Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs
Identifieur interne : 000E80 ( Istex/Curation ); précédent : 000E79; suivant : 000E81Solution structure of a DNA double helix incorporating four consecutive non-Watson-Crick base-pairs
Auteurs : Shan-Ho Chou [Taïwan] ; Ko-Hsin Chin [Taïwan]Source :
- Journal of Molecular Biology [ 0022-2836 ] ; 2001.
English descriptors
- KwdEn :
- Teeft :
- Abundant noes, Academic press, Adenosine bases, Backbone, Backbone torsion angles, Backbone torsional angles, Biochemistry, Biol, Capital letters, Characteristic noes, Chemical shift, Chemical shifts, Chou, Complex points, Consecutive figure, Consecutive mismatches, Consecutive table, Constraint, Crossstrand, Crystal structure, Curve program, Dihedral angles, Distance bounds, Distance constraints, Distance geometry, Double helix, Duplex, Duplex structure, Easier sample preparation, Exchangeable protons, Hairpin, Hairpin ribozyme, Helical, Helical axis, Helix, Heteronuclear correlation, High resolution, Human centromeres, Human signal recognition particle, Imino, Imino proton, Imino protons, Important genomic regions, Initial structures, Internal loop, Internal loop region, Internal loop sequence, Internal loops, Limited repertoire, Lower case letters, Mismatch, Molecular dynamics, Molecular dynamics calculations, National science council, Natl acad, Nature struct, Noesy, Noesy data, Noesy experiments, Nuclear overhauser effect, Nucleic acid structure, Oligomer, Oligomers, Phosphate group, Phosphorous atoms, Present study, Proton, Proton pairs, Proton resonances, Relaxation delay, Residue numbers, Salt buffer condition, Sheared, Sheared pair, Sheared pairing, Sheared type, Solution structure, Spectral width, Strong noes, Struct, Structural studies, Such noes, Such sequences, Supplementary material, Tandem, Temperature controller, Terminal residue, Torsion angles, Torsional, Torsional angle, Torsional angle constraints, Torsional angles, Tppi mode, Trans domain, Unusual motif, Unusual structures.
Abstract
Abstract: A series of DNA 21-mers containing a variety of the 4 × 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°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ 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.
Url:
DOI: 10.1006/jmbi.2001.4964
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<affiliation wicri:level="1"><mods:affiliation>Institute of Biochemistry, National Chung-Hsing University, Taichung, 40227 Taiwan</mods:affiliation>
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<term>DQ-COSY</term>
<term>MD</term>
<term>NOE</term>
<term>NOESY</term>
<term>consecutive mismatches</term>
<term>ppm</term>
<term>sheared A·C pair</term>
<term>sheared G·A pair</term>
<term>wobble A·C pair</term>
<term>wobble G·T pair</term>
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<keywords scheme="Teeft" xml:lang="en"><term>Abundant noes</term>
<term>Academic press</term>
<term>Adenosine bases</term>
<term>Backbone</term>
<term>Backbone torsion angles</term>
<term>Backbone torsional angles</term>
<term>Biochemistry</term>
<term>Biol</term>
<term>Capital letters</term>
<term>Characteristic noes</term>
<term>Chemical shift</term>
<term>Chemical shifts</term>
<term>Chou</term>
<term>Complex points</term>
<term>Consecutive figure</term>
<term>Consecutive mismatches</term>
<term>Consecutive table</term>
<term>Constraint</term>
<term>Crossstrand</term>
<term>Crystal structure</term>
<term>Curve program</term>
<term>Dihedral angles</term>
<term>Distance bounds</term>
<term>Distance constraints</term>
<term>Distance geometry</term>
<term>Double helix</term>
<term>Duplex</term>
<term>Duplex structure</term>
<term>Easier sample preparation</term>
<term>Exchangeable protons</term>
<term>Hairpin</term>
<term>Hairpin ribozyme</term>
<term>Helical</term>
<term>Helical axis</term>
<term>Helix</term>
<term>Heteronuclear correlation</term>
<term>High resolution</term>
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<term>Imino proton</term>
<term>Imino protons</term>
<term>Important genomic regions</term>
<term>Initial structures</term>
<term>Internal loop</term>
<term>Internal loop region</term>
<term>Internal loop sequence</term>
<term>Internal loops</term>
<term>Limited repertoire</term>
<term>Lower case letters</term>
<term>Mismatch</term>
<term>Molecular dynamics</term>
<term>Molecular dynamics calculations</term>
<term>National science council</term>
<term>Natl acad</term>
<term>Nature struct</term>
<term>Noesy</term>
<term>Noesy data</term>
<term>Noesy experiments</term>
<term>Nuclear overhauser effect</term>
<term>Nucleic acid structure</term>
<term>Oligomer</term>
<term>Oligomers</term>
<term>Phosphate group</term>
<term>Phosphorous atoms</term>
<term>Present study</term>
<term>Proton</term>
<term>Proton pairs</term>
<term>Proton resonances</term>
<term>Relaxation delay</term>
<term>Residue numbers</term>
<term>Salt buffer condition</term>
<term>Sheared</term>
<term>Sheared pair</term>
<term>Sheared pairing</term>
<term>Sheared type</term>
<term>Solution structure</term>
<term>Spectral width</term>
<term>Strong noes</term>
<term>Struct</term>
<term>Structural studies</term>
<term>Such noes</term>
<term>Such sequences</term>
<term>Supplementary material</term>
<term>Tandem</term>
<term>Temperature controller</term>
<term>Terminal residue</term>
<term>Torsion angles</term>
<term>Torsional</term>
<term>Torsional angle</term>
<term>Torsional angle constraints</term>
<term>Torsional angles</term>
<term>Tppi mode</term>
<term>Trans domain</term>
<term>Unusual motif</term>
<term>Unusual structures</term>
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<front><div type="abstract" xml:lang="en">Abstract: A series of DNA 21-mers containing a variety of the 4 × 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°C even though five out of ten base-pairs in the stem adopt non-Watson-Crick pairs. However, the 4 × 4 internal loop still fits into a B-DNA double helix very well without significant change in the backbone torsion angles; only ζ 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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