Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

Mohanty, D and Bansal, M (1995) Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study. In: Biophysical Journal, 69 (3). pp. 1046-1067.

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Abstract

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Item Type:	Journal Article
Publication:	Biophysical Journal
Publisher:	Elsevier Science
Additional Information:	Copyright of this article belongs to Elsevier Science.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	27 Apr 2011 07:25
Last Modified:	27 Apr 2011 07:25
URI:	http://eprints.iisc.ac.in/id/eprint/37226

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