Talk abstracts

Talk on Friday 01:50-02:10pm submitted by Kirill Afonin

Generating New Specific RNA Interaction Interfaces Using C-loops

Kirill A. Afonin (Department of Chemistry, BGSU), Neocles B. Leontis (Department of Chemistry, BGSU)

Abstract:
Modular RNA motifs that mediate tertiary interactions have been used to engineer artificial self-assembling RNA molecules to form nano- and meso-scopic structures, including closed cooperative oligomeric complexes, long, straight fibers, and two-dimensional arrays. Individual RNA tertiary interactions, such as the ubiquitous hairpin loop/receptor motifs, are relatively weak and readily reversible – with generally fast on- and off-rates – and are therefore promising components for designing RNA molecular machines. To achieve intermolecular self-assembly at sub-micromolar concentrations, loop/receptor interactions must be used in pairs. Each molecule must present two loop or receptor motifs, properly oriented for interaction with the cognate motifs in the partner molecule. Using two different binding loops, GAAA (L1) and GGAA (L2) and their cognate receptors, R1 and R2, only two unique, non-self-associating, helical inter-molecular interfaces can be engineered for directional assembly. To be correctly oriented for interaction the motifs must be separated by an integral number of helical turns. Strongest binding occurs with loops and receptors separated by one helical turn (~11 bp). One way to increase the combinatorial possibilities for RNA self-assembly using loop-receptor interactions is to find additional, loop-receptor interaction motifs that interact with the same geometry and that exhibit orthogonal specificity to existing motifs. Here we explore a second strategy, suggested by the identification in crystal structures of a new recurrent RNA motif, the C-loop, which locally increases the helical twist of an RNA helix in which it is embedded. With one embedded C-loop, a helix completes one turn in about nine base stacking layers, i.e. seven Watson-Crick basepairs and two base-triples belonging to the C-loop. We show that the same loop/receptor motif pairs could be used with C-loops to generate molecules that associate preferentially with other C-loop-containing molecules as compared to molecules having the same motifs but lacking C-loops.

Keywords: Tectons, C-loop, Assembly