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.

Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures

“…The results generated from the COGNAC searches for each type of sextuple were deposited into the Interactions in RNA Structures Database (InterRNA) and can be accessed at http://mfrlab.org/interrna/. Each database entry is retrievable using an identification code referred to as the INTERRNA ID [6]. The flowchart for the data analysis and filtering process to sub-classify each type of sextuple is provided in Figure 2a.…”

“…The methodology that employs the COGNAC computer program used in this study has been proven to be able to identify hydrogen bond-connected bases from pairings to interactions involving six bases [1,6]. Although the COGNAC approach was reported to be able to extract novel motifs without the need for prior knowledge of the tertiary base arrangements involved, it has the distinct limitation of being able to only search for arrangements in which the bases are connected by hydrogen bonds.…”

“…Various types of smaller base arrangements consisting of triples, quadruples, and quintuples that can form tertiary-level motifs (3D motifs) have been observed, reported, and archived [4][5][6]. However, to our knowledge, there has been no systematic study to identify larger arrangements composed of six base clusters and beyond, despite their possible importance as building-block modules Figure 1.…”

Aberrant translation of proteins implicated in Alzheimer�s disease pathology

“…This complex then scans the 5'UTR of the messenger RNA in a 5ʹ to 3ʹ direction until a start codon is recognised and synthesis is initiated (reviewed in depth by Jackson et al 1 ); the process of translation then progresses through three stages: initiation, elongation, and termination. The cap-binding complex that forms at the initiation step is an assembly of a multitude of translation initiation factors, while the 5'-untranslated region (5'UTR) may differ in length, possess features such as tertiary structures, upstream open reading frames (uORFs) and RNA proteinbinding sites [2][3][4] . Importantly, each feature may act as a regulatory element independently enhancing or repressing the rate of protein synthesis (see Jackson et al 1 ).…”

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs

“…Some RNA modules have received a specific attention such as GNRA loops, Kink-turns, Gbulges, and the various types of A-minors. Moreover, several works have been presented, proposing computational methods to detect RNA modules in tertiary structures using either geometry or graph-based approaches [10][11][12][13][14][15][16][17][18][19][20][21][22]. A coarse grain graph representation of the secondary structure with its pseudoknots has already shown the modularity of ribosomal structures [23], and has been used recently for fragment based design applications [24].…”