Structural analysis of single-point mutations given an RNA sequence: a case study with RNAMute

Authors:
Alexander Churkin;Danny Barash
Affiliations:
Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel;Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel and Genome Diversity Center, Institute of Evolution, University of Haifa, Israel
Venue:
EURASIP Journal on Applied Signal Processing
Year:
2006

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Abstract

We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.