Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gotte M, Marquet R, Isel C, Anderson V E, Keith G, Gross H J, Ehresmann C, Ehresmann B, Heumann H
Probing the higher order structure of RNA with peroxonitrous acid Article de journal
Dans: FEBS Lett, vol. 390, no. 2, p. 226-228, 1996, ISBN: 8706865, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Probing the higher order structure of RNA with peroxonitrous acid},
author = {M Gotte and R Marquet and C Isel and V E Anderson and G Keith and H J Gross and C Ehresmann and B Ehresmann and H Heumann},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8706865},
isbn = {8706865},
year = {1996},
date = {1996-01-01},
journal = {FEBS Lett},
volume = {390},
number = {2},
pages = {226-228},
abstract = {Potassium peroxonitrite (ONOOK) and [Fe(EDTA)]2- were used to analyze the influence of chemically entirely different hydroxyl radical sources on tRNA cleavage profiles. [Fe(EDTA)]2- gives rise to hydroxyl radicals via a Fenton-like reaction during the oxidation of chelated Fe2+, while ONOOK generates hydroxyl radicals via its conjugate acid (ONOOH) when adding a stable alkaline solution of ONOOK in samples buffered at neutral pH. [Fe(EDTA)]2- is known to induce oxidative strand scission at sugar moieties thought to be solvent accessible, while those residues located in the 'inside' of structured RNAs are protected. Although ONOOH is neutral and significantly smaller than the metal complex, both reagents generate the same protection pattern on tRNAs, suggesting that access of the commonly formed hydroxyl radical, rather than access of its source, is the determining factor when probing the higher order structure of RNA. Strong difference in reactivity is only seen at the modified 2-thiouridine S34 of tRNA(Lys3) which shows hyperreactivity towards ONOOK treatment. This particular reaction may require interaction between the peroxonitrite anion and the thiocarbonyl group of the base, since hyperreactivity is not observed when probing the dethiolated tRNA(Lys3).},
note = {0014-5793
Journal Article},
keywords = {Animals Chelating Agents Edetic Acid Hydroxyl Radical/chemistry Molecular Probes Molecular Structure *Nitrates RNA, Fungal/chemistry RNA, Lys/chemistry RNA, MARQUET, Non-U.S. Gov't, Phe/chemistry Rabbits Saccharomyces cerevisiae/chemistry Support, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Heyman T, Agoutin B, Fix C, Dirheimer G, Keith G
Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU Article de journal
Dans: FEBS Lett, vol. 347, no. 2-3, p. 143-146, 1994, ISBN: 8033992, (0014-5793 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN
@article{,
title = {Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU},
author = {T Heyman and B Agoutin and C Fix and G Dirheimer and G Keith},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8033992},
isbn = {8033992},
year = {1994},
date = {1994-01-01},
journal = {FEBS Lett},
volume = {347},
number = {2-3},
pages = {143-146},
abstract = {The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.},
note = {0014-5793
Journal Article},
keywords = {Anticodon Base Sequence Culture Media Galactose Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization RNA Probes RNA, Fungal/*chemistry RNA, Ser/analysis/*chemistry Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Felden B, Florentz C, McPherson A, Giege R
A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA Article de journal
Dans: Nucleic Acids Res, vol. 22, no. 15, p. 2882-2886, 1994, ISBN: 8065897, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support
@article{,
title = {A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA},
author = {B Felden and C Florentz and A McPherson and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8065897},
isbn = {8065897},
year = {1994},
date = {1994-01-01},
journal = {Nucleic Acids Res},
volume = {22},
number = {15},
pages = {2882-2886},
abstract = {A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.},
note = {0305-1048
Journal Article},
keywords = {Acylation Base Sequence Comparative Study Histidine/*metabolism Histidine-tRNA Ligase/metabolism Kinetics Molecular Sequence Data *Nucleic Acid Conformation Phylogeny RNA, FLORENTZ, His/metabolism RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry RNA, Unité ARN, Viral/*chemistry Saccharomyces cerevisiae/enzymology Sequence Homology Support},
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}
}