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Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes

Chowdhury, Shibasish and Bansal, Manju (2001) Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes. In: Journal of Biosciences, 26 (5). pp. 649-665.

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Abstract

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimmer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Indian Academy of Sciences.
Keywords: d(GGC/GCC)5; d(CAG/CTG)5; hairpin structure; model building; molecular mechanics; quadruplex structure.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 06 Jan 2011 06:44
Last Modified: 06 Jan 2011 06:44
URI: http://eprints.iisc.ernet.in/id/eprint/34621

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