A computational study of expanded heterocyclic nucleosides in DNA.
Identifieur interne : 002A38 ( Main/Merge ); précédent : 002A37; suivant : 002A39A computational study of expanded heterocyclic nucleosides in DNA.
Auteurs : Peter I. O'Daniel [États-Unis] ; Malcolm Jefferson ; Olaf Wiest ; Katherine L. Seley-RadtkeSource :
- Journal of biomolecular structure & dynamics [ 0739-1102 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Purine Nucleosides.
- Computer Simulation, Models, Molecular, Molecular Conformation, Molecular Structure, Static Electricity.
Abstract
The first molecular dynamics study of a series of heterospacer-expanded tricyclic bases in DNA using modified force field parameters in AMBER is detailed. The expanded purine nucleoside monomers have been designed to probe the effects of a heteroaromatic spacer ring on the structure, function, and dynamics of the DNA helix. The heterobase scaffold has been expanded with a furan, pyrrole, or thiophene spacer ring. This structural modification increases the polarizability of the bases and provides an additional hydrogen bond donor with the amine hydrogen of the pyrrole ring or hydrogen bond acceptor with the furan or thiophene ring free electron pairs. The polarizability of the expanded bases were determined by AM1 calculations and the results of the MD simulations of 20-mers predict that the modified curvature of the expanded base leads to a much larger major groove, while the effect on the minor groove is negligible. Overall, the structure resembles A-DNA. MD simulations of 10-mers suggest that the balance between base pairing vs. base stacking and intercalation can be shifted towards the latter due to the increased surface area and polarizability of the expanded bases.
DOI: 10.1080/07391102.2008.10507243
PubMed: 18808194
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pubmed:18808194Le document en format XML
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<wicri:regionArea>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250</wicri:regionArea>
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<placeName><settlement type="city">College Park (Maryland)</settlement>
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<author><name sortKey="Jefferson, Malcolm" sort="Jefferson, Malcolm" uniqKey="Jefferson M" first="Malcolm" last="Jefferson">Malcolm Jefferson</name>
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<author><name sortKey="Wiest, Olaf" sort="Wiest, Olaf" uniqKey="Wiest O" first="Olaf" last="Wiest">Olaf Wiest</name>
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<author><name sortKey="Seley Radtke, Katherine L" sort="Seley Radtke, Katherine L" uniqKey="Seley Radtke K" first="Katherine L" last="Seley-Radtke">Katherine L. Seley-Radtke</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">A computational study of expanded heterocyclic nucleosides in DNA.</title>
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<affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250</wicri:regionArea>
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<author><name sortKey="Seley Radtke, Katherine L" sort="Seley Radtke, Katherine L" uniqKey="Seley Radtke K" first="Katherine L" last="Seley-Radtke">Katherine L. Seley-Radtke</name>
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<series><title level="j">Journal of biomolecular structure & dynamics</title>
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<term>Molecular Conformation</term>
<term>Molecular Structure</term>
<term>Purine Nucleosides (chemistry)</term>
<term>Static Electricity</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term>
<term>Conformation moléculaire</term>
<term>Modèles moléculaires</term>
<term>Nucléoside purique ()</term>
<term>Simulation numérique</term>
<term>Structure moléculaire</term>
<term>Électricité statique</term>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
<term>Purine Nucleosides</term>
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<keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term>
<term>Models, Molecular</term>
<term>Molecular Conformation</term>
<term>Molecular Structure</term>
<term>Static Electricity</term>
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<keywords scheme="MESH" xml:lang="fr"><term>ADN</term>
<term>Conformation moléculaire</term>
<term>Modèles moléculaires</term>
<term>Nucléoside purique</term>
<term>Simulation numérique</term>
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<front><div type="abstract" xml:lang="en">The first molecular dynamics study of a series of heterospacer-expanded tricyclic bases in DNA using modified force field parameters in AMBER is detailed. The expanded purine nucleoside monomers have been designed to probe the effects of a heteroaromatic spacer ring on the structure, function, and dynamics of the DNA helix. The heterobase scaffold has been expanded with a furan, pyrrole, or thiophene spacer ring. This structural modification increases the polarizability of the bases and provides an additional hydrogen bond donor with the amine hydrogen of the pyrrole ring or hydrogen bond acceptor with the furan or thiophene ring free electron pairs. The polarizability of the expanded bases were determined by AM1 calculations and the results of the MD simulations of 20-mers predict that the modified curvature of the expanded base leads to a much larger major groove, while the effect on the minor groove is negligible. Overall, the structure resembles A-DNA. MD simulations of 10-mers suggest that the balance between base pairing vs. base stacking and intercalation can be shifted towards the latter due to the increased surface area and polarizability of the expanded bases.</div>
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