Abstract
If lambda DNA replication is blocked by mutation in any one of several genes essential for replication, intracellular lambda DNA often shows short three-stranded regions called D loops. In this report we show that one arm of a D loop is an RNA . DNA hybrid, whereas the remaining arm is made up of single-stranded DNA. The RNA can be partially removed by RNase A and totally removed by RNase H. Also, D loops do not appear if infections are made in cells treated with rifampin, a potent inhibitor of transcription by Escherichia coli RNA polymerase. Several genes associated with recombination, including the host recA gene, are not essential for D-loop formation.
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- Baas P. D., Keegstra W., Teertstra W. R., Jansz H. S. R-loops in bacteriophage phiX174 RF DNA. J Mol Biol. 1978 Oct 25;125(2):187–205. doi: 10.1016/0022-2836(78)90344-3. [DOI] [PubMed] [Google Scholar]
- Brown W. M., Shine J., Goodman H. M. Human mitochondrial DNA: analysis of 7S DNA from the origin of replication. Proc Natl Acad Sci U S A. 1978 Feb;75(2):735–739. doi: 10.1073/pnas.75.2.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chattoraj D. K., Inman R. B. Origin and direction of replication of bacteriophage 186 DNA. Proc Natl Acad Sci U S A. 1973 Jun;70(6):1768–1771. doi: 10.1073/pnas.70.6.1768. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gefter M. L., Hirota Y., Kornberg T., Wechsler J. A., Barnoux C. Analysis of DNA polymerases II and 3 in mutants of Escherichia coli thermosensitive for DNA synthesis. Proc Natl Acad Sci U S A. 1971 Dec;68(12):3150–3153. doi: 10.1073/pnas.68.12.3150. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Holloman W. K., Radding C. M. Recombination promoted by superhelical DNA and the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1976 Nov;73(11):3910–3914. doi: 10.1073/pnas.73.11.3910. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Holloman W. K., Wiegand R., Hoessli C., Radding C. M. Uptake of homologous single-stranded fragments by superhelical DNA: a possible mechanism for initiation of genetic recombination. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2394–2398. doi: 10.1073/pnas.72.6.2394. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ikeda H., Matsumoto T. Transcription promotes recA-independent recombination mediated by DNA-dependent RNA polymerase in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4571–4575. doi: 10.1073/pnas.76.9.4571. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kasamatsu H., Vinograd J. Replication of circular DNA in eukaryotic cells. Annu Rev Biochem. 1974;43(0):695–719. doi: 10.1146/annurev.bi.43.070174.003403. [DOI] [PubMed] [Google Scholar]
- McEntee K., Weinstock G. M., Lehman I. R. Initiation of general recombination catalyzed in vitro by the recA protein of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2615–2619. doi: 10.1073/pnas.76.6.2615. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McMacken R., Kornberg A. A multienzyme system for priming the replication of phiX174 viral DNA. J Biol Chem. 1978 May 10;253(9):3313–3319. [PubMed] [Google Scholar]
- McMilin K. D., Russo V. E. Maturation and recombination of bacteriophage lambda DNA molecules in the absence of DNA duplication. J Mol Biol. 1972 Jul 14;68(1):49–55. doi: 10.1016/0022-2836(72)90261-6. [DOI] [PubMed] [Google Scholar]
- Radding C. M. Genetic recombination: strand transfer and mismatch repair. Annu Rev Biochem. 1978;47:847–880. doi: 10.1146/annurev.bi.47.070178.004215. [DOI] [PubMed] [Google Scholar]
- Schnös M., Inman R. B. Position of branch points in replicating lambda DNA. J Mol Biol. 1970 Jul 14;51(1):61–73. doi: 10.1016/0022-2836(70)90270-6. [DOI] [PubMed] [Google Scholar]
- Shen C. K., Hearst J. E. Psoralen-crosslinked secondary structure map of single-stranded virus DNA. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2649–2653. doi: 10.1073/pnas.73.8.2649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shibata T., DasGupta C., Cunningham R. P., Radding C. M. Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1638–1642. doi: 10.1073/pnas.76.4.1638. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stahl F. W., McMilin K. D., Stahl M. M., Crasemann J. M., Lam S. The distribution of crossovers along unreplicated lambda bacteriophage chromosomes. Genetics. 1974 Jul;77(3):395–408. doi: 10.1093/genetics/77.3.395. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
- Thomas M., White R. L., Davis R. W. Hybridization of RNA to double-stranded DNA: formation of R-loops. Proc Natl Acad Sci U S A. 1976 Jul;73(7):2294–2298. doi: 10.1073/pnas.73.7.2294. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thompson B. J., Camien M. N., Warner R. C. Kinetics of branch migration in double-stranded DNA. Proc Natl Acad Sci U S A. 1976 Jul;73(7):2299–2303. doi: 10.1073/pnas.73.7.2299. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tomizawa J., Sakakibara Y., Kakefuda T. Replication of colicin E1 plasmid DNA in cell extracts. Origin and direction of replication. Proc Natl Acad Sci U S A. 1974 Jun;71(6):2260–2264. doi: 10.1073/pnas.71.6.2260. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang J. C. Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. J Mol Biol. 1969 Jul 14;43(1):25–39. doi: 10.1016/0022-2836(69)90076-x. [DOI] [PubMed] [Google Scholar]
- Wiesmeyer H. Prophage repression as a model for the study of gene regulation. I. Titration of the lambda repressor. J Bacteriol. 1966 Jan;91(1):89–94. doi: 10.1128/jb.91.1.89-94.1966. [DOI] [PMC free article] [PubMed] [Google Scholar]