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Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis

Mukherjee, Shayantani and Bansal, Manju and Bhattacharyya, Dhananjay (2006) Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. In: Journal of Computer-Aided Molecular Design, 20 (10-11). pp. 629-645.

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Non-canonical base pairs contribute immensely to the structural and functional variability of RNA, which calls for a detailed characterization of their spatial conformation. Intra-base pair parameters, namely propeller, buckle, open-angle, stagger, shear and stretch describe structure of base pairs indicating planarity and proximity of association between the two bases. In order to study the conformational specificities of non-canonical base pairs occurring in RNA crystal structures, we have upgraded NUPARM software to calculate these intra-base pair parameters using a new base pairing edge specific axis system. Analysis of base pairs and base triples with the new edge specific axis system indicate the presence of specific structural signatures for different classes of non-canonical pairs and triples. Differentiating features could be identified for pairs in cis or trans orientation, as well as those involving sugar edges or C-H-mediated hydrogen bonds. It was seen that propeller for all types of base pairs in cis orientation are generally negative, while those for trans base pairs do not have any preference. Formation of a base triple is seen to reduce propeller of the associated base pair along with reduction of overall flexibility of the pairs. We noticed that base pairs involving sugar edge are generally more nonplanar, with large propeller or buckle values, presumably to avoid steric clash between the bulky sugar moieties. These specific conformational signatures often provide an insight into their role in the structural and functional context of RNA.

Item Type: Journal Article
Publication: Journal of Computer-Aided Molecular Design
Publisher: Spinger
Additional Information: Copyright of this article belongs to Spinger
Keywords: Base pair conformation; RNA structure; Non-Watson-Crick; Intra-base pair parameters; Propeller twist;
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 06 Mar 2007
Last Modified: 19 Sep 2010 04:34
URI: http://eprints.iisc.ac.in/id/eprint/9586

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