☆ 4.7 Article

Adventures with RNA graphs

METHODS (2018)

期刊

METHODS

卷 143, 期 -, 页码 16-33

出版社

ACADEMIC PRESS INC ELSEVIER SCIENCE

DOI: 10.1016/j.ymeth.2018.03.009

关键词

RNA structure; Graphs; Coarse-grained modeling; RNA secondary structure; Mathematical biology; RNA design

类别

Biochemical Research Methods Biochemistry & Molecular Biology

资金

NIH NIGMS [R01GM100469, R35GM122562]

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Protocol

Reagent

摘要

The structure of RNA has been a natural subject for mathematical modeling, inviting many innovative computational frameworks. This single-stranded polynucleotide chain can fold upon itself in numerous ways to form hydrogen-bonded segments, imperfect with single-stranded loops. Illustrating these paired and non paired interaction networks, known as RNA's secondary (2D) structure, using mathematical graph objects has been illuminating for RNA structure analysis. Building upon such seminal work from the 1970s and 1980s, graph models are now used to study not only RNA structure but also describe RNA's recurring modular units, sample the conformational space accessible to RNAs, predict RNA's three-dimensional folds, and apply the combined aspects to novel RNA design. In this article, we outline the development of the RNA-As Graphs (or RAG) approach and highlight current applications to RNA structure prediction and design. (C) 2018 Elsevier Inc. All rights reserved.

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