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Immunologie, Immunopathologie et Chimie Thérapeutique
Publications
2009
Burnouf D. Y., Wagner J. E.
Kinetics of deoxy-CTP incorporation opposite a dG-C8-N-2-aminofluorene adduct by a high-fidelity DNA polymerase Article de journal
Dans: J Mol Biol, vol. 386, non 4, p. 951-61, 2009, (1089-8638 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Résumé | BibTeX | Étiquettes: Adducts, Bacillus, Catalytic, Cytidine, Deoxyguanosine/*metabolism, DNA, DNA-Directed, Domain, DUMAS, Elements, Fluorenes/*metabolism, Guanine, Kinetics, Oligonucleotides/metabolism, Phosphorothioate, Polymerase/*metabolism, Specificity, stearothermophilus/enzymology, Substrate, Titrimetry, Triphosphate/*metabolism
@article{,
title = {Kinetics of deoxy-CTP incorporation opposite a dG-C8-N-2-aminofluorene adduct by a high-fidelity DNA polymerase},
author = { D. Y. Burnouf and J. E. Wagner},
year = {2009},
date = {2009-01-01},
journal = {J Mol Biol},
volume = {386},
number = {4},
pages = {951-61},
abstract = {The model carcinogen N-2-acetylaminofluorene covalently binds to the C8 position of guanine to form two adducts, the N-(2'-deoxyguanosine-8-yl)-aminofluorene (G-AF) and the N-2-(2'-deoxyguanosine-8-yl)-acetylaminofluorene (G-AAF). Although they are chemically closely related, their biological effects are strongly different and they are processed by different damage tolerance pathways. G-AF is bypassed by replicative and high-fidelity polymerases, while specialized polymerases ensure synthesis past of G-AAF. We used the DNA polymerase I fragment of a Bacillus stearothermophilus strain as a model for a high-fidelity polymerase to study the kinetics of incorporation of deoxy-CTP (dCTP) opposite a single G-AF. Pre-steady-state kinetic experiments revealed a drastic reduction in dCTP incorporation performed by the G-AF-modified ternary complex. Two populations of these ternary complexes were identified: (i) a minor productive fraction (20%) that readily incorporates dCTP opposite the G-AF adduct with a rate similar to that measured for the adduct-free ternary complexes and (ii) a major fraction of unproductive complexes (80%) that slowly evolve into productive ones. In the light of structural data, we suggest that this slow rate reflects the translocation of the modified base within the active site, from the pre-insertion site into the insertion site. By making this translocation rate limiting, the G-AF lesion reveals a novel kinetic step occurring after dNTP binding and before chemistry.},
note = {1089-8638 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Adducts, Bacillus, Catalytic, Cytidine, Deoxyguanosine/*metabolism, DNA, DNA-Directed, Domain, DUMAS, Elements, Fluorenes/*metabolism, Guanine, Kinetics, Oligonucleotides/metabolism, Phosphorothioate, Polymerase/*metabolism, Specificity, stearothermophilus/enzymology, Substrate, Titrimetry, Triphosphate/*metabolism},
pubstate = {published},
tppubtype = {article}
}
The model carcinogen N-2-acetylaminofluorene covalently binds to the C8 position of guanine to form two adducts, the N-(2'-deoxyguanosine-8-yl)-aminofluorene (G-AF) and the N-2-(2'-deoxyguanosine-8-yl)-acetylaminofluorene (G-AAF). Although they are chemically closely related, their biological effects are strongly different and they are processed by different damage tolerance pathways. G-AF is bypassed by replicative and high-fidelity polymerases, while specialized polymerases ensure synthesis past of G-AAF. We used the DNA polymerase I fragment of a Bacillus stearothermophilus strain as a model for a high-fidelity polymerase to study the kinetics of incorporation of deoxy-CTP (dCTP) opposite a single G-AF. Pre-steady-state kinetic experiments revealed a drastic reduction in dCTP incorporation performed by the G-AF-modified ternary complex. Two populations of these ternary complexes were identified: (i) a minor productive fraction (20%) that readily incorporates dCTP opposite the G-AF adduct with a rate similar to that measured for the adduct-free ternary complexes and (ii) a major fraction of unproductive complexes (80%) that slowly evolve into productive ones. In the light of structural data, we suggest that this slow rate reflects the translocation of the modified base within the active site, from the pre-insertion site into the insertion site. By making this translocation rate limiting, the G-AF lesion reveals a novel kinetic step occurring after dNTP binding and before chemistry.
2002
Westhof E
Group I introns and RNA folding Article de journal
Dans: Biochem Soc Trans, vol. 30, non Pt 6, p. 1149-1152, 2002, ISBN: 12440993, (0300-5127 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence *Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA Splicing RNA, Catalytic, Unité ARN, WESTHOF
@article{,
title = {Group I introns and RNA folding},
author = {E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12440993},
isbn = {12440993},
year = {2002},
date = {2002-01-01},
journal = {Biochem Soc Trans},
volume = {30},
number = {Pt 6},
pages = {1149-1152},
abstract = {Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine cofactors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.},
note = {0300-5127
Journal Article
Review
Review, Tutorial},
keywords = {Base Sequence *Introns Molecular Sequence Data *Nucleic Acid Conformation RNA/*chemistry RNA Splicing RNA, Catalytic, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine cofactors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.