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.
Highlights
For the first two decades of the Protein Data Bank’s (PDB) existence, the number of RNA structure entries did not exceed 1000 structures [1]
The downloaded structures were annotated for specific base arrangement patterns of known tertiary motifs using the program NASSAM and for clusters of three to six bases that are interconnected by hydrogen bonds using the program COGNAC
As more RNA structures are deposited in the PDB, value added information that could be extracted from the structural data with regard to the motifs and arrangements of the bases could be useful
Summary
For the first two decades of the Protein Data Bank’s (PDB) existence, the number of RNA structure entries did not exceed 1000 structures [1]. Examples of secondary structural motifs include the various hairpin, internal and junction loops, whereas tertiary structural motifs include interactions such as the A-minor motifs, ribosezippers, loop-receptor motifs and several others [11,12] These interactions are largely involved in stabilizing the tertiary structure of RNA [12,13] while some have been implicated in functional roles [14,15]. Its classification scheme is based on a directed acyclic graph, allowing a node to have multiple parents Another resource, the RNAJunction database, contains structure and sequence information for RNA junctions, kissing loops, internal loops and bulges [18]. None of these databases provides annotation on RNA base interaction clusters or a mapping of the interactions between the bases in forming specific 3D arrangements These interactions can potentially act as structural motifs and have functional or structural stabilization roles. This database is a repository of 3D base arrangements and clusters of hydrogen bonded base interactions that were the result of annotations by the NASSAM [22,23] and COGNAC [16] computer programs
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