2D Meets 4G: G-quadruplexes in RNA Secondary Structure Prediction

IEEE/ACM Trans Comput Biol Bioinform. Jul-Aug 2013;10(4):832-44. doi: 10.1109/TCBB.2013.7.

Abstract

G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters, we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead. Stable G-quadruplexes are strongly enriched, however, in the 5'UTR of protein coding mRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Base Sequence
  • Computational Biology
  • G-Quadruplexes*
  • Humans
  • Nucleic Acid Conformation*
  • RNA Folding
  • RNA, Messenger / chemistry*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Thermodynamics

Substances

  • 5' Untranslated Regions
  • RNA, Messenger