Poster abstracts

Poster number 29 submitted by Laura Jones

Comprehensive thermodynamic parameter analysis of 3' double overhangs on terminal wobble base pairs

Laura Jones (Chemistry Department, Allegheny College), Stacy Miller (Chemistry Department, Allegheny College), Karen Giovanetti (Chemistry Department, Allegheny College), Dr. Martin J Serra (Chemistry Department, Allegheny College)

Abstract:
Comprehensive thermodynamic parameter analysis of 3' double overhangs on terminal wobble base pairs |Thermodynamic parameters are reported for 32 self-complimentary RNA duplexes in 1 M NaCl. Twenty-four sequences contain wobble terminal base pairs (GU) with 3'double-nucleotide overhangs, mimicking the structures of short interfering RNA's (siRNA) and microRNAs (miRNA), and eight sequences contain 3' single-nucleotide overhangs. Results from this study allow for the development of a refined nearest-neighbor model to predict the influence of 3' double overhangs on wobble terminal base pairs on the stability of duplex formation. Three of eight possible 3' single-nucleotide overhangs on a wobble terminal base pair have a significant stabilizing effect (CUG/G, CGA/U, and CGG/U) of 0.4 or more kcal/mol relative to 3' single-nucleotide overhangs on Watson-Crick terminal base pairs. Of 24 completed sequences, three 3' double-nucleotide overhangs on wobble terminal base pairs also have a stabilizing effect of 0.4 or more kcal/mol (CGGC/U, CUUA/G, and CUUC/G) relative to 3' single-nucleotide overhangs on Watson-Crick terminal base pairs. The thermodynamic parameters are also reported for 8 self-complimentary RNA duplexes in 1 M NaCl that contain 5' single-nucleotide overhangs on wobble terminal base pairs. Compared to 5' single-nucleotide overhangs on Watson-crick terminal base pairs, no significant stabilization is observed, nor a significant different in stabilizing effects.

Keywords: thermodynamics, wobble, overhangs