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R-loop
An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA (ssDNA). R-loops may be formed in a variety of circumstances, and may be tolerated or cleared by cellular components. The term "R-loop" was given to reflect the similarity of these structures to D-loops; the "R" in this case represents the involvement of an RNA moiety.
In the laboratory, R-loops may also be created by the hybridization of mature mRNA with double-stranded DNA under conditions favoring the formation of a DNA-RNA hybrid; in this case, the intron regions (which have been spliced out of the mRNA) form single-stranded loops, as they cannot hybridize with complementary sequence in the mRNA.
== History ==
R-looping was first described in 1976.〔Thomas M, White RL, Davis RW. “Hybridization of RNA to double-stranded DNA: formation of R-loops”. Proc. Natl Acad. Sci. USA. 1976; 73:2294–2298.〕 Independent R-looping studies from the laboratories of Richard J. Roberts and Phillip A. Sharp showed that protein coding adenovirus genes contained DNA sequences that were not present in the mature mRNA.〔Berget SM, Moore C, Sharp PA. “Spliced segments at the 5′ terminus of adenovirus 2 late mRNA”. Proc Natl Acad Sci USA. 1977; 8:3171–3175. doi: 10.1073/pnas.74.8.3171.〕〔Chow LT, Gelinas RE, Broker TR, Roberts RJ. “An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA”. Cell. 1977; 12(1):1-8.〕 Roberts and Sharp were awarded the Nobel Prize in 1993 for independently discovering introns. After their discovery in adenovirus, introns were found in a number of eukaryotic genes such as the eukaryotic ovalbumin gene (first by the O'Malley laboratory, then confirmed by other groups) 〔Lai EC, Woo SL, Dugaiczyk A, Catterall JF, O'Malley BW (1978) "The ovalbumin gene: structural sequences in native chicken DNA are not contiguous" Proc Natl Acad Sci U S A. 1978 May;75(5):2205-9〕〔O’Hare K, Breathnach R, Benoist C, Chambon P (1979). “No more than seven interruptions in the ovalbumin gene: comparison of genomic and double-stranded cDNA sequences.” Oxford Journals, 7(2): 321-334.〕 hexon DNA,〔Berget SM, Moore C, Sharp PA. “Spliced segments at the 5′ terminus of adenovirus 2 late mRNA”. Proc Natl Acad Sci USA. 1977; 8:3171–3175. doi: 10.1073/pnas.74.8.3171.〕 and extrachromosomal rRNA genes of Tetrahymena thermophila.〔Cech TR and Rio DC (1979). “Localization of transcribed regions on extrachromosomal ribosomal RNA genes of Tetrahymena thermophila by R-loop mapping.” Proc Natl Acad Sci USA. 76, (10): 5051-5055.〕
In the mid-1980's, development of an antibody that binds specifically to the R-loop structure opened the door for immunofluorescence studies, as well as genome-wide characterization of R-loop formation by DRIP-seq.〔Boguslawski SJ et al (1986). "Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids". ''J Immunol Methods''. 1;89(1):123-30.〕
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