MersV1, PubMed, Corpus, bibRecord, 002609

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.

Identifieur interne : 002609 ( PubMed/Corpus ); précédent : 002608; suivant : 002610

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.

Auteurs : L. Ayadi ; C. Coulombeau ; R. Lavery

Source :

Biophysical journal [ 0006-3495 ] ; 1999.

RBID : pubmed:10585943

English descriptors

KwdEn :
- Base Pairing, Base Sequence, Biophysical Phenomena, Biophysics, DNA (chemistry), Models, Molecular, Nucleic Acid Conformation, Thermodynamics.
MESH :
- chemical , chemistry : DNA.
- Base Pairing, Base Sequence, Biophysical Phenomena, Biophysics, Models, Molecular, Nucleic Acid Conformation, Thermodynamics.

Abstract

Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature.

DOI: 10.1016/S0006-3495(99)77152-3
PubMed: 10585943

Links to Exploration step

pubmed:10585943

Le document en format XML

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<author><name sortKey="Ayadi, L" sort="Ayadi, L" uniqKey="Ayadi L" first="L" last="Ayadi">L. Ayadi</name>
<affiliation><nlm:affiliation>Laboratoire d'Etudes Dynamiques et Structurales de la Sélectivité, Laboratoire de Chimie Bioorganique, Université Joseph Fourier, F-38041 Grenoble, Cedex 9, France.</nlm:affiliation>
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<author><name sortKey="Coulombeau, C" sort="Coulombeau, C" uniqKey="Coulombeau C" first="C" last="Coulombeau">C. Coulombeau</name>
</author>
<author><name sortKey="Lavery, R" sort="Lavery, R" uniqKey="Lavery R" first="R" last="Lavery">R. Lavery</name>
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<author><name sortKey="Ayadi, L" sort="Ayadi, L" uniqKey="Ayadi L" first="L" last="Ayadi">L. Ayadi</name>
<affiliation><nlm:affiliation>Laboratoire d'Etudes Dynamiques et Structurales de la Sélectivité, Laboratoire de Chimie Bioorganique, Université Joseph Fourier, F-38041 Grenoble, Cedex 9, France.</nlm:affiliation>
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<author><name sortKey="Coulombeau, C" sort="Coulombeau, C" uniqKey="Coulombeau C" first="C" last="Coulombeau">C. Coulombeau</name>
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<author><name sortKey="Lavery, R" sort="Lavery, R" uniqKey="Lavery R" first="R" last="Lavery">R. Lavery</name>
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<term>Base Sequence</term>
<term>Biophysical Phenomena</term>
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<front><div type="abstract" xml:lang="en">Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature.</div>
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<Title>Biophysical journal</Title>
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<Abstract><AbstractText>Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature.</AbstractText>
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Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.

Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki