Puglisi J D, Putz J, Florentz C, Giege R
Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 1, p. 41-49, 1993, ISBN: 8441619, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN
@article{,
title = {Influence of tRNA tertiary structure and stability on aminoacylation by yeast aspartyl-tRNA synthetase},
author = {J D Puglisi and J Putz and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8441619},
isbn = {8441619},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {1},
pages = {41-49},
abstract = {Mutations have been designed that disrupt the tertiary structure of yeast tRNA(Asp). The effects of these mutations on both tRNA structure and specific aspartylation by yeast aspartyl-tRNA synthetase were assayed. Mutations that disrupt tertiary interactions involving the D-stem or D-loop result in destabilization of the base-pairing in the D-stem, as monitored by nuclease digestion and chemical modification studies. These mutations also decrease the specificity constant (kcat/Km) for aspartylation by aspartyl-tRNA synthetase up to 10(3)-10(4) fold. The size of the T-loop also influences tRNA(Asp) structure and function; change of its T-loop to a tetraloop (-UUCG-) sequence results in a denatured D-stem and an almost 10(4) fold decrease of kcat/Km for aspartylation. The negative effects of these mutations on aspartylation activity are significantly alleviated by additional mutations that stabilize the D-stem. These results indicate that a critical role of tertiary structure in tRNA(Asp) for aspartylation is the maintenance of a base-paired D-stem.},
note = {0305-1048
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/*metabolism Base Sequence Kinetics Molecular Sequence Data Mutation *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't Temperature, Transfer/*chemistry/metabolism Saccharomyces cerevisiae/enzymology Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Poterszman A, Plateau P, Moras D, Blanquet S, Mazauric M H, Kreutzer R, Kern D
Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus. Implications for the structure of prokaryotic aspartyl-tRNA synthetases Article de journal
Dans: FEBS Lett, vol. 325, no. 3, p. 183-186, 1993, ISBN: 8319804, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN
@article{,
title = {Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus. Implications for the structure of prokaryotic aspartyl-tRNA synthetases},
author = {A Poterszman and P Plateau and D Moras and S Blanquet and M H Mazauric and R Kreutzer and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8319804},
isbn = {8319804},
year = {1993},
date = {1993-01-01},
journal = {FEBS Lett},
volume = {325},
number = {3},
pages = {183-186},
abstract = {The genes of aspartyl-tRNA synthetase (AspRS) from two Thermus thermophilus strain VK-1 and HB8, have been cloned and sequenced. Their nucleotidic sequences code for the same protein which displays the three characteristic motifs of class II aminoacyl-tRNA synthetases. This enzyme shows 50% identity with Escherichia coli AspRS, over the totality of the chain (580 amino acids). A comparison with the eukaryotic yeast cytoplasmic AspRS indicates the presence in the prokaryotic AspRS of an extra domain between motifs 2 and 3 much larger than in the eukaryotic ones. When its gene is under the control of the tac promoter of the expression vector pKK223-3, the protein is efficiently overexpressed as a thermostable protein in E. coli. It can be further purified to homogeneity using a heat treatment followed by a single anion exchange chromatography. Single crystals of the pure protein, diffracting at least to 2.2 A resolution (space group P2(1)2(1)2(1)},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Podyminogin M A, Vlassov V V, Giege R
Synthetic RNA-cleaving molecules mimicking ribonuclease A active center. Design and cleavage of tRNA transcripts Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 25, p. 5950-5956, 1993, ISBN: 7507235, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/*metabolism Ribonuclease, Base Sequence Binding Sites Hydrogen-Ion Concentration Molecular Sequence Data Nucleic Acid Conformation RNA/metabolism RNA, Genetic, Non-U.S. Gov't Temperature Transcription, Pancreatic/antagonists & inhibitors/chemical synthesis/*metabolism Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Synthetic RNA-cleaving molecules mimicking ribonuclease A active center. Design and cleavage of tRNA transcripts},
author = {M A Podyminogin and V V Vlassov and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507235},
isbn = {7507235},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {25},
pages = {5950-5956},
abstract = {RNA cleaving molecules were synthesized by conjugating imidazole residues imitating the essential imidazoles in the active center of pancreatic ribonuclease to an intercalating compound, derivative of phenazine capable of binding to the double stranded regions of polynucleotides. Action of the molecules on tRNA was investigated. It was found, that some of the compounds bearing two imidazole residues cleave tRNA under physiological conditions. The cleavage reaction shows a bell-shaped pH dependence with a maximum at pH 7.0 indicating participation of protonated and non-protonated imidazole residues in the process. Under the conditions stabilizing the tRNA structure, a tRNAAsp transcript was cleaved preferentially at the junctions of the stem and loop regions of the cloverleaf tRNA fold, at the five positions C56, C43, C20.1, U13, and U8, with a marked preference for C56. This cleavage pattern is consistent with a hydrolysis mechanism involving non-covalent binding of the compounds to the double-stranded regions of tRNA followed by an attack of the imidazole residues at the juxtaposed flexible single-stranded regions of the molecule. The compounds provide new probes for the investigation of RNA structure in solution and potential reactive groups for antisense oligonucleotide derivatives.},
note = {0305-1048
Journal Article},
keywords = {Asp/*metabolism Ribonuclease, Base Sequence Binding Sites Hydrogen-Ion Concentration Molecular Sequence Data Nucleic Acid Conformation RNA/metabolism RNA, Genetic, Non-U.S. Gov't Temperature Transcription, Pancreatic/antagonists & inhibitors/chemical synthesis/*metabolism Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pochart P, Agoutin B, Fix C, Keith G, Heyman T
A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 7, p. 1517-1521, 1993, ISBN: 8386834, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA Transposable Elements/*physiology Electrophoresis, Gel, Met/metabolism RNA, Ser/*metabolism RNA, Transfer, Two-Dimensional Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*metabolism Retroviridae/*growth & development Saccharomyces cerevisiae/metabolism
@article{,
title = {A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles},
author = {P Pochart and B Agoutin and C Fix and G Keith and T Heyman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8386834},
isbn = {8386834},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {7},
pages = {1517-1521},
abstract = {The analysis of the tRNAs associated to the virus-like particles produced by the Ty1 element revealed the specific packaging of three major tRNA species, in about equal amounts: the replication primer initiator tRNA(Met), the tRNA(Ser)AGA and a tRNA undetected until now as an expressed species in yeast. The latter tRNA is coded by the already described tDNA(Ser)GCT. This tRNA is enriched more than 150 fold in the particles as compared to its content in total cellular tRNA where it represents less than 0.1% (initiator tRNA(Met) and tRNA(Ser)AGA being 11 and 4 fold enriched respectively). This tRNA is the only species coded by the tDNA(Ser)GCT gene which is found in three copies per genome since no other corresponding expressed tRNA could be detected. This gene is thus very poorly expressed. The high concentration of tRNA(Ser)GCU in the particles compared to its very low cellular content led us to consider its possible implication in Ty specific processes.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence DNA Transposable Elements/*physiology Electrophoresis, Gel, Met/metabolism RNA, Ser/*metabolism RNA, Transfer, Two-Dimensional Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*metabolism Retroviridae/*growth & development Saccharomyces cerevisiae/metabolism},
pubstate = {published},
tppubtype = {article}
}
Philippe C, Eyermann F, Benard L, Portier C, Ehresmann B, Ehresmann C
Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 10, p. 4394-4398, 1993, ISBN: 7685101, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site},
author = {C Philippe and F Eyermann and L Benard and C Portier and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685101},
isbn = {7685101},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {10},
pages = {4394-4398},
abstract = {From genetic and biochemical evidence, we previously proposed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops. Here, we use "toeprint" experiments with Moloney murine leukemia virus reverse transcriptase to analyze the effect of S15 on the formation of the ternary mRNA-30S-tRNA(fMet) complex. We show that the binding of the 30S subunit on the mRNA stops reverse transcriptase near position +10, corresponding to the 3' terminus of the pseudoknot, most likely by stabilizing the pseudoknot conformation. Furthermore, S15 is found to stabilize the binary 30S-mRNA complex. When the ternary 30S-mRNA-tRNA(fMet) complex is formed, a toeprint is observed at position +17. This toeprint progressively disappears when the ternary complex is formed in the presence of increasing concentrations of S15, while a shift from position +17 to position +10 is observed. Beside, RNase T1 footprinting experiments reveal the simultaneous binding of S15 and 30S subunit on the mRNA. Otherwise, we show by filter binding assays that initiator tRNA remains bound to the 30S subunit even in the presence of S15. Our results indicate that S15 prevents the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, the ribosome being trapped in a preternary 30S-mRNA-tRNA(fMet) complex.},
note = {0027-8424
Journal Article},
keywords = {Bacterial Molecular Sequence Data Nucleic Acid Conformation Operator Regions (Genetics) *Peptide Chain Initiation RNA, Bacterial/genetics RNA, Base Sequence Escherichia coli/*genetics *Gene Expression Regulation, Messenger/genetics RNA, Met/metabolism Ribosomal Proteins/*genetics Ribosomes/*metabolism Structure-Activity Relationship Support, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pellequer J L, Westhof E, Regenmortel M H Van
Correlation between the location of antigenic sites and the prediction of turns in proteins Article de journal
Dans: Immunol Lett, vol. 36, no. 1, p. 83-99, 1993, ISBN: 7688347, (0165-2478 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Databases, Factual Epitopes/*chemistry Molecular Sequence Data Protein Conformation Protein Folding *Protein Structure, Secondary Proteins/*chemistry, Unité ARN
@article{,
title = {Correlation between the location of antigenic sites and the prediction of turns in proteins},
author = {J L Pellequer and E Westhof and M H Van Regenmortel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7688347},
isbn = {7688347},
year = {1993},
date = {1993-01-01},
journal = {Immunol Lett},
volume = {36},
number = {1},
pages = {83-99},
abstract = {In the present study, we developed new turn scales based on the occurrence of amino acids at each of the four positions of a turn using a structural database comprised of 87 proteins. We found that the scales correctly predicted a fraction of the turn regions in proteins with approximately 80% confidence. We used the turn scales for predicting the location of antigenic sites in proteins. The method was developed with the specific aim of predicting only a few peaks for each protein (two or three). We found that it leads to a high level of accurate prediction (70% of correct prediction of known epitopes). Our method should be useful for selecting protein regions to be synthesized in order to produce anti-peptide antibodies cross-reacting with the parent protein.},
note = {0165-2478
Journal Article},
keywords = {Amino Acid Sequence Databases, Factual Epitopes/*chemistry Molecular Sequence Data Protein Conformation Protein Folding *Protein Structure, Secondary Proteins/*chemistry, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pellequer J L, Westhof E
PREDITOP: a program for antigenicity prediction Article de journal
Dans: J Mol Graph, vol. 11, no. 3, p. 204-210, 191-202, 1993, ISBN: 7509182, (0263-7855 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Antigens/*chemistry Computer Graphics Epitopes/chemistry Proteins/*chemistry/*immunology *Software Software Design, Unité ARN
@article{,
title = {PREDITOP: a program for antigenicity prediction},
author = {J L Pellequer and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7509182},
isbn = {7509182},
year = {1993},
date = {1993-01-01},
journal = {J Mol Graph},
volume = {11},
number = {3},
pages = {204-210, 191-202},
abstract = {A program (PREDITOP) for predicting the location of antigenic regions (or epitopes) on proteins is described. This program and the associated ones are written in Turbo Pascal and run on IBM-PC compatibles. The program contains 22 normalized scales, corresponding to hydrophilicity, accessibility, flexibility, or secondary structure propensities. New scales are easily implemented. An hydrophobic moment procedure has also been implemented in order to determine amphiphilic helices. The program generates a result file where the values represent a particular physicochemical aspect of the studied protein. PREDITOP can display one or several result files by simple graphical super-imposition. Curve combinations can be done by the ADDITIO or MULTIPLI routines which create a new result file by adding or multiplying previously calculated files representing several propensities. The program is useful and efficient for identifying potential antigenic regions in a protein with the aim of raising antibodies against synthesized peptides which cross-react with the native protein.},
note = {0263-7855
Journal Article},
keywords = {Antigens/*chemistry Computer Graphics Epitopes/chemistry Proteins/*chemistry/*immunology *Software Software Design, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Paoletti J, Mougel M, Tounekti N, Girard P M, Ehresmann C, Ehresmann B
Spontaneous dimerization of retroviral MoMuLV RNA Article de journal
Dans: Biochimie, vol. 75, no. 8, p. 681-686, 1993, ISBN: 8286441, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Biopolymers Molecular Sequence Data Moloney murine leukemia virus/*genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry Support
@article{,
title = {Spontaneous dimerization of retroviral MoMuLV RNA},
author = {J Paoletti and M Mougel and N Tounekti and P M Girard and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8286441},
isbn = {8286441},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {8},
pages = {681-686},
abstract = {The genome of the Moloney murine leukemia virus (MoMuLV) is composed of two identical RNA molecules joined at their 5' ends by the dimer linkage structure (DLS). Dimerization sequences are located within the PSI encapsidation domain. We present here an overview of the work we have performed on spontaneous dimerization of a MoMuLV RNA fragment encompassing the PSI domain in order to understand the mechanism by which retroviral RNA dimerization takes place. We present kinetical, thermodynamical and conformational evidence which leads to the conclusion that the PSI domain is a structurally independent domain and that conformational changes are triggered by the dimerization process. We conclude that at least one particular region (nucleotides 278-309) of the RNA is directly involved in the process while the conformation of some other regions is changed probably because of a long-range effect.},
note = {0300-9084
Journal Article},
keywords = {Base Sequence Biopolymers Molecular Sequence Data Moloney murine leukemia virus/*genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry Support},
pubstate = {published},
tppubtype = {article}
}
Oguiza J A, Malumbres M, Eriani G, Pisabarro A, Mateos L M, Martin F, Martin J F
Dans: J Bacteriol, vol. 175, no. 22, p. 7356-7362, 1993, ISBN: 8226683, (0021-9193 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN
@article{,
title = {A gene encoding arginyl-tRNA synthetase is located in the upstream region of the lysA gene in Brevibacterium lactofermentum: regulation of argS-lysA cluster expression by arginine},
author = {J A Oguiza and M Malumbres and G Eriani and A Pisabarro and L M Mateos and F Martin and J F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8226683},
isbn = {8226683},
year = {1993},
date = {1993-01-01},
journal = {J Bacteriol},
volume = {175},
number = {22},
pages = {7356-7362},
abstract = {The Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an M(r) of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria.},
note = {0021-9193
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Myslinski E, Schuster C, Krol A, Carbon P
Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements Article de journal
Dans: J Mol Biol, vol. 234, no. 2, p. 311-318, 1993, ISBN: 7693950, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN
@article{,
title = {Promoter strength and structure dictate module composition in RNA polymerase III transcriptional activator elements},
author = {E Myslinski and C Schuster and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7693950},
isbn = {7693950},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {2},
pages = {311-318},
abstract = {RNA polymerase III transcription of genes with external promoters only (e.g. U6 snRNA) or containing in addition an internal B box (selenocysteine tRNA(Sec)) is stimulated by upstream elements; a distal sequence element (DSE) for U6 or an activator element in the tRNA(Sec) gene. In contrast to the composite structure of the DSE which requires an octamer motif, the Xenopus tRNA(Sec) activator element contains an SPH motif only. In vivo transcription is optimally stimulated by SPH in an absolute octamer-independent manner since adding octamer does not induce superstimulation. Experiments performed in the work presented here led to the following observations. Co-operation between SPH and octamer motifs can be detected in two distinct cases: first when these motifs are placed in front of B box-less tRNA(Sec) or U6 external promoters and second, if either element of the external promoter (proximal sequence element or TATA element), or the SPH motif itself, are altered. Altogether, our data provide evidence that an SPH motif can function alone in an optimized promoter only. In contrast, an octamer becomes indispensable when the basal promoter is weak or disabled. It follows that module composition of Pol III transcriptional activator elements is dependent on the structure and strength of the promoter. This reveals the existence of cross-talk between activator and promoter elements, mediated by the bound transcription factors, which are thus able to compensate for each other in order to allow successful assembly of the transcription complex.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Molecular Sequence Data Mutagenesis, Genetic/*physiology Xenopus laevis, Non-U.S. Gov't Transcription, Nucleic Acid/*physiology Selenocysteine/genetics Support, Site-Directed Oocytes/metabolism Promoter Regions (Genetics)/*genetics RNA/*genetics RNA Polymerase III/*metabolism RNA, Small Nuclear/genetics RNA, Transfer/genetics Regulatory Sequences, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Myslinski E, Schuster C, Huet J, Sentenac A, Krol A, Carbon P
Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 25, p. 5852-5858, 1993, ISBN: 8290344, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid-Specific/*genetics/metabolism Recombinant Proteins/metabolism Support, Animals Base Sequence DNA/metabolism DNA-Binding Proteins/*metabolism Molecular Sequence Data *Point Mutation Protein Binding RNA Polymerase III/*metabolism RNA, Genetic Xenopus laevis, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factors/*metabolism *Transcription, Transfer, Unité ARN
@article{,
title = {Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP},
author = {E Myslinski and C Schuster and J Huet and A Sentenac and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8290344},
isbn = {8290344},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {25},
pages = {5852-5858},
abstract = {The selenocysteine tRNA(Sec) gene possesses two external promoter elements, one of which is constituted by a strong TATA box. Point mutant analysis performed in this study led to the conclusion that the functional TATA promoter actually encompasses the sequence -34 GGGTATAAAAGG-23. Individual changes at T-31 do not affect transcription much. Position T-29 is less permissive to mutation since transversion to a G, for example, is less well tolerated than at T-31. Interestingly, a double point mutation, converting GG(-33/-32) to TT, causes abrogation of transcription in vivo and severe reduction of transcription in vitro with human TBP. Therefore, data obtained underscore the fact that, in the Xenopus tRNA(Sec), these two Gs are an integral part of the TATA promoter. Gel retardation experiments indicate that the GG to TT substitution, which led human TBP to lose its ability to support efficient transcription in vitro, correlates with the appearance of an altered pattern of retarded complexes. Altogether, the data presented in this report support a model in which TBP interacts directly with the TATA element of the tRNA(Sec) gene, in contrast to the type of interaction proposed for classical TATA-less tRNA genes.},
note = {0305-1048
Journal Article},
keywords = {Amino Acid-Specific/*genetics/metabolism Recombinant Proteins/metabolism Support, Animals Base Sequence DNA/metabolism DNA-Binding Proteins/*metabolism Molecular Sequence Data *Point Mutation Protein Binding RNA Polymerase III/*metabolism RNA, Genetic Xenopus laevis, Non-U.S. Gov't *TATA Box TATA-Box Binding Protein Transcription Factors/*metabolism *Transcription, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Muller G, Gaspin C, Etienne A, Westhof E
Automatic display of RNA secondary structures Article de journal
Dans: Comput Appl Biosci, vol. 9, no. 5, p. 551-561, 1993, ISBN: 7507400, (0266-7061 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN
@article{,
title = {Automatic display of RNA secondary structures},
author = {G Muller and C Gaspin and A Etienne and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507400},
isbn = {7507400},
year = {1993},
date = {1993-01-01},
journal = {Comput Appl Biosci},
volume = {9},
number = {5},
pages = {551-561},
abstract = {A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.},
note = {0266-7061
Journal Article},
keywords = {16S/chemistry/genetics RNA, 5S/chemistry/genetics Ribonuclease P *Software, Algorithms Bacillus subtilis/chemistry/genetics Base Sequence *Computer Graphics Endoribonucleases/genetics Escherichia coli/chemistry/genetics Molecular Sequence Data Nucleic Acid Conformation RNA/*chemistry/genetics RNA, Bacterial/genetics RNA, Catalytic/genetics RNA, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mougel M, Tounekti N, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C
Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 20, p. 4677-4684, 1993, ISBN: 8233816, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology
@article{,
title = {Conformational analysis of the 5' leader and the gag initiation site of Mo-MuLV RNA and allosteric transitions induced by dimerization},
author = {M Mougel and N Tounekti and J L Darlix and J Paoletti and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8233816},
isbn = {8233816},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {20},
pages = {4677-4684},
abstract = {Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translation, encapsidation and reverse transcription. Here, we have derived a secondary structure model of nucleotides upstream from psi and of the gag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, using chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place between U5 and 5' leader sequences. The U5-PBS subdomain can fold in two mutually exclusive conformations: a very stable and extended helical structure (E form) in which 17 of the 18 nucleotides of the PBS are paired, or an irregular three-branch structure (B form) in which 10 nucleotides of the PBS are paired. The dimeric RNA adopts the B conformation. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerization, it may facilitate annealing of the primer tRNAPro to the PBS by lowering the free energy required for melting the PBS. Furthermore, dimerization induces allosteric rearrangements around the SD site and the gag initiation region.},
note = {0305-1048
Journal Article},
keywords = {Allosteric Regulation Base Sequence Biopolymers *Genes, gag Molecular Sequence Data Moloney murine leukemia virus/*genetics *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Unité ARN, Viral/*chemistry/genetics Sequence Homology},
pubstate = {published},
tppubtype = {article}
}
Mougel M, Allmang C, Eyermann F, Cachia C, Ehresmann B, Ehresmann C
Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition Article de journal
Dans: Eur J Biochem, vol. 215, no. 3, p. 787-792, 1993, ISBN: 7689052, (0014-2956 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN
@article{,
title = {Minimal 16S rRNA binding site and role of conserved nucleotides in Escherichia coli ribosomal protein S8 recognition},
author = {M Mougel and C Allmang and F Eyermann and C Cachia and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7689052},
isbn = {7689052},
year = {1993},
date = {1993-01-01},
journal = {Eur J Biochem},
volume = {215},
number = {3},
pages = {787-792},
abstract = {Escherichia coli ribosomal protein S8 was previously shown to bind a 16S rRNA fragment (nucleotides 584-756) with the same affinity as the complete 16S rRNA, and to shield an irregular helical region (region C) [Mougel, M., Eyermann, F., Westhof, E., Romby, P., Expert-Bezancon, Ebel, J. P., Ehresmann, B. & Ehresmann, C. (1987). J. Mol. Biol. 198, 91-107]. Region C was postulated to display characteristic features: three bulged adenines (A595, A640 and A642), a non-canonical U598-U641 pair surrounded by two G.C pairs. In order to delineate the minimal RNA binding site, deletions were introduced by site-directed mutagenesis and short RNA fragments were synthesized. Their ability to bind S8 was assayed by filter binding. Our results show that the RNA binding site can be restricted to a short helical stem (588-605/633-651) containing region C. The second part of the work focused on region C and on the role of conserved nucleotides as potential determinants of S8 recognition. Single and double mutations were introduced by site-directed mutagenesis in fragment 584-756, and their effect on S8 binding was measured. It was found that the three bulged positions are essential and that adenines are required at positions 640 and 642. U598 is also crucial and the highly conserved G597.C643 pair cannot be inverted. These conserved nucleotides are either directly involved in the recognition process as direct contacts or required to maintain a specific conformation. The strong evolutionary pressure and the small number of positive mutants stress the high stringency of the recognition process.},
note = {0014-2956
Journal Article},
keywords = {16S/*metabolism Ribosomal Proteins/genetics/*metabolism Support, Adenine/metabolism Bacterial Proteins/metabolism Base Composition Base Sequence Binding Sites Conserved Sequence Escherichia coli/*metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Bacterial/metabolism RNA, Non-U.S. Gov't, Ribosomal, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Martin F, Eriani G, Eiler S, Moras D, Dirheimer G, Gangloff J
Overproduction and purification of native and queuine-lacking Escherichia coli tRNA(Asp). Role of the wobble base in tRNA(Asp) acylation Article de journal
Dans: J Mol Biol, vol. 234, no. 4, p. 965-974, 1993, ISBN: 8263943, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Activation Anticodon Aspartate-tRNA Ligase/metabolism Base Composition Base Sequence Cloning, Asp/chemistry/*metabolism Saccharomyces cerevisiae/metabolism Structure-Activity Relationship Support, ERIANI, Molecular Comparative Study Crystallography, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray Escherichia coli/*metabolism Guanine/*analogs & derivatives/chemistry Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Overproduction and purification of native and queuine-lacking Escherichia coli tRNA(Asp). Role of the wobble base in tRNA(Asp) acylation},
author = {F Martin and G Eriani and S Eiler and D Moras and G Dirheimer and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8263943},
isbn = {8263943},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {4},
pages = {965-974},
abstract = {Escherichia coli tRNA(Asp) was overproduced in E. coli up to 15-fold from a synthetic tRNA(Asp) gene placed in a plasmid under the dependence of an isopropyl-beta,D-thiogalactopyranoside-inducible promoter. Purification to nearly homogeneity (95%) was achieved after two HPLC DEAE-cellulose columns. E. coli tRNA(Asp)[G34] (having guanine instead of queuine at position 34) was obtained by the same procedure except that it was overproduced in a strain lacking the enzyme responsible for queuine modification. Nucleoside analysis showed that, except for the replacement of Q34 by G34 in mutant-derived tRNA(Asp), the base modification levels of both tRNAs are the same as those in wild-type E. coli tRNA(Asp). Kinetic properties of tRNA(Asp)[Q34] and [G34] with yeast AspRS compared to those in the homologous reactions in yeast and E. coli clearly indicate that the major identity elements are the same in both organisms: the conserved discriminant base and the anticodon triplet. In connection with this, we explored by site-directed mutagenesis the functional role of the interactions which, as revealed by the crystallographic structure, occur between the wobble base of yeast tRNA(Asp) and two residues of yeast AspRS. Their absence strongly affected aspartylation and the kd of tRNA(Asp). Each contact individually restores almost completely the wild-type acylation properties of the enzyme; thus, wobble base recognition in yeast appears to be more protected against mutational events than in E. coli, where only one contact is thought to occur at position 34.},
note = {0022-2836
Journal Article},
keywords = {*Amino Acid Activation Anticodon Aspartate-tRNA Ligase/metabolism Base Composition Base Sequence Cloning, Asp/chemistry/*metabolism Saccharomyces cerevisiae/metabolism Structure-Activity Relationship Support, ERIANI, Molecular Comparative Study Crystallography, Non-U.S. Gov't, Transfer, Unité ARN, X-Ray Escherichia coli/*metabolism Guanine/*analogs & derivatives/chemistry Molecular Sequence Data Nucleic Acid Conformation RNA},
pubstate = {published},
tppubtype = {article}
}
Marquet R, Ehresmann C, Ehresmann B
Higher Order Structures of HIV-1 RNA as Sites for Drug Actions. Chapitre d'ouvrage
Dans: Crooke, S T; Lebleu, B (Ed.): Antisense Research and Applications, p. 401-414, CRC Press, 1993.
Liens | BibTeX | Étiquettes: MARQUET, Unité ARN
@inbook{,
title = {Higher Order Structures of HIV-1 RNA as Sites for Drug Actions.},
author = {R Marquet and C Ehresmann and B Ehresmann},
editor = {S T Crooke and B Lebleu},
url = {http://www.crcpress.com/product/isbn/9780849347054},
year = {1993},
date = {1993-01-01},
booktitle = {Antisense Research and Applications},
pages = {401-414},
publisher = {CRC Press},
keywords = {MARQUET, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Lorber B, Skouri M, Munch J P, Giege R
Influence of impurities on protein crystallization: the case of lysozyme. Article de journal
Dans: J Crystal Growth, vol. 128, no. 1-4, part 2, p. 1203-1211, 1993, ISBN: 10.1016/S0022-0248(07)80124-2, (Proceedings of the Tenth International Conference on Crystal Growth).
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Influence of impurities on protein crystallization: the case of lysozyme.},
author = {B Lorber and M Skouri and J P Munch and R Giege},
url = {http://www.sciencedirect.com/science/article/pii/S0022024807801242},
isbn = {10.1016/S0022-0248(07)80124-2},
year = {1993},
date = {1993-01-01},
journal = {J Crystal Growth},
volume = {128},
number = {1-4, part 2},
pages = {1203-1211},
abstract = {Several batches of hen egg white lysozyme were compared on the basis of their biochemical purity and homogeneity as well as of their ability to crystallize in the tetragonal space group in the presence of sodium chloride and sodium acetate at pH 4.5. Trace amounts (< 2% (w/w)) of detectable protein impurities and inactive lysozyme molecules interfere with the nucleation and crystal growth processes. The presence of impurities significantly decreases solubility of lysozyme preparations. The intentional addition of ovalbumin or bovine serum albumin to pure lysozyme is correlated with an increase of the proportion of twinned crystals. Thus, reproductibility of lysozyme crystallization is dependent upon the presence of impurities.},
note = {Proceedings of the Tenth International Conference on Crystal Growth},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Keith G, Yusupov M, Briand C, Moras D, Kern D, Brion C
Sequence of tRNA(Asp) from Thermus thermophilus HB8 Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 18, p. 4399, 1993, ISBN: 7692402, (0305-1048 Journal Article).
Liens | BibTeX | Étiquettes: Asp/chemistry/*genetics Thermus thermophilus/*genetics, Bacterial/chemistry/genetics RNA, Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {Sequence of tRNA(Asp) from Thermus thermophilus HB8},
author = {G Keith and M Yusupov and C Briand and D Moras and D Kern and C Brion},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7692402},
isbn = {7692402},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {18},
pages = {4399},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry/*genetics Thermus thermophilus/*genetics, Bacterial/chemistry/genetics RNA, Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Keith G, Heitzler J, el Adlouni C, Glasser A L, Fix C, Desgres J, Dirheimer G
The primary structure of cytoplasmic initiator tRNA(Met) from Schizosaccharomyces pombe Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 12, p. 2949, 1993, ISBN: 8332511, (0305-1048 Journal Article).
Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data RNA, Fungal/*chemistry RNA, Met/*chemistry Schizosaccharomyces/*genetics, Transfer, Unité ARN
@article{,
title = {The primary structure of cytoplasmic initiator tRNA(Met) from Schizosaccharomyces pombe},
author = {G Keith and J Heitzler and C el Adlouni and A L Glasser and C Fix and J Desgres and G Dirheimer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8332511},
isbn = {8332511},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {12},
pages = {2949},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Molecular Sequence Data RNA, Fungal/*chemistry RNA, Met/*chemistry Schizosaccharomyces/*genetics, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Jaeger L, Westhof E, Michel F
Dans: J Mol Biol, vol. 234, no. 2, p. 331-346, 1993, ISBN: 8230218, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacteriophage T4/*genetics Base Sequence Enzyme Activation Enzyme Stability Introns/*physiology Models, Catalytic/drug effects/*metabolism/radiation effects RNA, Molecular Molecular Sequence Data Nucleic Acid Denaturation/physiology RNA, Non-U.S. Gov't Thermodynamics Ultraviolet Rays, Unité ARN, Viral/drug effects/*metabolism/radiation effects Support
@article{,
title = {Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components},
author = {L Jaeger and E Westhof and F Michel},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8230218},
isbn = {8230218},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {234},
number = {2},
pages = {331-346},
abstract = {We have studied the mechanism by which the 3' terminal domain of the sunY intron of bacteriophage T4 activates the group I ribozyme core of this intron, from which it is separated by some 800 nucleotides. As shown by monitoring either UV absorbance or self-splicing reaction kinetics as a function of temperature, intron transcripts undergo highly cooperative unfolding/inactivation upon heating: the two methods yield similar estimates of the thermodynamic parameters associated with this process. Such cooperativity makes it possible in turn to assess the energetic contribution of specific interactions to the overall structure, by comparing the sensitivity to heat inactivation of molecules carrying various nucleotide substitutions. By combining this approach with chemical modification, we have probed several proven or putative interactions between the core and 3' terminal domain of the intron and conclude that the role of the 3' terminal domain is to stabilize the active form of the ribozyme. Interestingly, the P9.0 interaction, which brings 3' terminal nucleotides next to the core site that binds the guanosine cofactor of the self-splicing reaction, is now shown to be composed in fact of two distinct pairings. An isolated base-pair (P9.0a), involving a residue located only six nucleotides upstream of the 3' splice site, participates in the stabilization of the ribozyme and appears to persist during the second stage of self-splicing (exon ligation). In contrast, formation of the previously demonstrated P9.0b pairing, which involves the two penultimate intron nucleotides, contributes no additional stability and results in no detectable rearrangement of the core structure. Implications for the concept of a static ribozyme are discussed in the light of a slightly revised three-dimensional model of the sunY intron.},
note = {0022-2836
Journal Article},
keywords = {Bacteriophage T4/*genetics Base Sequence Enzyme Activation Enzyme Stability Introns/*physiology Models, Catalytic/drug effects/*metabolism/radiation effects RNA, Molecular Molecular Sequence Data Nucleic Acid Denaturation/physiology RNA, Non-U.S. Gov't Thermodynamics Ultraviolet Rays, Unité ARN, Viral/drug effects/*metabolism/radiation effects Support},
pubstate = {published},
tppubtype = {article}
}
Isel C, Marquet R, Keith G, Ehresmann C, Ehresmann B
Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription Article de journal
Dans: J Biol Chem, vol. 268, no. 34, p. 25269-25272, 1993, ISBN: 7503978, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/metabolism Base Sequence Binding Sites Comparative Study DNA Primers HIV-1/genetics/*metabolism HIV-1 Reverse Transcriptase HIV-2/genetics/metabolism Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Genetic *Transcription, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*biosynthesis RNA-Directed DNA Polymerase/*metabolism SIV/genetics/metabolism Support
@article{,
title = {Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription},
author = {C Isel and R Marquet and G Keith and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7503978},
isbn = {7503978},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {34},
pages = {25269-25272},
abstract = {In all retroviruses, reverse transcription is primed by a tRNA whose 3' end 18 nucleotides are complementary to the so called viral primer binding site. Previous work showed that reverse transcription of HIV-1 RNA is initiated by tRNA(3Lys). Using a variety of chemical and enzymatic structural probes, we investigated the interactions between HIV-1 RNA and its natural primer tRNA(3Lys). In addition to the predictable contacts between the viral primer binding site and the 3' end of tRNA(3Lys), a specific interaction takes place between an A-rich loop located upstream of the primer binding site region and the anticodon loop of tRNA(3Lys). This AAAA/Umcm5s2UUU loop-loop interaction is not observed when the natural primer is replaced by an in vitro synthesized tRNA(3Lys) transcript. Furthermore, dethiolation of the modified nucleotide mcm5s2U at position 34 of tRNA(3Lys) strongly destabilizes this interaction. Sequence and structure comparisons indicate that the primer/template loop-loop interaction is conserved in all HIV-1 isolates, and possibly also in HIV-2 and SIV.},
note = {0021-9258
Journal Article},
keywords = {Anticodon/genetics/metabolism Base Sequence Binding Sites Comparative Study DNA Primers HIV-1/genetics/*metabolism HIV-1 Reverse Transcriptase HIV-2/genetics/metabolism Molecular Sequence Data Nucleic Acid Conformation RNA, Genetic, Genetic *Transcription, Lys/*metabolism RNA, MARQUET, Non-U.S. Gov't Templates, Transfer, Unité ARN, Viral/*biosynthesis RNA-Directed DNA Polymerase/*metabolism SIV/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Hou Y M, Westhof E, Giege R
An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 14, p. 6776-6780, 1993, ISBN: 8341698, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acyl-tRNA Ligases/*metabolism Base Sequence Escherichia coli/*chemistry/genetics/metabolism Hydrogen Bonding Models, Cys/*chemistry/genetics/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA},
author = {Y M Hou and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8341698},
isbn = {8341698},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {14},
pages = {6776-6780},
abstract = {The nucleotides in a tRNA that specifically interact with the cognate aminoacyl-tRNA synthetase have been found largely located in the helical stems, the anticodon, or the discriminator base, where they vary from one tRNA to another. The conserved and semiconserved nucleotides that are responsible for the tRNA tertiary structure have been shown to have little role in synthetase recognition. Here we report that aminoacylation of Escherichia coli tRNA(Cys) depends on the anticodon, the discriminator base, and a tertiary interaction between the semiconserved nucleotides at positions 15 and 48. While all other tRNAs contain a purine at position 15 and a complementary pyrimidine at position 48 that establish the tertiary interaction known as the Levitt pair, E. coli tRNA(Cys) has guanosine -15 and -48. Replacement of guanosine -15 or -48 with cytidine virtually eliminates aminoacylation. Structural analyses with chemical probes suggest that guanosine -15 and -48 interact through hydrogen bonds between the exocyclic N-2 and ring N-3 to stabilize the joining of the two long helical stems of the tRNA. This tertiary interaction is different from the traditional base pairing scheme in the Levitt pair, where hydrogen bonds would form between N-1 and O-6. Our results provide evidence for a role of RNA tertiary structure in synthetase recognition.},
note = {0027-8424
Journal Article},
keywords = {Amino Acyl-tRNA Ligases/*metabolism Base Sequence Escherichia coli/*chemistry/genetics/metabolism Hydrogen Bonding Models, Cys/*chemistry/genetics/metabolism Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gilmer D, Allmang C, Ehresmann C, Guilley H, Richards K, Jonard G, Ehresmann B
The secondary structure of the 5'-noncoding region of beet necrotic yellow vein virus RNA 3: evidence for a role in viral RNA replication Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 6, p. 1389-1395, 1993, ISBN: 8464729, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Gene Expression Hydrogen Bonding Molecular Sequence Data Mutagenesis, Messenger/genetics RNA, Site-Directed Nucleic Acid Conformation Plant Viruses/*genetics/ultrastructure Promoter Regions (Genetics) RNA Viruses/*genetics/ultrastructure RNA, Unité ARN, Viral/chemistry/*genetics/ultrastructure Vegetables *Virus Replication
@article{,
title = {The secondary structure of the 5'-noncoding region of beet necrotic yellow vein virus RNA 3: evidence for a role in viral RNA replication},
author = {D Gilmer and C Allmang and C Ehresmann and H Guilley and K Richards and G Jonard and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8464729},
isbn = {8464729},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {6},
pages = {1389-1395},
abstract = {Secondary structure-sensitive chemical and enzymatic probes have been used to produce a model for the folding of the first 312 residues of the long 5'-noncoding region of beet necrotic yellow vein virus RNA 3. The structure consists of two major domains, one of which includes long distance base-pairing interactions between two short sequence elements (Box I and Box II) situated between positions 237 and 292 and complementary elements (Box I' and II') near the 5'-terminus. Previous studies have shown that base pairing between these sequence elements (in either the plus-strand or minus-strand RNA) is important for RNA 3 accumulation during infection. RNA 3 transcripts were produced containing mutations which preferentially disrupted Box II-II' base pairing in either the plus- or minus-strand. In infection experiments, transcripts with mutations which disrupted the Box II-II' interaction in the plus-strand structure replicated less efficiently than mutants in which the Box II-II' interaction was disrupted in the minus-strand. These findings indicate that the complex 5'-proximal plus-strand structure to which the Box II-II' interaction contributes comprises at least part of the promoter for plus-strand RNA synthesis.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Gene Expression Hydrogen Bonding Molecular Sequence Data Mutagenesis, Messenger/genetics RNA, Site-Directed Nucleic Acid Conformation Plant Viruses/*genetics/ultrastructure Promoter Regions (Genetics) RNA Viruses/*genetics/ultrastructure RNA, Unité ARN, Viral/chemistry/*genetics/ultrastructure Vegetables *Virus Replication},
pubstate = {published},
tppubtype = {article}
}
Giege R, Puglisi J D, Florentz C
tRNA structure and aminoacylation efficiency Article de journal
Dans: Prog Nucleic Acid Res Mol Biol, vol. 45, p. 129-206, 1993, ISBN: 8341800, (0079-6603 Journal Article Review Review, Academic).
Liens | BibTeX | Étiquettes: Acylation Amino Acids/metabolism Amino Acyl-tRNA Ligases/metabolism Animals Base Sequence Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry/metabolism Support, Unité ARN
@article{,
title = {tRNA structure and aminoacylation efficiency},
author = {R Giege and J D Puglisi and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8341800},
isbn = {8341800},
year = {1993},
date = {1993-01-01},
journal = {Prog Nucleic Acid Res Mol Biol},
volume = {45},
pages = {129-206},
note = {0079-6603
Journal Article
Review
Review, Academic},
keywords = {Acylation Amino Acids/metabolism Amino Acyl-tRNA Ligases/metabolism Animals Base Sequence Dna Human Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Non-U.S. Gov't, Transfer/*chemistry/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giege R, Florentz C, Dreher T W
The TYMV tRNA-like structure Article de journal
Dans: Biochimie, vol. 75, no. 7, p. 569-582, 1993, ISBN: 8268257, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Transfer/*chemistry/metabolism RNA, Unité ARN, Viral/*chemistry/metabolism Tymovirus/*genetics
@article{,
title = {The TYMV tRNA-like structure},
author = {R Giege and C Florentz and T W Dreher},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268257},
isbn = {8268257},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {7},
pages = {569-582},
abstract = {The genomic RNA from turnip yellow mosaic virus presents a 3'-end functionally and structurally related to tRNAs. This report summarizes our knowledge about the peculiar structure of the tRNA-like domain and its interaction with tRNA specific proteins, like RNAse P, tRNA nucleotidyl-transferase, aminoacyl-tRNA synthetases, and elongation factors. It discusses also the biological role of this structure in the viral life cycle. A brief survey of our knowledge of other tRNA mimicries in biological systems, as well as their relevance for understanding canonical tRNA, will also be presented.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Molecular Sequence Data *Nucleic Acid Conformation RNA, FLORENTZ, Transfer/*chemistry/metabolism RNA, Unité ARN, Viral/*chemistry/metabolism Tymovirus/*genetics},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Florentz C, Schimmel P, Giege R
Triple aminoacylation specificity of a chimerized transfer RNA Article de journal
Dans: Biochemistry, vol. 32, no. 50, p. 14053-14061, 1993, ISBN: 8268184, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Triple aminoacylation specificity of a chimerized transfer RNA},
author = {M Frugier and C Florentz and P Schimmel and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8268184},
isbn = {8268184},
year = {1993},
date = {1993-01-01},
journal = {Biochemistry},
volume = {32},
number = {50},
pages = {14053-14061},
abstract = {We report here the rational design and construction of a chimerized transfer RNA with tripartite aminoacylation specificity. A yeast aspartic acid specific tRNA was transformed into a highly efficient acceptor of alanine and phenylalanine and a moderate acceptor of valine. The transformation was guided by available knowledge of the requirements for aminoacylation by each of the three amino acids and was achieved by iterative changes in the local sequence context and the structural framework of the variable loop and the two variable regions of the dihydrouridine loop. The changes introduced to confer efficient acceptance of the three amino acids eliminate aminoacylation with aspartate. The interplay of determinants and antideterminants for different specific aminoacylations, and the constraints imposed by the structural framework, suggest that a tRNA with an appreciable capacity for more than three efficient aminoacylations may be inherently difficult to achieve.},
note = {0006-2960
Journal Article},
keywords = {Acylation Alanine/metabolism Base Sequence Chimera Escherichia coli/genetics Molecular Sequence Data Mutation Nucleic Acid Conformation Phenylalanine/metabolism RNA, Asp/chemistry/genetics/*metabolism Saccharomyces cerevisiae/genetics Support, ERIANI, FLORENTZ, FRUGIER, Non-U.S. Gov't Support, P.H.S. Valine/metabolism, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fritsch V, Ravishanker G, Beveridge D L, Westhof E
Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations Article de journal
Dans: Biopolymers, vol. 33, no. 10, p. 1537-1552, 1993, ISBN: 8218922, (0006-3525 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Chemistry, Physical Comparative Study Computer Simulation Molecular Sequence Data Poly dA-dT/*chemistry Solvents Thermodynamics, Unité ARN
@article{,
title = {Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations},
author = {V Fritsch and G Ravishanker and D L Beveridge and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8218922},
isbn = {8218922},
year = {1993},
date = {1993-01-01},
journal = {Biopolymers},
volume = {33},
number = {10},
pages = {1537-1552},
abstract = {The program AMBER 3.0 has been used to generate molecular dynamics trajectories of a poly(dA).poly(dT) decamer. The simulations were performed using different methods to treat solvent effects. Results of a simulation including 18 counterions NH4+ and 4109 water molecules under (N, P, T) conditions were compared to simulation runs with implicit solvent representation in which solvent screening effects were represented by the use of a sigmoidal distance-dependent dielectric function. In the latter case, the system was simulated under microcanonical (N, V, E) and canonical (N, V, T) conditions. For the fully hydrated system simulation, a preequilibration protocol was developed since it was observed that long and progressive periods of heating and equilibration on the overall system were necessary in order to avoid energetic collisions between the solute and the solvent molecules, leading to severe irreversible deformation of the solute. A detailed analysis of DNA conformations, sugar puckers, and stability of the hydrogen bonds, Watson-Crick and three-center H bonds, is reported. The results show that DNA remains essentially in the B conformer with a tendency in the hydrated model to adopt a slightly distorted, unwound, and stretched conformation in comparison to standard B-DNA. Concerning sugar puckers, the mean pseudorotation phases of the adenine residues are systematically higher than those of the thymine residues, except in the case of the hydrated model for which a articular behavior is observed for the adenine strand. In this case, the terminal bases oscillate between C2'-endo and O4'-endo and the central ones stay in the C3'-endo domain. The mean lifetimes of the internal Watson-Crick H-bond (A) HN6.O4(T) are also dependent on the base pairs included in the calculation, excepted for the implicit solvent simulation at constant temperature. The three-center H bonds have very small mean lifetimes in all three cases of MD simulation. In the minor groove of the hydrated model, a spine of hydration is found as observed by x-ray crystallography and other theoretical simulations. On the basis of the rms deviations, it appears that the fully hydrated simulation has not reached a plateau at the end of the run, while the implicit simulation at constant energy seems to have converged. At constant temperature, very large oscillations in rms deviations are observed.},
note = {0006-3525
Journal Article},
keywords = {Base Sequence Chemistry, Physical Comparative Study Computer Simulation Molecular Sequence Data Poly dA-dT/*chemistry Solvents Thermodynamics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, Westhof E, Giege R
Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA Article de journal
Dans: Biochimie, vol. 75, no. 12, p. 1143-1157, 1993, ISBN: 8199250, (0300-9084 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Bromovirus/*genetics Computer Simulation Genome, FLORENTZ, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Promoter Regions (Genetics) RNA, Non-U.S. Gov't Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism RNA, Unité ARN, Viral Models, Viral/*chemistry/genetics/metabolism Structure-Activity Relationship Support
@article{,
title = {Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA},
author = {B Felden and C Florentz and E Westhof and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199250},
isbn = {8199250},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {12},
pages = {1143-1157},
abstract = {A 3-D model of the tyrosylable tRNA-like domain of the genomic brome mosaic virus RNAs was built by computer modelling based on solution probing of the molecule with different chemical and enzymatic reagents. This model encompasses four major structural domains, including two peculiar substructures oriented perpendicularly and mimicking a tRNA structure, and a fifth domain which makes the connection with the rest of the viral RNA. After recalling the different steps that led to the present structural knowledge of the BMV tRNA-like domain, we review its novel structural features revealed by the modelling and that did not appear in older versions of 3-D models of this structure. These features comprise additional base-pairs, hairpin loops, new tertiary long-range interactions, and a second pseudoknot. The main goal of this paper is to strengthen the validity of the model by establishing correlations between the putative 3-D conformation and the functional properties of the domain. For that, we show how the present structural model rationalises mutagenic and footprinting data that have established the importance of specific regions of the RNA for its recognition and aminoacylation by yeast tyrosyl-tRNA synthetase. We discuss further how the model corroborates mutational analyses performed to understand recognition of this RNA domain by the (ATP,CTP):tRNA nucleotidyl-transferase and by the viral replicase. The published mutants of the BMV tRNA-like domain fall into two classes. In one class, the mutants leave unchanged the overall architecture of the molecule, thereby affecting functions directly. In the second class, the overall architecture of the mutants is perturbed, and thus functions are affected indirectly.},
note = {0300-9084
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence Bromovirus/*genetics Computer Simulation Genome, FLORENTZ, Molecular Molecular Sequence Data Mutation/genetics Nucleic Acid Conformation Promoter Regions (Genetics) RNA, Non-U.S. Gov't Tyrosine-tRNA Ligase/chemistry/*metabolism, Transfer/*chemistry/genetics/metabolism RNA, Unité ARN, Viral Models, Viral/*chemistry/genetics/metabolism Structure-Activity Relationship Support},
pubstate = {published},
tppubtype = {article}
}
Eriani G, Cavarelli J, Martin F, Dirheimer G, Moras D, Gangloff J
Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 22, p. 10816-10820, 1993, ISBN: 8248175, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/metabolism Saccharomyces cerevisiae/chemistry Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*chemistry Fungal Proteins/chemistry Kinetics Macromolecular Systems Models, ERIANI, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Proline/chemistry Protein Binding Protein Conformation RNA, Transfer, Unité ARN
@article{,
title = {Role of dimerization in yeast aspartyl-tRNA synthetase and importance of the class II invariant proline},
author = {G Eriani and J Cavarelli and F Martin and G Dirheimer and D Moras and J Gangloff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8248175},
isbn = {8248175},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {22},
pages = {10816-10820},
abstract = {Cytoplasmic aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) from yeast is, as are most class II synthetases, an alpha 2 dimer. The only invariant amino acid in signature motif 1 of this class is Pro-273; this residue is located at the dimer interface. To understand the role of Pro-273 in the conserved dimeric configuration, we tested the effect of a Pro-273-->Gly (P273G) substitution on the catalytic properties of homo- and heterodimeric AspRS. Heterodimers of AspRS were produced in vivo by overexpression of their respective subunit variants from plasmid-encoded genes and purified to homogeneity in one HPLC step. The homodimer containing the P273G shows an 80% inactivation of the enzyme and an affinity decrease for its cognate tRNA(Asp) of one order of magnitude. The P273G-mutated subunit recovered wild-type enzymatic properties when associated with a native subunit or a monomer otherwise inactivated having an intact dimeric interface domain. These results, which can be explained by the crystal structure of the native enzyme complexed with its substrates, confirm the structural importance of Pro-273 for dimerization and clearly establish the functional interdependence of the AspRS subunits. More generally, the dimeric conformation may be a structural prerequisite for the activity of mononucleotide binding sites constructed from antiparallel beta strands.},
note = {0027-8424
Journal Article},
keywords = {Asp/metabolism Saccharomyces cerevisiae/chemistry Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*chemistry Fungal Proteins/chemistry Kinetics Macromolecular Systems Models, ERIANI, Molecular Mutagenesis, Non-U.S. Gov't, Site-Directed Proline/chemistry Protein Binding Protein Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
el Adlouni C, Keith G, Dirheimer G, Szarkowski J W, Przykorska A
Rye nuclease I as a tool for structural studies of tRNAs with large variable arms Article de journal
Dans: Nucleic Acids Res, vol. 21, no. 4, p. 941-947, 1993, ISBN: 8383845, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Anticodon Base Sequence Cattle Molecular Sequence Data Nucleic Acid Conformation *Nucleotidases RNA, Leu/chemistry RNA, Non-U.S. Gov't, Ser/chemistry Saccharomyces cerevisiae Secale cereale/*enzymology Support, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Rye nuclease I as a tool for structural studies of tRNAs with large variable arms},
author = {C el Adlouni and G Keith and G Dirheimer and J W Szarkowski and A Przykorska},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8383845},
isbn = {8383845},
year = {1993},
date = {1993-01-01},
journal = {Nucleic Acids Res},
volume = {21},
number = {4},
pages = {941-947},
abstract = {A single-strand-specific nuclease from rye germ (Rn nuclease I) was used for secondary and tertiary structure investigations of tRNAs with large variable arms (class II tRNAs). We have studied the structure in solution of two recently sequenced tRNA(Leu): yeast tRNA(Leu)(ncm5UmAA) and bovine tRNA(Leu)(XmAA) as well as yeast tRNA(Leu)(UAG), tRNA(Leu)(m5CAA) and tRNA(Ser)(IGA). The latter is the only tRNA with a long variable arm for which the secondary and tertiary structure has already been studied by use of chemical probes and computer modelling. The data obtained in this work showed that the general model of class II tRNAs proposed by others for tRNA(Ser) can be extended to tRNAs(Leu) as well. However interesting differences in the structure of tRNAs(Leu) versus tRNA(Ser)(IGA) were also noticed. The main difference was observed in the accessibility of the variable loops to nucleolytic attack of Rn nuclease I: variable loops of all studied tRNA(Leu) species were cut by Rn nuclease I, while that of yeast tRNA(Ser)(IGA) was not. This could be due to differences in stability of the variable arms and the lengths of their loops which are 3 and 4 nucleotides in tRNA(Ser)(IGA) and tRNAs(Leu) respectively.},
note = {0305-1048
Journal Article},
keywords = {Animals Anticodon Base Sequence Cattle Molecular Sequence Data Nucleic Acid Conformation *Nucleotidases RNA, Leu/chemistry RNA, Non-U.S. Gov't, Ser/chemistry Saccharomyces cerevisiae Secale cereale/*enzymology Support, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brunel C, Romby P, Moine H, Caillet J, Grunberg-Manago M, Springer M, Ehresmann B, Ehresmann C
Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains Article de journal
Dans: Biochimie, vol. 75, no. 12, p. 1167-1179, 1993, ISBN: 8199252, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*genetics Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) Point Mutation Protein Structure, Base Sequence Escherichia coli/*enzymology/genetics Gene Deletion Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism RNA, Met/chemistry/metabolism Ribosomes/metabolism Structure-Activity Relationship Support, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism Translation, ROMBY, Secondary RNA, Transfer, Unité ARN
@article{,
title = {Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains},
author = {C Brunel and P Romby and H Moine and J Caillet and M Grunberg-Manago and M Springer and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8199252},
isbn = {8199252},
year = {1993},
date = {1993-01-01},
journal = {Biochimie},
volume = {75},
number = {12},
pages = {1167-1179},
abstract = {Previous work showed that E coli threonyl-tRNA synthetase (ThrRS) binds to the leader region of its own mRNA and represses its translation by blocking ribosome binding. The operator consists of four distinct domains, one of them (domain 2) sharing structural analogies with the anticodon arm of the E coli tRNA(Thr). The regulation specificity can be switched by using tRNA identity rules, suggesting that the operator could be recognized by ThrRS as a tRNA-like structure. In the present paper, we investigated the relative contribution of the four domains to the regulation process by using deletions and point mutations. This was achieved by testing the effects of the mutations on RNA conformation (by probing experiments), on ThrRS recognition (by footprinting experiments and measure of the competition with tRNA(Thr) for aminoacylation), on ribosome binding and ribosome/ThrRS competition (by toeprinting experiments). It turns out that: i) the four domains are structurally and functionally independent; ii) domain 2 is essential for regulation and contains the major structural determinants for ThrRS binding; iii) domain 4 is involved in control and ThrRS recognition, but to a lesser degree than domain 2. However, the previously described analogies with the acceptor-like stem are not functionally significant. How it is recognized by ThrRS remains to be resolved; iv) domain 1, which contains the ribosome loading site, is not involved in ThrRS recognition. The binding of ThrRS probably masks the ribosome binding site by steric hindrance and not by direct contacts. This is only achieved when ThrRS interacts with both domains 2 and 4; and v) the unpaired domain 3, which connects domains 2 and 4, is not directly involved in ThrRS recognition. It should serve as an articulation to provide an appropriate spacing between domains 2 and 4. Furthermore, it is possibly involved in ribosome binding.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*genetics Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) Point Mutation Protein Structure, Base Sequence Escherichia coli/*enzymology/genetics Gene Deletion Gene Expression Regulation, Genetic, Messenger/chemistry/metabolism RNA, Met/chemistry/metabolism Ribosomes/metabolism Structure-Activity Relationship Support, Non-U.S. Gov't Threonine-tRNA Ligase/chemistry/*genetics/metabolism Translation, ROMBY, Secondary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baudin F, Marquet R, Isel C, Darlix J L, Ehresmann B, Ehresmann C
Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains Article de journal
Dans: J Mol Biol, vol. 229, no. 2, p. 382-397, 1993, ISBN: 8429553, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Sequence Electrophoresis, Genetic, MARQUET, Non-U.S. Gov't Translation, Polyacrylamide Gel HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*chemistry/metabolism Rabbits Support
@article{,
title = {Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains},
author = {F Baudin and R Marquet and C Isel and J L Darlix and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8429553},
isbn = {8429553},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {229},
number = {2},
pages = {382-397},
abstract = {The 5' region of HIV-1 RNA contains functional elements involved in key steps of the retroviral cycle, such as genomic RNA transcription, splicing, translation, dimerization or initiation of reverse transcription. In the present work, we investigated the conformation of the first 500 nucleotides covering the RNA leader and the 5' gag coding sequences of HIV-MAL, using chemical probing. We provide detailed information on almost each nucleotide at one of their Watson-Crick positions and on position N-7 of purines. Experiments were conducted on two in vitro transcribed RNA fragments (1 to 707 and 1 to 311). A secondary structure model was derived by combining the experimental data, computer predictions and sequence comparison. Under conditions favoring dimerization (high salt concentration), HIV-1 RNA folds into independent structural domains that can be related to defined functional regions. The first domain corresponds to TAR forming a stable stem-loop. Intrinsic structural features are found to stabilize the TAR hairpin loop. The second domain (nucleotides 56 to 299) contains the PBS sequence, which is located in a stable subdomain constrained by a four stem junction (nucleotides 139 to 218). Although the MAL isolate has an insertion near the PBS, probably resulting from the duplication of a 23-nucleotide sequence, the structural organization of this subdomain is conserved in all other HIV-1 isolates. The third domain (nucleotides 300 to 404) contains the splice donor site, packaging and dimerization elements and the AUG initiation codon of gag. A major result is the structural versatility of this region. Two mutually exclusive structures, both equally in agreement with probing data, could modulate the different functions involving this domain. The reduced accessibility of the gag translational initiation site possibly accounts for the low efficiency of the in vitro translation of the dimer. Finally, the 5' gag coding sequences form a metastable domain.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Sequence Electrophoresis, Genetic, MARQUET, Non-U.S. Gov't Translation, Polyacrylamide Gel HIV-1/*genetics Molecular Sequence Data Nucleic Acid Conformation RNA, Unité ARN, Viral/*chemistry/metabolism Rabbits Support},
pubstate = {published},
tppubtype = {article}
}
Baron C, Westhof E, Bock A, Giege R
Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser) Article de journal
Dans: J Mol Biol, vol. 231, no. 2, p. 274-292, 1993, ISBN: 8510147, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adenine/chemistry Aspergillus Nuclease S1/pharmacology Base Sequence Comparative Study Escherichia coli/*chemistry Guanine/chemistry Lead/pharmacology Models, Amino Acid-Specific/*chemistry/drug effects RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Ser/*chemistry/drug effects Selenocysteine/*metabolism Sequence Homology, Transfer, Unité ARN
@article{,
title = {Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser)},
author = {C Baron and E Westhof and A Bock and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8510147},
isbn = {8510147},
year = {1993},
date = {1993-01-01},
journal = {J Mol Biol},
volume = {231},
number = {2},
pages = {274-292},
abstract = {Selenocysteine-inserting tRNAs (or tRNA(Sec)) are structurally untypical tRNAs that are charged by seryl-tRNA synthetase before being recognized by the selenocysteine synthase that converts serine into selenocysteine. tRNA(Sec) from Escherichia coli contains 95 nucleotides and is the longest tRNA known to date, in contrast to canonical tRNA(Ser), 88 nucleotides-long. We have studied its solution conformation by chemical and enzymatic probing. Global structural features were obtained by cobra venom and S1 nuclease mapping, as well as by probing with Pb2+. Accessibilities of phosphate groups were measured by ethylnitrosourea probing. Information about positions in bases involved in Watson-Crick pairing, in stacking or in tertiary interactions were obtained by chemical probing with dimethylsulfate, diethylpyrocarbonate, kethoxal and carbodiimide. On the basis of these chemical data, a three-dimensional model was constructed by computer modeling and compared to that of canonical tRNA(Ser). tRNA(Sec) resembles tRNA(Ser) at the level of its T-arm and anticodon-arm conformations, as well as at the joining of the D- and T-loops by a tertiary Watson-Crick G19-C56 interaction. Its extra-long variable arm is a double-stranded structure closed by a four nucleotide loop that is linked to the body of the tRNA in a way different from that found in tRNA(Ser). As anticipated from the peculiar features of the sequence in the D-loop and at the junction of amino acid and D-arms, tRNA(Sec) possesses a novel but restricted set of tertiary interactions in the core of its three-dimensional structure: a G8-A21-U14 triple pair and a novel interaction between C16 of the D-loop and C59 of the T-loop. A third triple interaction involving C15-G20a-G48 is suggested but some experimental evidence for it is still lacking. It is furthermore concluded that the D-arm has six base-pairs instead of three, as in canonical class II tRNA(Ser), with the D-loop containing only four nucleotides. Finally, the amino acid accepting arm forms a stack of eight Watson-Crick base-pairs (instead of 7 in other tRNAs). The biological relevance of this model with regard to interaction with seryl-tRNA synthetase and enzymes from the selenocysteine metabolism is discussed.},
note = {0022-2836
Journal Article},
keywords = {Adenine/chemistry Aspergillus Nuclease S1/pharmacology Base Sequence Comparative Study Escherichia coli/*chemistry Guanine/chemistry Lead/pharmacology Models, Amino Acid-Specific/*chemistry/drug effects RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't, Nucleic Acid Support, Ser/*chemistry/drug effects Selenocysteine/*metabolism Sequence Homology, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baranowski W, Tomaszewski J, Keith G
[Methylation of DNA in tissue of ovarian malignant tumors in women] Article de journal
Dans: Ginekol Pol, vol. 64, no. 4, p. 169-173, 1993, ISBN: 8282237, (0017-0011 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adult Carcinoma/genetics DNA, Neoplasm/*metabolism English Abstract Female Human Methylation Middle Aged Ovarian Neoplasms/*genetics Sertoli Cell Tumor/genetics, Unité ARN
@article{,
title = {[Methylation of DNA in tissue of ovarian malignant tumors in women]},
author = {W Baranowski and J Tomaszewski and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8282237},
isbn = {8282237},
year = {1993},
date = {1993-01-01},
journal = {Ginekol Pol},
volume = {64},
number = {4},
pages = {169-173},
abstract = {DNA methylation level from woman ovarian malignant tissues was investigated by 32P postlabeling of the single nucleotides, separation on TLC with followed autoradiography and Cerenkov counting. Slight differences in DNA methylation extent were found in malignant ovarian tumors as compared to normal myometrium and benign uterine tumor [myomas]. Lowest level of m5dC in relation to C and also in relation to total DNA was found in carcinoma embryonal tissue whereas maximal DNA methylation level was obtained in folliculoma tissue. This preliminary report needs further investigation of particularly genes methylation.},
note = {0017-0011
Journal Article},
keywords = {Adult Carcinoma/genetics DNA, Neoplasm/*metabolism English Abstract Female Human Methylation Middle Aged Ovarian Neoplasms/*genetics Sertoli Cell Tumor/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baranowski W, Tomaszewski J, Keith G
Unusual deficiency of the modified purine base queuine in transfer ribonucleic acid from the human placenta as tested by enzymatic assay Article de journal
Dans: Am J Obstet Gynecol, vol. 169, no. 3, p. 581-582, 1993, ISBN: 8372867, (0002-9378 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Female Guanine/*analogs & derivatives/chemistry Human Placenta/*chemistry Pregnancy RNA, Transfer/*chemistry, Unité ARN
@article{,
title = {Unusual deficiency of the modified purine base queuine in transfer ribonucleic acid from the human placenta as tested by enzymatic assay},
author = {W Baranowski and J Tomaszewski and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8372867},
isbn = {8372867},
year = {1993},
date = {1993-01-01},
journal = {Am J Obstet Gynecol},
volume = {169},
number = {3},
pages = {581-582},
abstract = {Transfer ribonucleic acid from rapidly growing tissues, particularly from neoplasia, is partially deficient in queuine, a highly modified transfer ribonucleic acid constituent. By means of an enzymatic assay we also found a queuine deficiency (14%) in human placenta transfer ribonucleic acid despite its high concentrations in the amniotic fluid. Proposed cause and significance of the results are discussed.},
note = {0002-9378
Journal Article},
keywords = {Female Guanine/*analogs & derivatives/chemistry Human Placenta/*chemistry Pregnancy RNA, Transfer/*chemistry, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pfeiffer P, Jung J L, Heitzler J, Keith G
Unusual structure of the double-stranded RNA associated with the '447' cytoplasmic male sterility in Vicia faba Article de journal
Dans: J Gen Virol, vol. 74, no. Pt 6, p. 1167-1173, 1993, ISBN: 7685375, (0022-1317 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Cytoplasm Extrachromosomal Inheritance/*genetics Fabaceae/*genetics Inclusion Bodies, Genetic, Medicinal Pollen/genetics RNA/*genetics/isolation & purification RNA Replicase/metabolism Transcription, Unité ARN, Viral Infertility/genetics Molecular Sequence Data *Plants
@article{,
title = {Unusual structure of the double-stranded RNA associated with the '447' cytoplasmic male sterility in Vicia faba},
author = {P Pfeiffer and J L Jung and J Heitzler and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685375},
isbn = {7685375},
year = {1993},
date = {1993-01-01},
journal = {J Gen Virol},
volume = {74},
number = {Pt 6},
pages = {1167-1173},
abstract = {The 16.7 kbp dsRNA specific to the '447' cytoplasmic male sterility (CMS) line of Vicia faba was labelled in vitro with [alpha-32P]ATP and poly(A) polymerase, and by T4 RNA ligase-mediated addition of [32P]pCp. Analysis of the reaction products under denaturing conditions revealed in both cases extensive labelling of a 4.5 kb ssRNA, already detected in previous experiments in which the RNA-dependent RNA polymerase associated with the dsRNA was allowed to pursue RNA synthesis on preinitiated complexes. Mobility shift analysis of total pCp-labelled dsRNA revealed not two but three different 3' termini. The most prominent sequencing pattern corresponded to the 4.5 kb ssRNA, indicating that this RNA species has a preferentially accessible, free 3' OH extremity. Northern blot analysis of the denatured dsRNA confirmed that the 4.5 kb ssRNA is a subgenomic mRNA and detected its counterpart of about 12 kb. Nearly all 16.7 kbp dsRNA molecules featured an interrupted positive-sense strand, indicating a marked prevalence of transcription over replication complexes. This unusual strategy of transcription by a strand displacement mechanism, following initiation at an internal discontinuity, is compared with that of other dsRNA viruses or defective viruses, and is discussed in relation to the expression of the CMS trait.},
note = {0022-1317
Journal Article},
keywords = {Base Sequence Cytoplasm Extrachromosomal Inheritance/*genetics Fabaceae/*genetics Inclusion Bodies, Genetic, Medicinal Pollen/genetics RNA/*genetics/isolation & purification RNA Replicase/metabolism Transcription, Unité ARN, Viral Infertility/genetics Molecular Sequence Data *Plants},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M L, Keith G, Fix C, Wilhelm F X
Pleiotropic effect of a point mutation in the yeast SUP4-o tRNA gene: in vivo pre-tRNA processing in S. cerevisiae Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 4, p. 791-796, 1992, ISBN: 1542574, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Blotting, Fungal/*genetics Genes, Fungal/genetics/metabolism RNA, Northern Genes, Suppressor/*genetics Introns/genetics Molecular Sequence Data Mutation/genetics RNA Precursors/*metabolism RNA, Transfer, Tyr/*genetics/metabolism Saccharomyces cerevisiae/*genetics/metabolism, Unité ARN
@article{,
title = {Pleiotropic effect of a point mutation in the yeast SUP4-o tRNA gene: in vivo pre-tRNA processing in S. cerevisiae},
author = {M L Wilhelm and G Keith and C Fix and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1542574},
isbn = {1542574},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {4},
pages = {791-796},
abstract = {The expression of mutant tyrosine-inserting ochre suppressor SUP4-o tRNA genes in vivo in S. cerevisiae was examined as a basis for further studies of tRNA transcription and processing. In vivo yeast precursor tRNAs have been identified by filter hybridization and primer extension analysis. We have previously shown that a mutant SUP4-o tRNA gene with a C52----A52 transversion at positive 52 (C52----A52(+IVS) allele) was transcribed but that the primary transcript was not processed correctly. We show here that 5' and 3' end processing as well as splicing are defective for this mutant but that the 5' end processing is restored when the intron is removed from the gene by oligonucleotide directed mutagenesis (C52----A52(-IVS) allele). Our results imply that the C52----A52 transversion by itself cannot account for the lack of susceptibility to RNase P cleavage but that the overall tertiary structure of the mutant tRNA precursor is destabilized by the intron/anticodon stem. A second consequence of the C52----A52 transversion is to prevent complete maturation of the tRNA precursor at its 3' end since intermediates containing incompletely processed 3' trailers accumulate in the yeast cells transformed with the C52----A52(-IVS) allele. A correct structure of the T stem might therefore define a structural feature required for the recognition of the 3' processing activity.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Blotting, Fungal/*genetics Genes, Fungal/genetics/metabolism RNA, Northern Genes, Suppressor/*genetics Introns/genetics Molecular Sequence Data Mutation/genetics RNA Precursors/*metabolism RNA, Transfer, Tyr/*genetics/metabolism Saccharomyces cerevisiae/*genetics/metabolism, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M L, Baranowski W, Keith G, Wilhelm F X
Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 15, p. 4106, 1992, ISBN: 1508703, (0305-1048 Journal Article).
Liens | BibTeX | Étiquettes: 5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN
@article{,
title = {Rapid transfer of small RNAs from a polyacrylamide gel onto a nylon membrane using a gel dryer},
author = {M L Wilhelm and W Baranowski and G Keith and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1508703},
isbn = {1508703},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {15},
pages = {4106},
note = {0305-1048
Journal Article},
keywords = {5S/*isolation & purification RNA, Acrylic Resins Human Nylons RNA, Ribosomal, Small Nuclear/*isolation & purification RNA, Transfer/*isolation & purification Yeasts/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Michel F
Some tertiary motifs of RNA foldings Chapitre d'ouvrage
Dans: Lilley, D M J; Heumann, H; Suck, D (Ed.): Structural Tools for the Analysis of Protein-Nucleic Acid Complexes (Advances in Life Sciences), p. 255-267, Birkhauser Verlag, Basel, 1992.
Liens | BibTeX | Étiquettes: Unité ARN
@inbook{,
title = {Some tertiary motifs of RNA foldings},
author = {E Westhof and F Michel},
editor = {D M J Lilley and H Heumann and D Suck},
url = {http://www.amazon.com/Structural-Analysis-Protein-Nucleic-Complexes-Advances/dp/0817627766},
year = {1992},
date = {1992-01-01},
booktitle = {Structural Tools for the Analysis of Protein-Nucleic Acid Complexes (Advances in Life Sciences)},
pages = {255-267},
publisher = {Birkhauser Verlag, Basel},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Westhof E, Jaeger L
RNA pseudoknots Article de journal
Dans: Curr Opin Struct Biol, vol. 2, no. 3, p. 327-333, 1992.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {RNA pseudoknots},
author = {E Westhof and L Jaeger},
url = {http://www.sciencedirect.com/science/article/pii/0959440X9290221R},
doi = {10.1016/0959-440X(92)90221-R},
year = {1992},
date = {1992-01-01},
journal = {Curr Opin Struct Biol},
volume = {2},
number = {3},
pages = {327-333},
abstract = {RNA pseudoknots result from Watson-Crick base pairing involving a stretch of bases located between paired strands and a distal single-stranded region. Recently, significant advances in our understanding of their structural and functional aspects have been accomplished. At the structural level, modelling and NMR studies have shown that a defined subset of pseudoknots may be considered as tertiary motifs in RNA foldings. At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E
Westhof's rule Article de journal
Dans: Nature, vol. 358, no. 6386, p. 459-460, 1992, ISBN: 1641036, (0028-0836 Letter).
Liens | BibTeX | Étiquettes: *Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF
@article{,
title = {Westhof's rule},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1641036},
isbn = {1641036},
year = {1992},
date = {1992-01-01},
journal = {Nature},
volume = {358},
number = {6386},
pages = {459-460},
note = {0028-0836
Letter},
keywords = {*Hydrogen Bonding *Nucleic Acid Conformation, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Tounekti N, Mougel M, Roy C, Marquet R, Darlix J L, Paoletti J, Ehresmann B, Ehresmann C
Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA Article de journal
Dans: J Mol Biol, vol. 223, no. 1, p. 205-220, 1992, ISBN: 1731069, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Comparative Study Hydrogen Bonding Macromolecular Systems Molecular Sequence Data Molecular Structure Moloney murine leukemia virus/*ultrastructure Nucleic Acid Conformation Phylogeny RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure Sequence Alignment Support
@article{,
title = {Effect of dimerization on the conformation of the encapsidation Psi domain of Moloney murine leukemia virus RNA},
author = {N Tounekti and M Mougel and C Roy and R Marquet and J L Darlix and J Paoletti and B Ehresmann and C Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1731069},
isbn = {1731069},
year = {1992},
date = {1992-01-01},
journal = {J Mol Biol},
volume = {223},
number = {1},
pages = {205-220},
abstract = {In Moloney murine leukemia virus, the encapsidation Psi element was shown to be necessary and sufficient to promote packaging of viral RNA, and to be required for dimerization. The conformation of the Psi domain (nucleotides 215 to 565) was investigated in solution by chemical probing. The four bases were monitored at one of their Watson-Crick positions with dimethylsulfate at cytosine N3 and adenosine N1, and with a carbodiimide derivative at guanosine N1 and uridine N3. Position N7 of adenine residues was probed with diethylpyrocarbonate. The analyses were conducted on in vitro transcribed fragments corresponding either to the isolated Psi domain or to the 5'-terminal 725 nucleotides. The RNA fragments were analyzed in their monomeric and dimeric forms. A secondary structure model was derived from probing data, computer prediction and sequence analysis of related murine retroviruses. One major result is that Psi forms an independent and highly structured domain. Dimerization induces an extensive reduction of reactivity in region 278 to 309 that can be interpreted as the result of intermolecular interactions and/or intramolecular conformational rearrangements. A second region (around position 215) was shown to display discrete reactivity changes upon dimerization. These two regions represent likely elements of dimerization. More unexpectedly, reactivity changes (essentially enhancement of reactivity) were also detected in another part of Psi (around position 480) not believed to contain elements of dimerization. These reactivity changes could be interpreted as dimerization-induced allosteric transitions.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence Comparative Study Hydrogen Bonding Macromolecular Systems Molecular Sequence Data Molecular Structure Moloney murine leukemia virus/*ultrastructure Nucleic Acid Conformation Phylogeny RNA, MARQUET, Non-U.S. Gov't, Unité ARN, Viral/chemistry/*ultrastructure Sequence Alignment Support},
pubstate = {published},
tppubtype = {article}
}
Sturchler C, Carbon P, Krol A
An additional long-range interaction in human U1 snRNA Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 6, p. 1215-1221, 1992, ISBN: 1532853, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Binding Sites Hela Cells Human Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Small Nuclear, Small Nuclear/*chemistry/metabolism Ribonucleases/metabolism Ribonucleoproteins/metabolism Ribonucleoproteins, Unité ARN
@article{,
title = {An additional long-range interaction in human U1 snRNA},
author = {C Sturchler and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1532853},
isbn = {1532853},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {6},
pages = {1215-1221},
abstract = {We present evidence for the existence of an additional long-range interaction in vertebrate U1 snRNAs. By submitting human U1 snRNP, HeLa nuclear extracts, authentic human or X. laevis in vitro transcribed U1 snRNAs to RNase V1, a nuclease specific for double-stranded regions, cleavages occurred in the sequence psi psi ACC (positions 5-9) residing in the 5' terminal region of the RNA. The RNase V1 sensitive region is insensitive to single-stranded probes, something unexpected knowing that it was considered single-stranded in order to base-pair to pre-mRNA 5' splice site. We have identified the sequence GGUAG (positions 132-136) as the only possible 3' partner. Mutants, either abolishing or restoring the interaction between the partners, coupled to an RNase V1 assay, served to substantiate this base-pairing model. The presence of this additional helix, even detected in nuclear extracts under in vitro splicing conditions, implies that a conformational change must occur to release a free U1 snRNA 5' end.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Binding Sites Hela Cells Human Molecular Sequence Data Mutagenesis, Site-Directed Nucleic Acid Conformation RNA, Small Nuclear, Small Nuclear/*chemistry/metabolism Ribonucleases/metabolism Ribonucleoproteins/metabolism Ribonucleoproteins, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Skouri M, Munch J P, Lorber B, Giege R, Candau S
Interaction between lysozyme molecules under precrystallization conditions studied by light scattering. Article de journal
Dans: J Crystal Growth, vol. 122, no. 1-4, p. 14-20, 1992, ISBN: 10.1016/0022-0248(92)90221-4.
Résumé | Liens | BibTeX | Étiquettes: Unité ARN
@article{,
title = {Interaction between lysozyme molecules under precrystallization conditions studied by light scattering.},
author = {M Skouri and J P Munch and B Lorber and R Giege and S Candau},
url = {http://www.sciencedirect.com/science/article/pii/0022024892902214},
isbn = {10.1016/0022-0248(92)90221-4},
year = {1992},
date = {1992-01-01},
journal = {J Crystal Growth},
volume = {122},
number = {1-4},
pages = {14-20},
abstract = {Lightscattering experiments were undertaken on lysozymeunder various solvent conditions. When the protein is undersaturated, attractive interparticular interactions are detected. They are enhanced when the temperature is decreased, but are much weaker in NaCl solutions in which the protein crystallizes than in ammonium sulfate solutions in which it forms amorphous precipitates. When the protein in a NaCl solution is brought to supersaturation by a temperature decrease, lightscattering measurements indicate the simultaneous presence of two scatter populations which can be assimilated to individual lysozymemolecules and to large particles. Kinetic experiments in which the temperature is quenched rapidly indicate that the apparent hydrodynamic radius of the large particles increases regularly with time up to a plateau value of about 2600A˚.},
keywords = {Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Senger B, Despons L, Walter P, Fasiolo F
The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 89, no. 22, p. 10768-10771, 1992, ISBN: 1438273, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon/genetics/*metabolism Base Sequence Kinetics Methionine/*metabolism Models, Genetic, Met/genetics/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN
@article{,
title = {The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA},
author = {B Senger and L Despons and P Walter and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1438273},
isbn = {1438273},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {22},
pages = {10768-10771},
abstract = {Previous work suggested that the presence of the anticodon CAU alone was enough to confer methionine acceptance to a tRNA. Conversions of Escherichia coli nonmethionine tRNAs to a methionine-accepting species were obtained by substitutions reconstructing the whole methionine anticodon loop together with preservation (or introduction) of the acceptor stem base A73. We show here that the CAU triplet alone is unable to confer methionine acceptance when transplanted into a yeast aspartic tRNA. Both non-anticodon bases of the anticodon loop of yeast tRNA(Met) and A73 are required in addition to CAU for methionine acceptance. The importance of these non-anticodon bases in other CAU-containing tRNA frameworks was also established. These specific non-anticodon base interactions make a substantial thermodynamic contribution to the methionine acceptance of a transfer RNA.},
note = {0027-8424
Journal Article},
keywords = {Anticodon/genetics/*metabolism Base Sequence Kinetics Methionine/*metabolism Models, Genetic, Met/genetics/*metabolism Saccharomyces cerevisiae/*genetics Support, Non-U.S. Gov't Transcription, Structural Molecular Sequence Data Nucleic Acid Conformation RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Puglisi J D, Putz J, Schatz D, Eckstein F, Florentz C, Giege R
Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 89, no. 13, p. 5882-5886, 1992, ISBN: 1631068, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN
@article{,
title = {Determinant nucleotides of yeast tRNA(Asp) interact directly with aspartyl-tRNA synthetase},
author = {J Rudinger and J D Puglisi and J Putz and D Schatz and F Eckstein and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1631068},
isbn = {1631068},
year = {1992},
date = {1992-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {89},
number = {13},
pages = {5882-5886},
abstract = {The interaction of wild-type and mutant yeast tRNA(Asp) transcripts with yeast aspartyl-tRNA synthetase (AspRS; EC 6.1.1.12) has been probed by using iodine cleavage of phosphorothioate-substituted transcripts. AspRS protects phosphates in the anticodon (G34, U35), D-stem (U25), and acceptor end (G73) that correspond to determinant nucleotides for aspartylation. This protection, as well as that in anticodon stem (C29, U40, G41) and D-stem (U11 to U13), is consistent with direct interaction of AspRS at these phosphates. Other protection, in the variable loop (G45), D-loop (G18, G19), and T-stem and loop (G53, U54, U55), as well as enhanced reactivity at G37, may result from conformational changes of the transcript upon binding to AspRS. Transcripts mutated at determinant positions showed a loss of phosphate protection in the region of the mutation while maintaining the global protection pattern. The ensemble of results suggests that aspartylation specificity arises from both protein-base and protein-phosphate contacts and that different regions of tRNA(Asp) interact independently with AspRS. A mutant transcript of yeast tRNA(Phe) that contains the set of identity nucleotides for specific aspartylation gave a phosphate protection pattern strikingly similar to that of wild-type tRNA(Asp). This confirms that a small number of nucleotides within a different tRNA sequence context can direct specific interaction with synthetase.},
note = {0027-8424
Journal Article},
keywords = {Asp/chemistry/*metabolism Saccharomyces cerevisiae/enzymology Structure-Activity Relationship Support, Aspartate-tRNA Ligase/*metabolism Base Sequence Binding Sites DNA Mutational Analysis Fungal Proteins/metabolism Molecular Sequence Data Protein Binding RNA, FLORENTZ, Fungal/chemistry/metabolism RNA, Non-U.S. Gov't, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rudinger J, Florentz C, Dreher T, Giege R
Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 8, p. 1865-1870, 1992, ISBN: 1579487, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support
@article{,
title = {Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA},
author = {J Rudinger and C Florentz and T Dreher and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1579487},
isbn = {1579487},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {8},
pages = {1865-1870},
abstract = {Mischarging of the valine specific tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA has been tested in the presence of purified arginyl-, aspartyl-, histidinyl-, and phenylalanyl-tRNA synthetases from bakers' yeast. Important mischarging of a 264 nucleotide-long transcript was found with histidinyl-tRNA synthetase which can acylate this fragment up to a level of 25% with a loss of specificity (expressed as Vmax/KM ratios) of only 100 fold as compared to a yeast tRNA(His) transcript. Experiments on transcripts of various lengths indicate that the minimal valylatable fragment (n = 88) is the most efficient substrate for histidinyl-tRNA synthetase, with kinetic characteristics similar to those found for the control tRNA(His) transcript. Mutations in the anticodon or adjacent to the 3' CCA that severely affect the valylation capacity of the 264 nucleotide long TYMV fragment are without negative effect on its mischarging, and for some cases even improve its efficiency. A short fragment (n = 42) of the viral RNA containing the pseudoknot and corresponding to the amino acid accepting branch of the molecule is an efficient histidine acceptor.},
note = {0305-1048
Journal Article},
keywords = {Base Sequence Codon/genetics Histidine-tRNA Ligase/*metabolism Kinetics Molecular Sequence Data Mosaic Viruses/enzymology/genetics/*metabolism Mutation/genetics Nucleic Acid Conformation RNA, FLORENTZ, His/*metabolism RNA, Non-P.H.S. Yeasts/enzymology, Non-U.S. Gov't Support, Transfer, U.S. Gov't, Unité ARN, Viral/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Romby P, Brunel C, Caillet J, Springer M, Grunberg-Manago M, Westhof E, Ehresmann C, Ehresmann B
Dans: Nucleic Acids Res, vol. 20, no. 21, p. 5633-5640, 1992, ISBN: 1280807, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN
@article{,
title = {Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules},
author = {P Romby and C Brunel and J Caillet and M Springer and M Grunberg-Manago and E Westhof and C Ehresmann and B Ehresmann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1280807},
isbn = {1280807},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {21},
pages = {5633-5640},
abstract = {We previously showed that: (i) E.coli threonyl-tRNA synthetase (ThrRS) binds to the leader of its mRNA and represses translation by preventing ribosome binding to its loading site; (ii) the translational operator shares sequence and structure similarities with tRNA(Thr); (iii) it is possible to switch the specificity of the translational control from ThrRS to methionyl-tRNA synthetase (MetRS) by changing the CGU anticodon-like sequence to CAU, the tRNA(Met) anticodon. Here, we show that the wild type (CGU) and the mutated (CAU) operators act as competitive inhibitors of tRNA(Thr) and tRNA(fMet) for aminoacylation catalyzed by E.coli ThrRS and MetRS, respectively. The apparent Kd of the MetRS/CAU operator complex is one order magnitude higher than that of the ThrRS/CGU operator complex. Although ThrRS and MetRS shield the anticodon- and acceptor-like domains of their respective operators, the relative contribution of these two domains differs significantly. As in the threonine system, the interaction of MetRS with the CAU operator occludes ribosome binding to its loading site. The present data demonstrate that the anticodon-like sequence is one major determinant for the identity of the operator and the regulation specificity. It further shows that the tRNA-like operator obeys to tRNA identity rules.},
note = {0305-1048
Journal Article},
keywords = {Acylation Anticodon Base Sequence Binding, Bacterial Methionine-tRNA Ligase/metabolism Molecular Sequence Data Mutation Nucleic Acid Conformation *Operator Regions (Genetics) RNA, Bacterial/metabolism RNA, Competitive Escherichia coli/enzymology/*genetics *Gene Expression Regulation, Genetic, Met/metabolism RNA, Non-U.S. Gov't Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/metabolism Translation, ROMBY, Thr/metabolism Repressor Proteins/*metabolism Ribosomes/metabolism Support, Transfer, Transfer/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rippe K, Fritsch V, Westhof E, Jovin T M
Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex Article de journal
Dans: EMBO J, vol. 11, no. 10, p. 3777-3786, 1992, ISBN: 1396571, (0261-4189 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF
@article{,
title = {Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex},
author = {K Rippe and V Fritsch and E Westhof and T M Jovin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1396571},
isbn = {1396571},
year = {1992},
date = {1992-01-01},
journal = {EMBO J},
volume = {11},
number = {10},
pages = {3777-3786},
abstract = {The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H.O6 and N6H.N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.},
note = {0261-4189
Journal Article},
keywords = {Base Sequence Circular Dichroism DNA/*chemistry Hydrogen Bonding Hydrogen-Ion Concentration Indicators and Reagents Magnesium Chloride Models, Fluorescence Spectrophotometry, MARQUET, Molecular Molecular Sequence Data *Nucleic Acid Conformation Oligodeoxyribonucleotides/*chemistry Spectrometry, PAILLART, Ultraviolet Structure-Activity Relationship Thermodynamics, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Przykorska A, el Adlouni C, Keith G, Szarkowski J W, Dirheimer G
Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp) Article de journal
Dans: Nucleic Acids Res, vol. 20, no. 4, p. 659-663, 1992, ISBN: 1542562, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/*metabolism RNA, Base Composition Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/*metabolism Secale cereale Substrate Specificity Support, Phe/chemistry/genetics/*metabolism Ribonuclease, Transfer, Unité ARN
@article{,
title = {Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp)},
author = {A Przykorska and C el Adlouni and G Keith and J W Szarkowski and G Dirheimer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1542562},
isbn = {1542562},
year = {1992},
date = {1992-01-01},
journal = {Nucleic Acids Res},
volume = {20},
number = {4},
pages = {659-663},
abstract = {A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry/genetics/*metabolism RNA, Base Composition Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA, Non-U.S. Gov't Yeasts/genetics, Pancreatic/*metabolism Secale cereale Substrate Specificity Support, Phe/chemistry/genetics/*metabolism Ribonuclease, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}