Poster abstracts

Poster number 1 submitted by Amal Abu Almakarem

Comprehensive Survey and Geometric Classification of Basetriples in RNA Structures

Amal Abu Almakarem (Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403), Jesse Stombaugh (Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403), Craig L. Zirbel (Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403), Neocles B. Leontis (Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403)

Abstract:

Structured RNAs fold into complex globular molecules composed of helices and loops (internal, hairpin, or junction). The helices are comprised of Watson-Crick basepairs, while the loop regions tend to involve non-Watson-Crick basepairs. These loop regions may also participate in long-range RNA-RNA interactions that stabilize the 3D RNA structure. These long-range interactions generally involve non-Watson-Crick basepair interactions. Pairwise interactions between RNA bases can be classified geometrically by their base edges that interact (Watson-Crick, Hoogsteen, and Sugar Edge) and the relative orientation of their glycosidic bonds (cis or trans). Thus, there are 12 geometric basepairing families. A basetriple is a set of three nucleotides making two or three basepairs with one another, one of which may be a Watson-Crick pair. In a basetriple, at least one nucleotide must be involved in two basepair interactions. We used our “Find RNA 3D” (FR3D) search program to find all instances of basetriples. By searching symbolically for all instances of three bases in which a Watson-Crick or non-Watson-Crick basepair occurred between the first and second bse, and between the second and third base. We classified these according to the nature of the first and second basepairs. Combinatorially, 108 different kinds of basetriples were expected,12 cWW,12 tWW, 10 cWH, 10 tWH, 8 cWS, 8 tWS, 8 cHW, 8 tHW, 6 cHH, 6 tHH,4 cHS, 4 tHS, 4 cSW, 4 tSW, 2 cSH, and 2 tSH of which 64 were actually observed in the current database. From a reduced-redundancy set of atomic level x-ray crystal structures, the FR3D program found a large number of basetriple interactions, which were classified into geometric families based on the interacting edges. We determined the sequence signatures and distinct geometries within each geometric family. This information is useful in understanding and predicting allowed sequence variation between related organisms to better understand mutational data.

Keywords: RNA basepair, FR3D, geometric search program