Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.
Identifieur interne : 000259 ( France/Analysis ); précédent : 000258; suivant : 000260Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.
Auteurs : L. Ayadi [France] ; C. Coulombeau ; R. LaverySource :
- Biophysical journal [ 0006-3495 ] ; 1999.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
Affiliations:
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pubmed:10585943Le document en format XML
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Ayadi</name><affiliation wicri:level="4"><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><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d'Etudes Dynamiques et Structurales de la Sélectivité, Laboratoire de Chimie Bioorganique, Université Joseph Fourier, F-38041 Grenoble, Cedex 9</wicri:regionArea><wicri:noRegion>Cedex 9</wicri:noRegion><orgName type="university">Université Joseph Fourier</orgName><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName></affiliation></author><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></author></analytic><series><title level="j">Biophysical journal</title><idno type="ISSN">0006-3495</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Biophysical Phenomena</term><term>Biophysics</term><term>DNA (chemistry)</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Appariement de bases</term><term>Biophysique</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Phénomènes biophysiques</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Biophysical Phenomena</term><term>Biophysics</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Appariement de bases</term><term>Biophysique</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Phénomènes biophysiques</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><affiliations><list><country><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li></settlement><orgName><li>Université Joseph Fourier</li></orgName></list><tree><noCountry><name sortKey="Coulombeau, C" sort="Coulombeau, C" uniqKey="Coulombeau C" first="C" last="Coulombeau">C. Coulombeau</name><name sortKey="Lavery, R" sort="Lavery, R" uniqKey="Lavery R" first="R" last="Lavery">R. Lavery</name></noCountry><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Ayadi, L" sort="Ayadi, L" uniqKey="Ayadi L" first="L" last="Ayadi">L. Ayadi</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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