Hybridization of RNA to double-stranded DNA: formation of R-loops.
RNA can hybridize to double-stranded DNA in the presence of 70% formamide by displacing the identical DNA strand. The resulting structure, called an R-loop, is formed in formamide probably because of the greater thermodynamic stability of the RNA-DNA hybrid when it is near the denaturation temperature of duplex DNA. The rate of R-loop formation is maximal at the temperature at which half of the duplex DNA is irreversibly converted to single-stranded DNA (the strand separation temperature of tss) of the duplex DNA and falls precipitously a few degrees above or below that temperature. This maximal rate is similar to the rate of hybridization of RNA to single-stranded DNA under the same conditions. At temperatures above the tss the rate is proportional to the RNA concentration. However, at temperatures below tss the rate of R-loop formation is less dependent upon the RNA concentration. Once formed, the R-loops display considerable stability; the formamide can be removed and the DNA can be cleaved with restriction endonucleases without loss of R-loop structures.
D003090:Coliphages; D004279:DNA, Viral; D005559:Formamides / Q000494:pharmacology; D007700:Kinetics; D008854:Microscopy, Electron; D009693:Nucleic Acid Hybridization / Q000187:drug effects; D009994:Osmolar Concentration; D012335:RNA, Ribosomal; D012441:Saccharomyces cerevisiae; D013696:Temperature
D004279:DNA, Viral; D005559:Formamides; D012335:RNA, Ribosomal