InterRNA: a database of base interactions in RNA structures

Abstract

A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the database InterRNA (INTERactions in RNA structures database-http://mfrlab.org/interrna/) that contains records of known RNA 3D motifs as well as records for clusters of bases that are interconnected by hydrogen bonds. The contents of the database were compiled from RNA structural annotations carried out by the NASSAM (http://mfrlab.org/grafss/nassam) and COGNAC (http://mfrlab.org/grafss/cognac) computer programs. An analysis of the database content and comparisons with the existing corpus of knowledge regarding RNA 3D motifs clearly show that InterRNA is able to provide an extension of the annotations for known motifs as well as able to provide novel interactions for further investigations.

Figure 1.

Tree graphs used by COGNAC to represent hydrogen bond connected base interactions where R denotes a base residue position (node) and the edges of the graphs are the lines connecting the nodes for (A) triples, (B) quadruples, (C) quintuples and (D) sextuples.

Figure 2.

Example of the user interface displaying an InterRNA database record; the JSMol panel enables browser embedded molecular visualization of the entry which in this example is a sextuple type 3 pattern in a generally planar arrangement. A summary of the hydrogen bonds involved in the interaction is also provided in the lower left panel.