Improving RNA secondary structure prediction with structure mapping data.
Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide.
Department of Biochemistry & Biophysics, University of Rochester Medical Center, Box 712, Rochester, New York, USA; Center for RNA Biology, University of Rochester Medical Center, Box 712, Rochester, New York, USA.
Michael F
MF
Sloma
Department of Biochemistry & Biophysics, University of Rochester Medical Center, Box 712, Rochester, New York, USA; Center for RNA Biology, University of Rochester Medical Center, Box 712, Rochester, New York, USA. Electronic address: David_Mathews@urmc.rochester.edu.
David H
DH
Mathews
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics; D057166:High-Throughput Screening Assays; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry; D012341:RNA, Ribosomal, 5S / Q000737:chemistry
D004798:Enzymes; D012329:RNA, Bacterial; D012341:RNA, Ribosomal, 5S; D012313:RNA
DMS; SHAPE; SNRNASM; Single nucleotide resolution nucleic acid structure mapping experiments