The single stranded RNA molecule folds on to itself to open up a possibility of forming a large variety of non-canonical base pairs, where two nucleobases interact with each other via any of the three distinct interacting edges - Watson Crick edge(W), Hoogsteen edge(H) and Sugar edge(S). In complex folded structures of RNA, often more than two bases get involved in edge-to-edge hydrogen bonding interactions to form base triples (involving 3 bases) and quartets (involving 4 bases) which, in turn, facilitate formation of local structural motifs or long range interactions and thus are recurrently observed in different RNA molecules. Comprehensive classification and nomenclature scheme for base pairs and base triples are already available. Here we have proposed a topology based classification and nomenclature scheme for base quartets.
QUARNA provides list of quartets present in non-redundant dataset of RNA structures obtained from HDRNAS and NDB as well as in a larger dataset obtained from RCSB PDB with 3.5 Angstrom resolution cut-off. It also provides an in-built quartet-finder program to detect nucleotide base quartets of different topology from a given pdb file.
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