MersV1, Main, Exploration, bibRecord, 002948

Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

Identifieur interne : 002948 ( Main/Exploration ); précédent : 002947; suivant : 002949

Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

Auteurs : Bruno Pagano [Italie] ; Carlo A. Mattia ; Luigi Cavallo ; Seiichi Uesugi ; Concetta Giancola ; Franca Fraternali

Source :

The journal of physical chemistry. B [ 1520-6106 ] ; 2008.

RBID : pubmed:18767769

Descripteurs français

KwdFr :
- ADN (), ADN (génétique), ARN (), ARN (génétique), Acides aminés (), Cations (), G-quadruplexes, Modèles moléculaires, Simulation numérique, Sodium (), Séquence nucléotidique.
MESH :
- génétique : ADN, ARN.
- ADN, ARN, Acides aminés, Cations, G-quadruplexes, Modèles moléculaires, Simulation numérique, Sodium, Séquence nucléotidique.

English descriptors

KwdEn :
- Amino Acids (chemistry), Base Sequence, Cations (chemistry), Computer Simulation, DNA (chemistry), DNA (genetics), G-Quadruplexes, Models, Molecular, RNA (chemistry), RNA (genetics), Sodium (chemistry).
MESH :
- chemical , chemistry : Amino Acids, Cations, DNA, RNA, Sodium.
- chemical , genetics : DNA, RNA.
- Base Sequence, Computer Simulation, G-Quadruplexes, Models, Molecular.

Abstract

Molecular dynamics simulations have been used to study the differences between two DNA and RNA 14-mer quadruplexes of analogous sequences. Their structures present a completely different fold: DNA forms a bimolecular quadruplex containing antiparallel strands and diagonal loops; RNA forms an intrastrand parallel quadruplex containing a G-tetrad and an hexad, which dimerizes by hexad stacking. We used a multiscale computational approach combining classical Molecular dynamics simulations and density functional theory calculations to elucidate the difference in stability of the 2-folds and their ability in coordinating cations. The presence of 2'-OH groups in the RNA promotes the formation of a large number of intramolecular hydrogen bonds that account for the difference in fold and stability of the two 14-mers. We observe that the adenines in the RNA quadruplex play a key role in conserving the geometry of the hexad. We predict the cation coordination mode of the two quadruplexes, not yet observed experimentally, and we offer a rationale for the corresponding binding energies involved.

DOI: 10.1021/jp804036j
PubMed: 18767769

Affiliations:

Italie

Le document en format XML

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<front><div type="abstract" xml:lang="en">Molecular dynamics simulations have been used to study the differences between two DNA and RNA 14-mer quadruplexes of analogous sequences. Their structures present a completely different fold: DNA forms a bimolecular quadruplex containing antiparallel strands and diagonal loops; RNA forms an intrastrand parallel quadruplex containing a G-tetrad and an hexad, which dimerizes by hexad stacking. We used a multiscale computational approach combining classical Molecular dynamics simulations and density functional theory calculations to elucidate the difference in stability of the 2-folds and their ability in coordinating cations. The presence of 2'-OH groups in the RNA promotes the formation of a large number of intramolecular hydrogen bonds that account for the difference in fold and stability of the two 14-mers. We observe that the adenines in the RNA quadruplex play a key role in conserving the geometry of the hexad. We predict the cation coordination mode of the two quadruplexes, not yet observed experimentally, and we offer a rationale for the corresponding binding energies involved.</div>
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Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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Pour générer des pages wiki

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