title: Simplified RNA secondary structure mapping by automation of SHAPE data analysis.
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.
authors.affiliation: Department of Medicine, Stanford University Medical Center, Palo Alto, CA, USA.
authors.forename: Phillip S
authors.initials: PS
authors.lastname: Pang
authors.forename: Menashe
authors.initials: M
authors.lastname: Elazar
authors.forename: Edward A
authors.initials: EA
authors.lastname: Pham
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Glenn
mesh_terms: D000215:Acylation; D000465:Algorithms; D001483:Base Sequence; D017931:DNA Primers; D019075:Electrophoresis, Capillary; D016174:Hepacivirus / Q000235:genetics; D008024:Ligands; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D015203:Reproducibility of Results; D012984:Software; D014758:Viral Core Proteins / Q000235:genetics
chemical_list: D017931:DNA Primers; D008024:Ligands; D012367:RNA, Viral; D014758:Viral Core Proteins; C069130:nucleocapsid protein, Hepatitis C virus; D012313:RNA