2D meets 4G: G-quadruplexes in RNA secondary structure prediction

Jing Qin, Ronny Lorrenz et al

Research output: Contribution to journalJournal articleResearchpeer-review

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 5ÊUTR of protein coding mRNAs.

Original languageEnglish
JournalI E E E - A C M Transactions on Computational Biology and Bioinformatics
Volume10
Issue number4
Pages (from-to)832-844
Number of pages12
ISSN1545-5963
DOIs
Publication statusPublished - Jul 2013

Keywords

  • Dynamic programming
  • RNA folding
  • ViennaRNA Package
  • RNA Folding
  • Humans
  • Computational Biology
  • Thermodynamics
  • Sequence Alignment
  • RNA, Messenger/chemistry
  • Sequence Analysis, RNA
  • 5' Untranslated Regions
  • Base Sequence
  • G-Quadruplexes
  • Nucleic Acid Conformation

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