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Nucleic Acids Research 2005 33(1):43-55; doi:10.1093/nar/gki143
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Published online 18 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Article

New insights into DNA triplexes: residual twist and radial difference as measures of base triplet non-isomorphism and their implication to sequence-dependent non-uniform DNA triplex

R. Thenmalarchelvi and N. Yathindra*

Department of Crystallography and Biophysics, University of Madras Guindy Campus, Chennai 600 025, India

*To whom correspondence should be addressed. Tel: +91 44 223 00 122; Fax: +91 44 223 52 494; Email: ny{at}vsnl.com

Received July 22, 2004. Revised November 19, 2004. Accepted December 2, 2004.

DNA triplexes are formed by both isomorphic (structurally alike) and non-isomorphic (structurally dissimilar) base triplets. It is espoused here that (i) the base triplet non-isomorphism may be articulated in structural terms by a residual twist ({Delta}t°), the angle formed by line joining the C1'...C1' atoms of the adjacent Hoogsteen or reverse Hoogsteen (RH) base pairs and the difference in base triplet radius ({Delta}r Å), and (ii) their influence on DNA triplex is largely mechanistic, leading to the prediction of a high (t + {Delta}t)° and low (t – {Delta}t)° twist at the successive steps of Hoogsteen or RH duplex of a parallel or antiparallel triplex. Efficacy of this concept is corroborated by molecular dynamics (MD) simulation of an antiparallel DNA triplex comprising alternating non-isomorphic G*GC and T*AT triplets. Conformational changes necessitated by base triplet non-isomorphism are found to induce an alternating (i) high anti and anti glycosyl and (ii) BII and an unusual BIII conformation resulting in a zigzag backbone for the RH strand. Thus, base triplet non-isomorphism causes DNA triplexes into exhibiting sequence-dependent non-uniform conformation. Such structural variations may be relevant in deciphering the specificity of interaction with DNA triplex binding proteins. Seemingly then, residual twist ({Delta}t°) and radial difference ({Delta}r Å) suffice as indices to define and monitor the effect of base triplet non-isomorphism in nucleic acid triplexes.

This article is dedicated to Professor M. Sundaralingam who, along with his wife, met with a tragic end in the recent tsunami disaster in Sri Lanka


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