Year: 2010
Type: article
Abstract: Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.
Source: Nucleic Acids Research
DOI: 10.1093/nar/gkq282
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,992
Awards: Computational Methods for Tertiary RNA Folding and Novel RNA Design, G132563423, G1336448005, G1572106353, G2135478056, G338944111, G3897559065, Toward RNA Genomics: A Pilot Study in the Analysis, Design, and Prediction of RNA Structures, G4408547596, G5019921669, G5094664921, G5292656900, Computational studies of in vitro selection of RNAs, G719843099, G969889393
OpenAlex ID: W2027589426