Adventures with RNA graphs

Research output: Contribution to journalReview article

Abstract

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.

Original languageEnglish (US)
Pages (from-to)16-33
Number of pages18
JournalMethods
Volume143
DOIs
StatePublished - Jul 1 2018

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

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