R-loop stability as a function of RNA structure and size

Raif Landgraf, Chi hong B. Chen, David S. Sigman

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


The sequence-specific formation of R-loops can be assayed using RNAs which overlap a HindIII cleavage site in a 3.5 kb plasmid. Chemical modification of the displaced DNA strand has permitted stabilization of these R-loops and allowed a systematic investigation of the dependence of these triple-stranded structures on the chain length and structure of the input RNA. RNAs as short as 50 nt form stable R-loops if 5-allylamine uridines (Uaa-RNA) are used in place of normal uridines; normal RNAs must be 100 nt long to form R-loops quantitatively. Since acetic anhydride decreases the hybridization efficiency of Uaa-RNAs, the positive charge of the RNAs must diminish the electrostatic repulsion of the three negatively charged phosphodiester backbones. The dependence of R-loop stability on the length of RNA can be simulated with a random walk model, which also applies to strand migration within Holiday junctions. R-loop hybridization provides a versatile method to generate single-stranded DNA in a sequence-selective manner.

Original languageEnglish (US)
Pages (from-to)3516-3523
Number of pages8
JournalNucleic acids research
Issue number17
StatePublished - Sep 11 1995
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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