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

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

Content Provider	Springer Nature Link
Author	Mukherjee, Shayantani Bansal, Manju Bhattacharyya, Dhananjay
Copyright Year	2006
Abstract	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 non-planar, 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.
Starting Page	629
Ending Page	645
Page Count	17
File Format	PDF
ISSN	0920654X
Journal	Journal of Computer-Aided Molecular Design
Volume Number	20
Issue Number	10-11
e-ISSN	15734951
Language	English
Publisher	Kluwer Academic Publishers
Publisher Date	2006-11-24
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Base pair conformation RNA structure Non-Watson-Crick Intra-base pair parameters Propeller twist Animal Anatomy / Morphology / Histology Computer Applications in Chemistry Physical Chemistry
Content Type	Text
Resource Type	Article
Subject	Drug Discovery Physical and Theoretical Chemistry Computer Science Applications

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