Biophysical Journal 69: 1046-1067 (1995)
© 1995 the Biophysical Society

This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Mohanty, D Articles by Bansal, M Search for Related Content PubMed PubMed Citation Articles by Mohanty, D Articles by Bansal, M

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

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

ABSTRACT

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG3) 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.

This article has been cited by other articles:

				S. A. Salisbury, S. E. Wilson, H. R. Powell, O. Kennard, P. Lubini, G. M. Sheldrick, N. Escaja, E. Alazzouzi, A. Grandas, and E. Pedroso The bi-loop, a new general four-stranded DNA motif PNAS, May 27, 1997; 94(11): 5515 - 5518. [Abstract] [Full Text] [PDF]