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Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Kiran, MR and Bansal, M (1997) Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study. In: Journal of Biomolecular Structure & Dynamics, 15 (2). pp. 333-345.

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Official URL: http://www.jbsdonline.com/Issue-February-2011-c430...

Abstract

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Adenine Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 28 Jan 2011 08:55
Last Modified: 28 Jan 2011 08:55
URI: http://eprints.iisc.ernet.in/id/eprint/35226

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