A computational study of expanded heterocyclic nucleosides in DNA.
Identifieur interne : 002020 ( PubMed/Checkpoint ); précédent : 002019; suivant : 002021A 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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O'Daniel</name><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><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Jefferson, Malcolm" sort="Jefferson, Malcolm" uniqKey="Jefferson M" first="Malcolm" last="Jefferson">Malcolm Jefferson</name></author><author><name sortKey="Wiest, Olaf" sort="Wiest, Olaf" uniqKey="Wiest O" first="Olaf" last="Wiest">Olaf Wiest</name></author><author><name sortKey="Seley Radtke, Katherine L" sort="Seley Radtke, Katherine L" uniqKey="Seley Radtke K" first="Katherine L" last="Seley-Radtke">Katherine L. 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O'Daniel</name><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><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Jefferson, Malcolm" sort="Jefferson, Malcolm" uniqKey="Jefferson M" first="Malcolm" last="Jefferson">Malcolm Jefferson</name></author><author><name sortKey="Wiest, Olaf" sort="Wiest, Olaf" uniqKey="Wiest O" first="Olaf" last="Wiest">Olaf Wiest</name></author><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></author></analytic><series><title level="j">Journal of biomolecular structure & dynamics</title><idno type="ISSN">0739-1102</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation</term><term>DNA (chemistry)</term><term>Models, Molecular</term><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></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Purine Nucleosides</term></keywords><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></keywords><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><term>Structure moléculaire</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18808194</PMID><DateCompleted><Year>2008</Year><Month>12</Month><Day>22</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0739-1102</ISSN><JournalIssue CitedMedium="Print"><Volume>26</Volume><Issue>3</Issue><PubDate><Year>2008</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Journal of biomolecular structure & dynamics</Title><ISOAbbreviation>J. Biomol. Struct. Dyn.</ISOAbbreviation></Journal><ArticleTitle>A computational study of expanded heterocyclic nucleosides in DNA.</ArticleTitle><Pagination><MedlinePgn>283-92</MedlinePgn></Pagination><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>O'Daniel</LastName><ForeName>Peter I</ForeName><Initials>PI</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jefferson</LastName><ForeName>Malcolm</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Wiest</LastName><ForeName>Olaf</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Seley-Radtke</LastName><ForeName>Katherine L</ForeName><Initials>KL</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM073645-03</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM 073645-01</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM073645-02</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM073645-01</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM073645</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM073645-04</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. 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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><name sortKey="Wiest, Olaf" sort="Wiest, Olaf" uniqKey="Wiest O" first="Olaf" last="Wiest">Olaf Wiest</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="O Daniel, Peter I" sort="O Daniel, Peter I" uniqKey="O Daniel P" first="Peter I" last="O'Daniel">Peter I. O'Daniel</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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