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Nucleic Acids Res. 2011 Dec;39(22):e151. doi: 10.1093/nar/gkr773. Epub 2011 Sep 30.

Simplified RNA secondary structure mapping by automation of SHAPE data analysis.

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1
Department of Medicine, Stanford University Medical Center, Palo Alto, CA, USA.

Abstract

SHAPE (Selective 2'-hydroxyl acylation analysed by primer extension) technology has emerged as one of the leading methods of determining RNA secondary structure at the nucleotide level. A significant bottleneck in using SHAPE is the complex and time-consuming data processing that is required. We present here a modified data collection method and a series of algorithms, embodied in a program entitled Fast Analysis of SHAPE traces (FAST), which significantly reduces processing time. We have used this method to resolve the secondary structure of the first ~900 nt of the hepatitis C virus (HCV) genome, including the entire core gene. We have also demonstrated the ability of SHAPE/FAST to detect the binding of a small molecule inhibitor to the HCV internal ribosomal entry site (IRES). In conclusion, FAST allows for high-throughput data processing to match the current high-throughput generation of data possible with SHAPE, reducing the barrier to determining the structure of RNAs of interest.

PMID:
21965531
PMCID:
PMC3239176
DOI:
10.1093/nar/gkr773
[Indexed for MEDLINE]
Free PMC Article
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