| A measure of bending in nucleic acids structures applied to A-tract DNA. | |
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MedLine Citation:
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PMID: 20123729 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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A method is proposed to measure global bending in DNA and RNA structures. It relies on a properly defined averaging of base-fixed coordinate frames, computes mean frames of suitably chosen groups of bases and uses these mean frames to evaluate bending. The method is applied to DNA A-tracts, known to induce considerable bend to the double helix. We performed atomistic molecular dynamics simulations of sequences containing the A(4)T(4) and T(4)A(4) tracts, in a single copy and in two copies phased with the helical repeat. Various temperature and salt conditions were investigated. Our simulations indicate bending by roughly 10 degrees per A(4)T(4) tract into the minor groove, and an essentially straight structure containing T(4)A(4), in agreement with electrophoretic mobility data. In contrast, we show that the published NMR structures of analogous sequences containing A(4)T(4) and T(4)A(4) tracts are significantly bent into the minor groove for both sequences, although bending is less pronounced for the T(4)A(4) containing sequence. The bending magnitudes obtained by frame averaging are confirmed by the analysis of superhelices composed of repeated tract monomers. |
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Authors:
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F Lankas; N Spacková; M Moakher; P Enkhbayar; J Sponer |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-01-31 |
Journal Detail:
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Title: Nucleic acids research Volume: 38 ISSN: 1362-4962 ISO Abbreviation: Nucleic Acids Res. Publication Date: 2010 Jun |
Date Detail:
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Created Date: 2010-06-03 Completed Date: 2010-06-22 Revised Date: 2010-09-27 |
Medline Journal Info:
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Nlm Unique ID: 0411011 Medline TA: Nucleic Acids Res Country: England |
Other Details:
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Languages: eng Pagination: 3414-22 Citation Subset: IM |
Affiliation:
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Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic. filip.lankas@uochb.cas.cz |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Adenine
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chemistry DNA / chemistry* Molecular Dynamics Simulation Nucleic Acid Conformation RNA / chemistry Thymine / chemistry |
| Grant Support | |
ID/Acronym/Agency:
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//Wellcome Trust |
| Chemical | |
Reg. No./Substance:
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63231-63-0/RNA; 65-71-4/Thymine; 73-24-5/Adenine; 9007-49-2/DNA |
| Comments/Corrections | |
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