title: Representation, searching and discovery of patterns of bases in complex RNA structures.
abstract: We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.
authors.affiliation: Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Harrison
authors.forename: Darren R
authors.initials: DR
authors.lastname: South
authors.forename: Peter
authors.initials: P
authors.lastname: Willett
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Artymiuk
mesh_terms: D020029:Base Pairing; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D010363:Pattern Recognition, Automated; D012313:RNA / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D012260:Ribonucleases; D012265:Ribonucleotides / Q000737:chemistry*
chemical_list: D012341:RNA, Ribosomal, 5S; D012265:Ribonucleotides; D012313:RNA; D012260:Ribonucleases