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Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Ravi Kiran, M and Bansal, Manju (1998) Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes. In: Journal of Biomolecular Structure & Dynamics, 16 (3). pp. 511-526.

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


Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Item Type: Journal Article
Publication: Journal of Biomolecular Structure & Dynamics
Publisher: Adenine Press
Additional Information: Copyright of this article belongs to Adenine Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 28 Jan 2011 09:05
Last Modified: 28 Jan 2011 09:05
URI: http://eprints.iisc.ac.in/id/eprint/35225

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