Evidence of RNA in D Loops of Intracellular Lambda DNA

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1980 Apr 1

PMID 6445565

Citations 8

Authors

D K Chattoraj

F W Stahl

Affiliations

Soon will be listed here.

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.

Citing Articles

A Sensitive and Nonoptical CRISPR Detection Mechanism by Sizing Double-Stranded λ DNA Reporter.

Mohammad N, Katkam S, Wei Q Angew Chem Int Ed Engl. 2022; 61(50):e202213920.

PMID: 36239984 PMC: 10100359. DOI: 10.1002/anie.202213920.

When DNA Topology Turns Deadly - RNA Polymerases Dig in Their R-Loops to Stand Their Ground: New Positive and Negative (Super)Twists in the Replication-Transcription Conflict.

Kuzminov A Trends Genet. 2017; 34(2):111-120.

PMID: 29179918 PMC: 5967978. DOI: 10.1016/j.tig.2017.10.007.

RNase HII Saves rnhA Mutant Escherichia coli from R-Loop-Associated Chromosomal Fragmentation.

Kouzminova E, Kadyrov F, Kuzminov A J Mol Biol. 2017; 429(19):2873-2894.

PMID: 28821455 PMC: 5610948. DOI: 10.1016/j.jmb.2017.08.004.

Arrest of Viral Proliferation by Ectopic Copies of Its Cognate Replication Origin.

Valenzuela M, Sharan C Genes (Basel). 2015; 6(2):436-50.

PMID: 26110319 PMC: 4488673. DOI: 10.3390/genes6020436.

Evidence for inclusion of regions of nonhomology in heteroduplex products of bacteriophage lambda recombination.

Lichten M, Fox M Proc Natl Acad Sci U S A. 1984; 81(22):7180-4.

PMID: 6239288 PMC: 392101. DOI: 10.1073/pnas.81.22.7180.

References

Wiesmeyer H . Prophage repression as a model for the study of gene regulation. I. Titration of the lambda repressor. J Bacteriol. 1966; 91(1):89-94. PMC: 315914. DOI: 10.1128/jb.91.1.89-94.1966. View

Wang J . Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. J Mol Biol. 1969; 43(1):25-39. DOI: 10.1016/0022-2836(69)90076-x. View

Schnos M, Inman R . Position of branch points in replicating lambda DNA. J Mol Biol. 1970; 51(1):61-73. DOI: 10.1016/0022-2836(70)90270-6. View

Gefter M, Hirota Y, Kornberg T, Wechsler J, 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; 68(12):3150-3. PMC: 389610. DOI: 10.1073/pnas.68.12.3150. View

McMilin K, Russo V . Maturation and recombination of bacteriophage lambda DNA molecules in the absence of DNA duplication. J Mol Biol. 1972; 68(1):49-55. DOI: 10.1016/0022-2836(72)90261-6. View

Chattoraj D, Inman R . Origin and direction of replication of bacteriophage 186 DNA. Proc Natl Acad Sci U S A. 1973; 70(6):1768-71. PMC: 433592. DOI: 10.1073/pnas.70.6.1768. View

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; 71(6):2260-4. PMC: 388431. DOI: 10.1073/pnas.71.6.2260. View

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. View

Stahl F, McMilin K, Stahl M, Crasemann J, Lam S . The distribution of crossovers along unreplicated lambda bacteriophage chromosomes. Genetics. 1974; 77(3):395-408. PMC: 1213136. DOI: 10.1093/genetics/77.3.395. View

10.

Holloman W, Wiegand R, Hoessli C, Radding C . 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; 72(6):2394-8. PMC: 432765. DOI: 10.1073/pnas.72.6.2394. View

11.

Thomas M, Davis R . Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975; 91(3):315-28. DOI: 10.1016/0022-2836(75)90383-6. View

12.

Thomas M, White R, Davis R . Hybridization of RNA to double-stranded DNA: formation of R-loops. Proc Natl Acad Sci U S A. 1976; 73(7):2294-8. PMC: 430535. DOI: 10.1073/pnas.73.7.2294. View

13.

Thompson B, CAMIEN M, Warner R . Kinetics of branch migration in double-stranded DNA. Proc Natl Acad Sci U S A. 1976; 73(7):2299-303. PMC: 430537. DOI: 10.1073/pnas.73.7.2299. View

14.

Shen C, Hearst J . Psoralen-crosslinked secondary structure map of single-stranded virus DNA. Proc Natl Acad Sci U S A. 1976; 73(8):2649-53. PMC: 430705. DOI: 10.1073/pnas.73.8.2649. View

15.

Holloman W, Radding C . Recombination promoted by superhelical DNA and the recA gene of Escherichia coli. Proc Natl Acad Sci U S A. 1976; 73(11):3910-4. PMC: 431262. DOI: 10.1073/pnas.73.11.3910. View

16.

Brown W, Shine J, Goodman H . Human mitochondrial DNA: analysis of 7S DNA from the origin of replication. Proc Natl Acad Sci U S A. 1978; 75(2):735-9. PMC: 411331. DOI: 10.1073/pnas.75.2.735. View

17.

McMacken R, Kornberg A . A multienzyme system for priming the replication of phiX174 viral DNA. J Biol Chem. 1978; 253(9):3313-9. View

18.

Radding C . Genetic recombination: strand transfer and mismatch repair. Annu Rev Biochem. 1978; 47:847-80. DOI: 10.1146/annurev.bi.47.070178.004215. View

19.

Baas P, Keegstra W, Teertstra W, Jansz H . R-loops in bacteriophage phiX174 RF DNA. J Mol Biol. 1978; 125(2):187-205. DOI: 10.1016/0022-2836(78)90344-3. View

20.

Shibata T, Dasgupta C, Cunningham R, Radding C . Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci U S A. 1979; 76(4):1638-42. PMC: 383445. DOI: 10.1073/pnas.76.4.1638. View