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

Ralf Landgraf, C. B. Chen -h., D. S. Sigman

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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
Pages (from-to)3516-3523
Number of pages8
JournalNucleic Acids Research
Volume23
Issue number17
StatePublished - Jan 1 1995
Externally publishedYes

Fingerprint

RNA
Uridine
DNA
Allylamine
Backbone
Electrostatics
Holidays
Migration
Overlap
Single-Stranded DNA
Random walk
Chemical modification
Stabilization
Static Electricity
Chain length
Charge
Decrease
Plasmids

ASJC Scopus subject areas

  • Genetics
  • Statistics, Probability and Uncertainty
  • Applied Mathematics
  • Health, Toxicology and Mutagenesis
  • Toxicology
  • Genetics(clinical)

Cite this

Landgraf, R., Chen -h., C. B., & Sigman, D. S. (1995). R-loop stability as a function of RNA structure and size. Nucleic Acids Research, 23(17), 3516-3523.

R-loop stability as a function of RNA structure and size. / Landgraf, Ralf; Chen -h., C. B.; Sigman, D. S.

In: Nucleic Acids Research, Vol. 23, No. 17, 01.01.1995, p. 3516-3523.

Research output: Contribution to journalArticle

Landgraf, R, Chen -h., CB & Sigman, DS 1995, 'R-loop stability as a function of RNA structure and size', Nucleic Acids Research, vol. 23, no. 17, pp. 3516-3523.
Landgraf, Ralf ; Chen -h., C. B. ; Sigman, D. S. / R-loop stability as a function of RNA structure and size. In: Nucleic Acids Research. 1995 ; Vol. 23, No. 17. pp. 3516-3523.
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