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

R Landgraf; C H Chen; D S Sigman

doi:10.1093/nar/23.17.3516

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

R Landgraf·C H Chen·D S Sigman

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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 stimulated 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.

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DNA DNA, Single-Stranded Glyoxal Nucleic Acid Denaturation Nucleic Acid Hybridization Oligodeoxyribonucleotides Plasmids RNA Restriction Mapping Structure-Activity Relationship Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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R Landgraf, C H Chen, D S Sigman. 1995-09-11. R-loop stability as a function of RNA structure and size.. https://doi.org/10.1093/nar%2F23.17.3516

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