Molecular mechanics studies on poly(purine) poly(pyrimidine) sequences in DNA: Polymorphism and local variability

Bansal, Manju and Pattabiraman, N (1989) Molecular mechanics studies on poly(purine) poly(pyrimidine) sequences in DNA: Polymorphism and local variability. In: Biopolymers, 28 (2). pp. 531-548.

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Abstract

Energy minimization has been carried out on three poly(purine). poly(pyrimidine) sequences $d(G)_{10}.d(C)_{10}, d(A)_{10} . d(T)_{10} and d(AG)_{5} . d(CT)_{5} $, using the molecular mechanics program AMBER (Assisted Model Building and Energy Refinement). In order to extensively scan the conformational space avaliable, five different helical models were studied, three of them being right handed helices while the other two were left helical. For all three sequences the right handed A- and B-type helices are energetically slightly preferred over the left helices, but the energy difference between the various right-handed helices is only marginal. A detailed analysis has been carried out to characterize the local structural variability in the refined structures, both in terms of torsion angles as well as other parameters such as base pair tilt, wedge roll, and wedge tilt, etc. All three sequences exhibit similar structural features for a particular form, but both the forms A and B show significyt deviations from fiber models. In particular, the A-form structures have higher unit rise (2.7 A), and lower unit twist (31 Deg) and base-pair tilt (12 Deg), compared to the fiber model, which has corresponding values of 2.56 A, 32.7 Deg, and 20 Deg, respectively. All these changes indicate that the refined models are closer to the A-form structure observed in crystals of oligonucleotides. In the refined B-for models, the helical parameters are close to the fiber B-form, although the torsion angles show considerable variations. None of the three sequences examined, including the $d(A)_n . d(T)_n $, sequence, show any pronounced curvature for the B-form structure.

Item Type:	Journal Article
Publication:	Biopolymers
Publisher:	John Wiley & Sons, Inc.
Additional Information:	The copyright belongs to John Wiley & Sons, Inc.
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	02 Dec 2005
Last Modified:	19 Sep 2010 04:21
URI:	http://eprints.iisc.ac.in/id/eprint/4107

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