Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.
Identifieur interne : 002546 ( PubMed/Checkpoint ); précédent : 002545; suivant : 002547Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.
Auteurs : C. Roll [France] ; C. Ketterlé ; V. Faibis ; G V Fazakerley ; Y. BoulardSource :
- Biochemistry [ 0006-2960 ] ; 1998.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- Base Composition, DNA Damage, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, Protons, Temperature, Thermodynamics, Water.
Abstract
We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. The continuous strand has the sequence 5'(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that the global conformation is very close to canonical B-form DNA, but it displays enhanced local flexibility. For the gap structure, we observe only one species in which the extra G is well stacked into the helix. The two half-helices around this residue also show a B-form conformation. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely. Using distance constraints, MD calculations show that the nick conformation is very close to a duplex with no lesion but is indeed more flexible in the central part. The gapped structure shows two families of conformations. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two cases.
DOI: 10.1021/bi972377w
PubMed: 9521727
Affiliations:
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Ketterlé</name></author><author><name sortKey="Faibis, V" sort="Faibis, V" uniqKey="Faibis V" first="V" last="Faibis">V. Faibis</name></author><author><name sortKey="Fazakerley, G V" sort="Fazakerley, G V" uniqKey="Fazakerley G" first="G V" last="Fazakerley">G V Fazakerley</name></author><author><name sortKey="Boulard, Y" sort="Boulard, Y" uniqKey="Boulard Y" first="Y" last="Boulard">Y. Boulard</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1998">1998</date><idno type="RBID">pubmed:9521727</idno><idno type="pmid">9521727</idno><idno type="doi">10.1021/bi972377w</idno><idno type="wicri:Area/PubMed/Corpus">002694</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002694</idno><idno type="wicri:Area/PubMed/Curation">002694</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002694</idno><idno type="wicri:Area/PubMed/Checkpoint">002546</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002546</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.</title><author><name sortKey="Roll, C" sort="Roll, C" uniqKey="Roll C" first="C" last="Roll">C. Roll</name><affiliation wicri:level="3"><nlm:affiliation>CEA, Service de Biochimie et de Génétique Moléculaire, Département de Biologie Cellulaire et Moléculaire, Gif-sur-Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CEA, Service de Biochimie et de Génétique Moléculaire, Département de Biologie Cellulaire et Moléculaire, Gif-sur-Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName></affiliation></author><author><name sortKey="Ketterle, C" sort="Ketterle, C" uniqKey="Ketterle C" first="C" last="Ketterlé">C. Ketterlé</name></author><author><name sortKey="Faibis, V" sort="Faibis, V" uniqKey="Faibis V" first="V" last="Faibis">V. Faibis</name></author><author><name sortKey="Fazakerley, G V" sort="Fazakerley, G V" uniqKey="Fazakerley G" first="G V" last="Fazakerley">G V Fazakerley</name></author><author><name sortKey="Boulard, Y" sort="Boulard, Y" uniqKey="Boulard Y" first="Y" last="Boulard">Y. Boulard</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="1998" type="published">1998</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term><term>DNA (chemistry)</term><term>DNA Damage</term><term>Models, Molecular</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Conformation</term><term>Nucleic Acid Heteroduplexes</term><term>Protons</term><term>Temperature</term><term>Thermodynamics</term><term>Water</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Altération de l'ADN</term><term>Composition en bases nucléiques</term><term>Conformation d'acide nucléique</term><term>Eau</term><term>Hétéroduplexes d'acides nucléiques</term><term>Modèles moléculaires</term><term>Protons</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Température</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 Composition</term><term>DNA Damage</term><term>Models, Molecular</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Conformation</term><term>Nucleic Acid Heteroduplexes</term><term>Protons</term><term>Temperature</term><term>Thermodynamics</term><term>Water</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Altération de l'ADN</term><term>Composition en bases nucléiques</term><term>Conformation d'acide nucléique</term><term>Eau</term><term>Hétéroduplexes d'acides nucléiques</term><term>Modèles moléculaires</term><term>Protons</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Température</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. The continuous strand has the sequence 5'(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that the global conformation is very close to canonical B-form DNA, but it displays enhanced local flexibility. For the gap structure, we observe only one species in which the extra G is well stacked into the helix. The two half-helices around this residue also show a B-form conformation. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely. Using distance constraints, MD calculations show that the nick conformation is very close to a duplex with no lesion but is indeed more flexible in the central part. The gapped structure shows two families of conformations. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two cases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">9521727</PMID><DateCompleted><Year>1998</Year><Month>04</Month><Day>30</Day></DateCompleted><DateRevised><Year>2013</Year><Month>11</Month><Day>21</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>37</Volume><Issue>12</Issue><PubDate><Year>1998</Year><Month>Mar</Month><Day>24</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Conformations of nicked and gapped DNA structures by NMR and molecular dynamic simulations in water.</ArticleTitle><Pagination><MedlinePgn>4059-70</MedlinePgn></Pagination><Abstract><AbstractText>We have analyzed and compared the molecular structures and dynamics of DNA duplexes containing a nick or a gap of one nucleotide where the base in front of the gap is a guanine. The continuous strand has the sequence 5'(CAGAGTCXCTGGCTC) where the residue X is absent for the nick, 14-mer, and where it is a G residue for the gap. Duplexes were formed with the two corresponding 7-mers. Neither of these is phosphorylated adjacent at the nick site, but it is a good model for a single strand break. For the nick structure, the quantitative NMR data show that the global conformation is very close to canonical B-form DNA, but it displays enhanced local flexibility. For the gap structure, we observe only one species in which the extra G is well stacked into the helix. The two half-helices around this residue also show a B-form conformation. As with the nick duplex, the adjacent G imino protons show enhanced exchange with solvent. The gap does not close completely. Using distance constraints, MD calculations show that the nick conformation is very close to a duplex with no lesion but is indeed more flexible in the central part. The gapped structure shows two families of conformations. One is close to B-DNA, the other is significantly kinked at the gap which reduces the size of the cavity. We observe a spine of hydration within the cavities, similar, but of different geometry in the two cases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Roll</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>CEA, Service de Biochimie et de Génétique Moléculaire, Département de Biologie Cellulaire et Moléculaire, Gif-sur-Yvette, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ketterlé</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Faibis</LastName><ForeName>V</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Fazakerley</LastName><ForeName>G V</ForeName><Initials>GV</Initials></Author><Author ValidYN="Y"><LastName>Boulard</LastName><ForeName>Y</ForeName><Initials>Y</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009692">Nucleic Acid Heteroduplexes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011522">Protons</NameOfSubstance></Chemical><Chemical><RegistryNumber>059QF0KO0R</RegistryNumber><NameOfSubstance UI="D014867">Water</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001482" MajorTopicYN="N">Base Composition</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004249" MajorTopicYN="Y">DNA Damage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019906" MajorTopicYN="N">Nuclear Magnetic Resonance, Biomolecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009692" MajorTopicYN="N">Nucleic Acid Heteroduplexes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011522" MajorTopicYN="N">Protons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="Y">Thermodynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014867" MajorTopicYN="Y">Water</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1998</Year><Month>5</Month><Day>2</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1998</Year><Month>5</Month><Day>2</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1998</Year><Month>5</Month><Day>2</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">9521727</ArticleId><ArticleId IdType="doi">10.1021/bi972377w</ArticleId><ArticleId IdType="pii">bi972377w</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Gif-sur-Yvette</li></settlement></list><tree><noCountry><name sortKey="Boulard, Y" sort="Boulard, Y" uniqKey="Boulard Y" first="Y" last="Boulard">Y. Boulard</name><name sortKey="Faibis, V" sort="Faibis, V" uniqKey="Faibis V" first="V" last="Faibis">V. Faibis</name><name sortKey="Fazakerley, G V" sort="Fazakerley, G V" uniqKey="Fazakerley G" first="G V" last="Fazakerley">G V Fazakerley</name><name sortKey="Ketterle, C" sort="Ketterle, C" uniqKey="Ketterle C" first="C" last="Ketterlé">C. Ketterlé</name></noCountry><country name="France"><region name="Île-de-France"><name sortKey="Roll, C" sort="Roll, C" uniqKey="Roll C" first="C" last="Roll">C. Roll</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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