On the occurrence of the T-loop RNA folding motif in large RNA molecules

Andrey S. Krasilnikov, Alfonso Mondragón*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

77 Scopus citations


The T-loop RNA folding motif may be considered as a five-nucleotide motif composed of a U-turn flanked by a noncanonical base pair. It was recently proposed that the flanking noncanonical base pair is always a UA trans Watson-Crick/Hoogsteen base pair stacked on a Watson-Crick base pair on one side. Here we show that structural analysis of several large RNA molecules, including the recently solved crystal structure of the specificity domain of Bacillus subtilis RNase P, combined with sequence analysis, indicates a broader sequence consensus for the motif. Additionally, we show that the flanking base pair does not necessarily stack on a Watson-Crick base pair and the 3′ terminus of the five-nucleotide motif is often followed by a sharp turn in the phosphate backbone rather than just a bulged base or bases.

Original languageEnglish (US)
Pages (from-to)640-643
Number of pages4
Issue number6
StatePublished - Jun 1 2003


  • Motif
  • RNA
  • Structure
  • T-loop
  • U-turn

ASJC Scopus subject areas

  • Molecular Biology


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