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Statistical mechanics of RNA folding: importance of alphabet size.

Authors
  • Mukhopadhyay, Ranjan
  • Emberly, Eldon
  • Tang, Chao
  • Wingreen, Ned S
Type
Published Article
Journal
Physical Review E
Publisher
American Physical Society (APS)
Publication Date
Oct 01, 2003
Volume
68
Issue
4 Pt 1
Pages
41904–41904
Identifiers
PMID: 14682970
Source
Medline
License
Unknown

Abstract

We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

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