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Modèles Insectes d’Immunité Innée
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2004
Weixlbaumer A, Werner A, Flamm C, Westhof E, Schroeder R
Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 17, p. 5126-5133, 2004, ISBN: 15459283, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Double-Stranded/chemistry RNA, Non-U.S. Gov't Thermodynamics Ultraviolet Rays, Unité ARN, Viral/*chemistry Sodium/chemistry Support, WESTHOF Base Pairing Base Sequence Dimerization HIV-1/*genetics Macromolecular Systems Magnesium/chemistry Molecular Sequence Data Nucleic Acid Conformation RNA Stability RNA
@article{,
title = {Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes},
author = {A Weixlbaumer and A Werner and C Flamm and E Westhof and R Schroeder},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15459283},
isbn = {15459283},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {17},
pages = {5126-5133},
abstract = {The HIV-1 type dimerization initiation signal (DIS) loop was used as a starting point for the analysis of the stability of Watson-Crick (WC) base pairs in a tertiary structure context. We used ultraviolet melting to determine thermodynamic parameters for loop-loop tertiary interactions and compared them with regular secondary structure RNA helices of the same sequences. In 1 M Na+ the loop-loop interaction of a HIV-1 DIS type pairing is 4 kcal/mol more stable than its sequence in an equivalent regular and isolated RNA helix. This difference is constant and sequence independent, suggesting that the rules governing the stability of WC base pairs in the secondary structure context are also valid for WC base pairs in the tertiary structure context. Moreover, the effect of ion concentration on the stability of loop-loop tertiary interactions differs considerably from that of regular RNA helices. The stabilization by Na+ and Mg2+ is significantly greater if the base pairing occurs within the context of a loop-loop interaction. The dependence of the structural stability on salt concentration was defined via the slope of a T(m)/log [ion] plot. The short base-paired helices are stabilized by 8 degrees C/log [Mg2+] or 11 degrees C/log [Na+], whereas base-paired helices forming tertiary loop-loop interactions are stabilized by 16 degrees C/log [Mg2+] and 26 degrees C/log [Na+]. The different dependence on ionic strength that is observed might reflect the contribution of specific divalent ion binding to the preformation of the hairpin loops poised for the tertiary kissing loop-loop contacts.},
note = {1362-4962
Journal Article},
keywords = {Double-Stranded/chemistry RNA, Non-U.S. Gov't Thermodynamics Ultraviolet Rays, Unité ARN, Viral/*chemistry Sodium/chemistry Support, WESTHOF Base Pairing Base Sequence Dimerization HIV-1/*genetics Macromolecular Systems Magnesium/chemistry Molecular Sequence Data Nucleic Acid Conformation RNA Stability RNA},
pubstate = {published},
tppubtype = {article}
}
The HIV-1 type dimerization initiation signal (DIS) loop was used as a starting point for the analysis of the stability of Watson-Crick (WC) base pairs in a tertiary structure context. We used ultraviolet melting to determine thermodynamic parameters for loop-loop tertiary interactions and compared them with regular secondary structure RNA helices of the same sequences. In 1 M Na+ the loop-loop interaction of a HIV-1 DIS type pairing is 4 kcal/mol more stable than its sequence in an equivalent regular and isolated RNA helix. This difference is constant and sequence independent, suggesting that the rules governing the stability of WC base pairs in the secondary structure context are also valid for WC base pairs in the tertiary structure context. Moreover, the effect of ion concentration on the stability of loop-loop tertiary interactions differs considerably from that of regular RNA helices. The stabilization by Na+ and Mg2+ is significantly greater if the base pairing occurs within the context of a loop-loop interaction. The dependence of the structural stability on salt concentration was defined via the slope of a T(m)/log [ion] plot. The short base-paired helices are stabilized by 8 degrees C/log [Mg2+] or 11 degrees C/log [Na+], whereas base-paired helices forming tertiary loop-loop interactions are stabilized by 16 degrees C/log [Mg2+] and 26 degrees C/log [Na+]. The different dependence on ionic strength that is observed might reflect the contribution of specific divalent ion binding to the preformation of the hairpin loops poised for the tertiary kissing loop-loop contacts.
1993
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}
}
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.