2008 Rustbelt RNA Meeting






Talk abstracts

Talk on Saturday 11:20-11:40am submitted by Irina Novikova

RNA Paranemic-Binding Motifs for Biosensing and Nano-assembly

Irina Novikova (Chemistry, Bowling Green State University), Kirill A. Afonin (Chemistry, Bowling Green State University), Evgeny O. Danilov (Chemistry, Bowling Green State University), Neocles B. Leontis (Chemistry, Bowling Green State University)

Paranemic crossover (PX) motifs provide specific, programmable and reversible binding interactions between pre-folded nucleic acid molecules (RNA or DNA). They involve inter-molecular Watson-Crick basepairing with minimal disruption of the secondary structures of the interacting nucleic acids.1 Minimal paranemic motifs involve two strand crossovers and can be programmed across the major or minor grooves of the interacting molecules.
We will present applications of PX self-assembly to RNA biosensing and RNA nanotechnology. Sequence-specific, label-free RNA biosensors (“TokenRNA”) targeting prefolded internal loop motifs (“Target RNA”) were constructed by coupling paranemic binding motifs to a Malachite Green (MG) aptamer obtained by SELEX.2 MG fluorophore added to the solution, only fluoresces when bound to the RNA aptamer. The aptamer-containing “TokenRNA” only binds MG in the presence of its RNA target. We show that this binding is sequence-specific as single-basepair mismatches in the paranemic binding motif disrupt the TokenRNA-Target interaction.3 We also explored the use of the paranemic motif as a cohesion tool for engineering linear RNA fibrils. Atomic Force Microscopy (AFM) showed that linear fibrils exceeding 2 micro-meters were obtained. The fibrils can be derivatized for multiple nanotechnology applications.

1. K. Afonin, D. Cieply, and N. Leontis (2008) J. Am. Chem. Soc. 130: 93.
2. D. Grate and C. Wilson (1999) Proc. Natl. Acad. Sci. USA 96, 6131.
3. K. Afonin, E. Danilov, I. Novikova, and N. Leontis (2008) Chembiochem. 9, 1902.

Keywords: Paranemic Motif, TokenRNA, Biosensor