Improving RNA secondary structure prediction with structure mapping data

Michael F Sloma; David H Mathews

doi:10.1016/bs.mie.2014.10.053

Improving RNA secondary structure prediction with structure mapping data

Methods Enzymol. 2015:553:91-114. doi: 10.1016/bs.mie.2014.10.053. Epub 2015 Feb 3.

Authors

Michael F Sloma¹, David H Mathews²

Affiliations

¹ 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.
² 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: [email protected].

PMID: 25726462
DOI: 10.1016/bs.mie.2014.10.053

Abstract

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.

Keywords: DMS; SHAPE; SNRNASM; Single nucleotide resolution nucleic acid structure mapping experiments.

MeSH terms

Algorithms
Computational Biology / methods*
Enzymes / chemistry
Enzymes / metabolism
Escherichia coli / genetics
High-Throughput Screening Assays
Models, Molecular*
Nucleic Acid Conformation
RNA / chemistry*
RNA / metabolism
RNA, Bacterial / chemistry
RNA, Ribosomal, 5S / chemistry

Substances

Enzymes
RNA, Bacterial
RNA, Ribosomal, 5S
RNA

Grants and funding

R01 GM076485/GM/NIGMS NIH HHS/United States