Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.
Identifieur interne : 002392 ( PubMed/Checkpoint ); précédent : 002391; suivant : 002393Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.
Auteurs : S H Chou [Taïwan] ; K H ChinSource :
- Journal of molecular biology [ 0022-2836 ] ; 2001.
Descripteurs français
- KwdFr :
- ADN (), ADN (génétique), ADN (métabolisme), ADN simple brin (), ADN simple brin (génétique), ADN simple brin (métabolisme), Appariement de bases, Dénaturation d'acide nucléique, Liaison hydrogène, Modèles moléculaires, Rayons ultraviolets, Résonance magnétique nucléaire biomoléculaire, Solutions, Séquence nucléotidique, Température, Thermodynamique.
- MESH :
- génétique : ADN, ADN simple brin.
- métabolisme : ADN, ADN simple brin.
- ADN, ADN simple brin, Appariement de bases, Dénaturation d'acide nucléique, Liaison hydrogène, Modèles moléculaires, Rayons ultraviolets, Résonance magnétique nucléaire biomoléculaire, Solutions, Séquence nucléotidique, Température, Thermodynamique.
English descriptors
- KwdEn :
- Base Pairing, Base Sequence, DNA (chemistry), DNA (genetics), DNA (metabolism), DNA, Single-Stranded (chemistry), DNA, Single-Stranded (genetics), DNA, Single-Stranded (metabolism), Hydrogen Bonding, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Denaturation, Solutions, Temperature, Thermodynamics, Ultraviolet Rays.
- MESH :
- chemical , chemistry : DNA, DNA, Single-Stranded.
- chemical , genetics : DNA, DNA, Single-Stranded.
- chemical , metabolism : DNA, DNA, Single-Stranded.
- Base Pairing, Base Sequence, Hydrogen Bonding, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acid Denaturation, Solutions, Temperature, Thermodynamics, Ultraviolet Rays.
Abstract
A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-CAAG-3'/3'-ACGT-5' were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C.A base-pair, a sheared A.C base-pair, a sheared A.G base-pair, and a wobble G.T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52 degrees C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 x 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only zeta torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche(-) domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.
DOI: 10.1006/jmbi.2001.4964
PubMed: 11575931
Affiliations:
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xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Biochemistry, National Chung-Hsing University, Taichung 40227</wicri:regionArea><wicri:noRegion>Taichung 40227</wicri:noRegion></affiliation></author><author><name sortKey="Chin, K H" sort="Chin, K H" uniqKey="Chin K" first="K H" last="Chin">K H Chin</name></author></analytic><series><title level="j">Journal of molecular biology</title><idno type="ISSN">0022-2836</idno><imprint><date when="2001" type="published">2001</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>DNA (chemistry)</term><term>DNA (genetics)</term><term>DNA (metabolism)</term><term>DNA, Single-Stranded (chemistry)</term><term>DNA, Single-Stranded (genetics)</term><term>DNA, Single-Stranded (metabolism)</term><term>Hydrogen Bonding</term><term>Models, Molecular</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Denaturation</term><term>Solutions</term><term>Temperature</term><term>Thermodynamics</term><term>Ultraviolet Rays</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (génétique)</term><term>ADN (métabolisme)</term><term>ADN simple brin ()</term><term>ADN simple brin (génétique)</term><term>ADN simple brin (métabolisme)</term><term>Appariement de bases</term><term>Dénaturation d'acide nucléique</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Rayons ultraviolets</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Solutions</term><term>Séquence nucléotidique</term><term>Température</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>DNA, Single-Stranded</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>ADN simple brin</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>ADN simple brin</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Hydrogen Bonding</term><term>Models, Molecular</term><term>Nuclear Magnetic Resonance, Biomolecular</term><term>Nucleic Acid Denaturation</term><term>Solutions</term><term>Temperature</term><term>Thermodynamics</term><term>Ultraviolet Rays</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>ADN simple brin</term><term>Appariement de bases</term><term>Dénaturation d'acide nucléique</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Rayons ultraviolets</term><term>Résonance magnétique nucléaire biomoléculaire</term><term>Solutions</term><term>Séquence nucléotidique</term><term>Température</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-CAAG-3'/3'-ACGT-5' were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C.A base-pair, a sheared A.C base-pair, a sheared A.G base-pair, and a wobble G.T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52 degrees C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 x 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only zeta torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche(-) domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">11575931</PMID><DateCompleted><Year>2001</Year><Month>10</Month><Day>25</Day></DateCompleted><DateRevised><Year>2006</Year><Month>11</Month><Day>15</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0022-2836</ISSN><JournalIssue CitedMedium="Print"><Volume>312</Volume><Issue>4</Issue><PubDate><Year>2001</Year><Month>Sep</Month><Day>28</Day></PubDate></JournalIssue><Title>Journal of molecular biology</Title><ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.</ArticleTitle><Pagination><MedlinePgn>769-81</MedlinePgn></Pagination><Abstract><AbstractText>A series of DNA 21-mers containing a variety of the 4 x 4 internal loop sequence 5'-CAAG-3'/3'-ACGT-5' were studied using nuclear magnetic resonance (NMR) methodology and distance geometry (DG)/molecular dynamics (MD) approaches. Such oligomers exhibit excellent resolution in the NMR spectra and reveal many unusual NOEs (nuclear Overhauser effect) that allow for the detailed characterization of a DNA hairpin incorporating a track of four different non-Watson-Crick base-pairs in the stem. These include a wobble C.A base-pair, a sheared A.C base-pair, a sheared A.G base-pair, and a wobble G.T base-pair. Significantly different twisting angles were observed between the base-pairs in internal loop that results with excellent intra-strand and inter-strand base stacking within the four consecutive mismatches and the surrounding canonical base-pairs. This explains why it melts at 52 degrees C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 x 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only zeta torsion angles between the tandem sheared base-pairs are changed to a great extent from the gauche(-) domain to the trans domain to accommodate the cross-strand base stacking in the internal loop. The observation that several consecutive non-canonical base-pairs can stably co-exist with Watson-Crick base-pairs greatly increases the limited repertoire of irregular DNA folds and reveals the possibility for unusual structural formation in the functionally important genomic regions that have potential to become single-stranded.</AbstractText><CopyrightInformation>Copyright 2001 Academic Press.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chou</LastName><ForeName>S H</ForeName><Initials>SH</Initials><AffiliationInfo><Affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan. shchou@dragon.nchu.edu.tw</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chin</LastName><ForeName>K H</ForeName><Initials>KH</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>England</Country><MedlineTA>J Mol Biol</MedlineTA><NlmUniqueID>2985088R</NlmUniqueID><ISSNLinking>0022-2836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004277">DNA, Single-Stranded</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012996">Solutions</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020029" MajorTopicYN="Y">Base Pairing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004277" MajorTopicYN="N">DNA, Single-Stranded</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</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="D009691" MajorTopicYN="N">Nucleic Acid Denaturation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012996" MajorTopicYN="N">Solutions</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013696" MajorTopicYN="N">Temperature</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014466" MajorTopicYN="N">Ultraviolet Rays</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2001</Year><Month>9</Month><Day>29</Day><Hour>10</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2001</Year><Month>10</Month><Day>26</Day><Hour>10</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2001</Year><Month>9</Month><Day>29</Day><Hour>10</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">11575931</ArticleId><ArticleId IdType="doi">10.1006/jmbi.2001.4964</ArticleId><ArticleId IdType="pii">S0022-2836(01)94964-2</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Taïwan</li></country></list><tree><noCountry><name sortKey="Chin, K H" sort="Chin, K H" uniqKey="Chin K" first="K H" last="Chin">K H Chin</name></noCountry><country name="Taïwan"><noRegion><name sortKey="Chou, S H" sort="Chou, S H" uniqKey="Chou S" first="S H" last="Chou">S H Chou</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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