Wittberger D, Berens C, Hammann C, Westhof E, Schroeder R
Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs Article de journal
Dans: J Mol Biol, vol. 300, no. 2, p. 339-352, 2000, ISBN: 10873469, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support
@article{,
title = {Evaluation of uranyl photocleavage as a probe to monitor ion binding and flexibility in RNAs},
author = {D Wittberger and C Berens and C Hammann and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10873469},
isbn = {10873469},
year = {2000},
date = {2000-01-01},
journal = {J Mol Biol},
volume = {300},
number = {2},
pages = {339-352},
abstract = {In order to evaluate uranyl photocleavage as a tool to identify and characterize structural and dynamic properties in RNA, we compared uranyl cleavage sites in five RNA molecules with known X-ray structures, namely the hammerhead and hepatitis delta virus ribozymes, the P4-P6 domain of the Tetrahymena group I intron, as well as tRNA(Phe) and tRNA(Asp) from yeast. Uranyl photocleavage was observed at specific positions in all molecules investigated. In order to characterize the sites, photocleavage was performed in the absence and in increasing amounts of MgCl(2). Uranyl photocleavage correlates well with sites of low calculated accessibility, suggesting that uranyl ions bind in tight RNA pockets formed by close approach of phosphate groups. RNA foldings require ion binding, usually magnesium ions. Thus, upon the adoption of the native structure, uranyl ions can no longer bind well except in flexible and open to the solvent regions that can undergo induced-fit without disrupting the native fold. Uranyl photocleavage was compared to N-ethyl-N-nitrosourea and lead-induced cleavages in the context of the three-dimensional X-ray structures. Overall, the regions protected from ENU attack are sites of uranyl cleavage, indicating sites of low accessibility which can form ion binding sites. On the contrary, lead cleavages occur at flexible and accessible sites and correlate with the unspecific cleavages prevalent in dynamic and open regions. Applied in a magnesium-dependent manner, and only in combination with other backbone probing agents such as N-ethyl-N-nitrosourea, lead and Fenton cleavage, uranyl probing has the potential to reveal high-affinity metal ion environments, as well as regions involved in conformational transitions.},
note = {0022-2836
Journal Article},
keywords = {Animals Base Pairing Base Sequence Ethylnitrosourea/metabolism Hepatitis Delta Virus/genetics Hydrogen Peroxide/metabolism Introns/genetics Ions/metabolism Iron/metabolism Lead/metabolism Magnesium Chloride/pharmacology Models, Asp/chemistry/genetics/metabolism RNA, Catalytic/chemistry/genetics/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation *Photolysis/drug effects Pliability RNA/*chemistry/genetics/*metabolism RNA, Non-U.S. Gov't Tetrahymena/genetics Uranyl Nitrate/*metabolism Yeasts/genetics, Phe/chemistry/genetics/metabolism RNA, Protozoan/chemistry/genetics/metabolism RNA, Transfer, Unité ARN, Viral/chemistry/genetics/metabolism Solvents Support},
pubstate = {published},
tppubtype = {article}
}
Aphasizhev R, Théobald-Dietrich A, Kostyuk D, Kochetkov S N, Kisselev L, Giege R, Fasiolo F
Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides Article de journal
Dans: RNA, vol. 3, no. 8, p. 893-904, 1997, ISBN: 9257648, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN
@article{,
title = {Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides},
author = {R Aphasizhev and A Théobald-Dietrich and D Kostyuk and S N Kochetkov and L Kisselev and R Giege and F Fasiolo},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9257648},
isbn = {9257648},
year = {1997},
date = {1997-01-01},
journal = {RNA},
volume = {3},
number = {8},
pages = {893-904},
abstract = {The contribution of the ribose 2'-hydroxyls to RNA structure and function has been analyzed, but still remains controversial. In this work, we report the use of a mutant T7 RNA polymerase as a tool in RNA studies, applied to the aspartate and methionine tRNA aminoacylation systems from yeast. Our approach consists of determining the effect of substituting natural ribonucleotides by deoxyribonucleotides in RNA and, thereby, defining the subset of important 2'-hydroxyl groups. We show that deoxyribose-containing RNA can be folded in a global conformation similar to that of natural RNA. Melting curves of tRNAs, obtained by temperature-gradient gel electrophoresis, indicate that in deoxyribo-containing molecules, the thermal stability of the tertiary network drops down, whereas the stability of the secondary structure remains unaltered. Nuclease footprinting reveals a significant increase in the accessibility of both single- and double-stranded regions. As to the functionality of the deoxyribose-containing tRNAs, their in vitro aminoacylation efficiency indicates striking differential effects depending upon the nature of the substituted ribonucleotides. Strongest decrease in charging occurs for yeast initiator tRNA(Met) transcripts containing dG or dC residues and for yeast tRNA(Asp) transcripts with dU or dG. In the aspartate system, the decreased aminoacylation capacities can be correlated with the substitution of the ribose moieties of U11 and G27, disrupting two hydrogen bond contacts with the synthetase. Altogether, this suggests that specific 2'-hydroxyl groups in tRNAs can act as determinants specifying aminoacylation identity.},
note = {1355-8382
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence DNA-Directed RNA Polymerases/genetics/metabolism Deoxyribonucleotides/chemistry/*metabolism Models, Genetic, Met/chemistry/genetics/metabolism Structure-Activity Relationship Support, Molecular Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Non-U.S. Gov't *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-9, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska and G Dirheimer and J W Szarkowski and A Przykorska},
editor = {Editor},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-9},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-9, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska 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=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-9},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Gabryszuk J, Keith G, Monko M, Kuligowska E, Dirheimer G, Szarkowski J W, Przykorska A
Structural specificity of nuclease from wheat chloroplasts stroma Article de journal
Dans: Nucleic Acids Symp Ser, no. 33, p. 115-119, 1995, ISBN: 8643343, (0261-3166 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer, Unité ARN
@article{,
title = {Structural specificity of nuclease from wheat chloroplasts stroma},
author = {J Gabryszuk and G Keith and M Monko and E Kuligowska 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=8643343},
isbn = {8643343},
year = {1995},
date = {1995-01-01},
journal = {Nucleic Acids Symp Ser},
number = {33},
pages = {115-119},
abstract = {A single-strand-specific nuclease from wheat chloroplasts (ChS nuclease) was tested as a tool for RNA secondary and tertiary structure investigations, using yeast tRNA(Phe) and yeast tRNA(Asp) as models. In tRNA(Phe) the nuclease introduced main primary cleavages at positions U33, A35 and A36 in the anticodon-loop and G18 and G19 in the D-loop. In tRNA(Asp) the main primary cleavages occurred at positions U33, G34 and U35 in the anticodon-loop and the lower one at position C20:1 in the D-loop. No primary cleavages were observed within the double-stranded stems. Because ChS nuclease has (i) a low molecular weight, (ii) a wide pH range of action (5.0 to 7.5) (iii) no divalent cation requirement in the reaction mixture and (iv) can be obtained as a pure protein in rather large quantities it appeared to be a very good tool for secondary and tertiary structural studies of RNAs.},
note = {0261-3166
Journal Article},
keywords = {Asp/chemistry/genetics/metabolism RNA, Base Sequence Binding Sites Chloroplasts/*enzymology Endonucleases/isolation & purification/*metabolism Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry/metabolism RNA, Fungal/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Triticum/*enzymology, Phe/chemistry/genetics/metabolism Substrate Specificity Support, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}