Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.
Identifieur interne : 002543 ( PubMed/Corpus ); précédent : 002542; suivant : 002544Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.
Auteurs : S H Chou ; K H ChinSource :
- Journal of molecular biology [ 0022-2836 ] ; 2001.
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
Links to Exploration step
pubmed:11575931Le document en format XML
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<author><name sortKey="Chou, S H" sort="Chou, S H" uniqKey="Chou S" first="S H" last="Chou">S H Chou</name>
<affiliation><nlm:affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan. shchou@dragon.nchu.edu.tw</nlm:affiliation>
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<author><name sortKey="Chin, K H" sort="Chin, K H" uniqKey="Chin K" first="K H" last="Chin">K H Chin</name>
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<term>DNA, Single-Stranded (chemistry)</term>
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<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
<term>DNA, Single-Stranded</term>
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<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>
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<Title>Journal of molecular biology</Title>
<ISOAbbreviation>J. Mol. Biol.</ISOAbbreviation>
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<ArticleTitle>Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs.</ArticleTitle>
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<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>
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