Click here to view fulltext PDF

Permanent link:
https://www.ias.ac.in/article/fulltext/jcsc/119/05/0525-0531

Base pairing of RNA; DNA sequence; interaction energy of RNA; RNA structures.

The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G^∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

Purshotam Sharma¹ Abhijit Mitra¹ Sitansh Sharma¹ Harjinder Singh¹

1. Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032

Published

September 2007

Manuscript received

5 May 2007

Accepted

6 June 2007