Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

Journal Article (Journal Article;Review)

Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathways, and dynamic adaptability of RNA. A new view is emerging in which tertiary interactions do not define RNA 3D structure, but rather, help select specific conformers from an already narrow, topologically pre-defined conformational distribution. Studies are providing fundamental insights into the nature of these topological constraints, how they are encoded by the RNA secondary structure, and how they interplay with other interactions, breathing new meaning to RNA secondary structure. New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. Topological constraints are also providing a much-needed framework for rationalizing and describing RNA dynamics and structural adaptation. Finally, studies suggest that topological constraints may play important roles in steering RNA folding pathways. Here, we review recent advances in our understanding of topological constraints encoded by the RNA secondary structure.

Full Text

Duke Authors

Cited Authors

  • Bailor, MH; Mustoe, AM; Brooks, CL; Al-Hashimi, HM

Published Date

  • June 2011

Published In

Volume / Issue

  • 21 / 3

Start / End Page

  • 296 - 305

PubMed ID

  • 21497083

Pubmed Central ID

  • PMC3319143

Electronic International Standard Serial Number (EISSN)

  • 1879-033X

Digital Object Identifier (DOI)

  • 10.1016/


  • eng

Conference Location

  • England