1. Simplified RNA secondary structure mapping by automation of SHAPE data analysis
- Author
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Phillip S. Pang, Jeffrey S. Glenn, Edward A. Pham, and Menashe Elazar
- Subjects
Acylation ,Hepacivirus ,Computational biology ,Biology ,Ligands ,Primer extension ,Nucleic acid secondary structure ,03 medical and health sciences ,Protein structure ,Genetics ,Protein secondary structure ,DNA Primers ,030304 developmental biology ,0303 health sciences ,Data processing ,Base Sequence ,Viral Core Proteins ,030302 biochemistry & molecular biology ,Electrophoresis, Capillary ,Reproducibility of Results ,RNA ,Molecular Sequence Annotation ,3. Good health ,Internal ribosome entry site ,Methods Online ,Nucleic Acid Conformation ,RNA, Viral ,Algorithms ,Software - 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.
- Published
- 2011
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