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

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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.

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Acknowledgments

We are grateful to the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT), India, for financial support. We are thankful to Ms Jhuma Das for technical support.

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Authors and Affiliations

  1. Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India

    Shayantani Mukherjee & Dhananjay Bhattacharyya

  2. Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India

    Manju Bansal

  3. Center for Applied Mathematics and Computational Science, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India

    Dhananjay Bhattacharyya

Authors
  1. Shayantani Mukherjee
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  2. Manju Bansal
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  3. Dhananjay Bhattacharyya
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Correspondence to Dhananjay Bhattacharyya.

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Mukherjee, S., Bansal, M. & Bhattacharyya, D. Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. J Comput Aided Mol Des 20, 629–645 (2006). https://doi.org/10.1007/s10822-006-9083-x

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  • DOI: https://doi.org/10.1007/s10822-006-9083-x

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