Hybridization of RNA to double-stranded DNA: formation of R-loops.

Abstract

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-oop, is fonned 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 dIlex DNA is irreversibly converted to single-stranded DNA (the strand separation temperature or ts) 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 t5s the rate is proportional to the RNA concentration. However, at temperatures below t55 the rate of Rloop 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. It has recently been observed by R. L. White and D. Hogness (manuscript in preparation) that rRNA can hybridize to duplex DNA that codes for rRNA (rDNA) of Drosophila melanogaster. As observed in the electron microscope, these R-loop structures appear similar to the D-loop structures reported by Robberson et al. (1). However, the duplex portion of the loop is an RNA-DNA hybrid rather than a DNA-DNA hybrid and has thus been termed an R-loop. In order to optimize the formation and utilization of R-loops observed by White and Hogness, we have studied their rate of formation and kinetic stability under a variety of conditions. The ability to form R-loops at high efficiency under controlled conditions may facilitate the mapping and isolation of DNA DNA cleaved with EcoRI endonuclease was placed in the Rloop formation buffer as described above. Samples of 4 AI each were taken at 10 intervals starting at 45°. Five minutes were allowed for equilibration between intervals. Each sample was diluted 20-fold into 0.35 M ammonium acetate at pH 8, 0.01 M Na3EDTA, and 75 Mg/ml of cytochrome c at 00. Samples were mounted for electron microscopy by the aqueous drop method. Drops of 25 Ml of the above DNA plus cytochrome solutions were placed on a polished teflon bar. A parlodioncoated microscope grid was touched to the side of each drop and was stained with uranyl acetate (2). At the strand separation temperature (tss) of a specific EcoRI DNA fragment, the duplex strands are converted into collapsed single-strand bushes. The tss of the RNA-DNA hybrid was determined in an identical manner, except that RNA was first hybridized to its EcoRIcleaved complementary DNA strand at 470 in the R-loop formation buffer.Our initial work on R-loop formation was complicated by DNA degradation and nonreproducible reaction rates. We believe this was the consequence of changes in the reaction constituents and their concentrations during the course of the reaction. The following revisions...

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