Document Type

Article

Publication Date

1-1-1997

Publication Title

Nucleic Acids Research

Volume

25

Issue Number

13

First Page

2562

Last Page

2565

DOI

10.1093/nar/25.13.2562

Keywords

base-amino acid, RNA

Disciplines

Biochemistry | Molecular Biology

Abstract

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TARTat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNAsynthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local structure considerations, such as groove width and α-helicity.

Comments

Copyright © 1997 Oxford University Press.The article was originally published in Nucleic Acids Research and can be found online at: http://dx.doi.org/10.1093/nar/25.13.2562.

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