Designing Structured RNA Pools for RNA inVitro Selection

Tuesday, October 30, 2007 - 6:15pm - 6:30pm
EE/CS 3-180
Hin Gan (New York University), Namhee Kim (New York University), Tamar Schlick (New York University)
In vitro selection is a versatile experimental tool for discovering novel
synthetic RNAs. However, most RNAs identified from random sequence pools
are small and simple folding motifs. To significantly increase the
probability of discovering novel RNAs, we develop an approach for
engineering sequence pools that links RNA sequence space regions with
corresponding structural distributions via a mixing matrix approach
combined with a graph theory analysis of RNA 2D structure space. Our pool
design method has been automated and made available through the web server
RAGPOOLS ( The RAGPOOLS serves as a guide
to researchers who aim to synthesize RNA pools with desired properties
and/or experiment in silico with various designs by our approach.