Plasmid DNA replication and topology as visualized by two-dimensional agarose gel electrophoresis

Plasmid

Volumn 63, Issue 1, 2010, Pages 1-10

  Schvartzman, J B ^a   Martinez Robles M L ^a   Hernandez P ^a   Krimer, D B ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

Catenation; DNA replication; Fork blockage; Knotting; Recombination; Supercoiling

Indexed keywords

PLASMID DNA;

AGAR GEL ELECTROPHORESIS; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA STRAND BREAKAGE; DNA STRUCTURE; DNA SUPERCOILING; ESCHERICHIA COLI; NONHUMAN; PLASMID; REVIEW; SACCHAROMYCES CEREVISIAE; STREPTOCOCCUS PYOGENES; TWO DIMENSIONAL GEL ELECTROPHORESIS;

DNA REPLICATION; DNA, CATENATED; DNA, SUPERHELICAL; ELECTROPHORESIS, AGAR GEL; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; NUCLEIC ACID CONFORMATION; PLASMIDS; REPLICATION ORIGIN;

EID: 72649095200     PISSN: 0147619X     EISSN: 10959890     Source Type: Journal    
DOI: 10.1016/j.plasmid.2009.11.001     Document Type: Review

References (74)

1. Bolívar F., et al. Origin of replication of pBR345 plasmid DNA. Proceedings of the National Academy of Sciences of the United States of America 74 (1977) 5265-5269
2. Bolívar F., et al. Construction and characterization of new cloning vehicles, II. A multipurpose cloning system. Gene 2 (1977) 95-113
3. Brewer B.J., and Fangman W.L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51 (1987) 463-471
4. Brewer B.J., and Fangman W.L. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55 (1988) 637-643
5. Brewer B.J., and Fangman W.L. Initiation at closely spaced replication origins in a yeast chromosome. Science 262 (1993) 1728-1731
6. Brewer B.J., and Fangman W.L. Initiation preference at a yeast origin of replication. Proceedings of the National Academy of Sciences of the United States of America 91 (1994) 3418-3422
7. Brewer B.J., et al. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Cancer Cells 6 (1988) 229-234
8. Caburet S., et al. Combing the genome for genomic instability. Trends in Biotechnology 20 (2002) 344-350
9. Ceglowski P., and Alonso J.C. Gene organization of the Streptococcus pyogenes plasmid pDB101: sequence analysis of the orf eta-copS region. Gene 145 (1994) 33-39
10. Ceglowski P., et al. Functional analysis of pSM19035-derived replicons in Bacillus subtilis. FEMS Microbiol Letters 109 (1993) 145-150
11. Cox M.M., et al. The importance of repairing stalled replication forks. Nature 404 (2000) 37-41
12. Delidakis C., and Kafatos F.C. Amplification enhancers and replication origins in the autosomal chrorion gene cluster of Drosophila. EMBO Journal 8 (1989) 891-901
13. deMassy B., et al. Inhibition of replication forks exiting the terminus region of the Escherichia coli chromosome occurs at two loci separated by 5 min. Proceedings of the National Academy of Sciences of the United States of America 84 (1987) 1759-1763
14. Deshpande A.M., and Newlon C.S. DNA replication fork pause sites dependent on transcription. Science 272 (1996) 1030-1033
15. Dubey D.D., et al. Three ARS elements contribute to the ura4 replication origin region in the fission yeast, Schizosaccharomyces pombe. EMBO Journal 13 (1994) 3638-3647
16. Fierro-Fernandez M., et al. Replication fork reversal occurs spontaneously after digestion but is constrained in supercoiled domains. Journal of Biological Chemistry 282 (2007) 18190-18196
17. Fierro-Fernandez M., et al. Topological locking restrains replication fork reversal. Proceedings of the National Academy of Sciences of the United States of America 104 (2007) 1500-1505
18. Friedman K.L., and Brewer B.J. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. In: Campbell J.L. (Ed). DNA Replication vol. 262 (1995), Academic Press Inc., 525 B Street, Suite 1900, San Diego, CA 92101-94495
19. Gahn T.A., and Schildkraut C.L. The Epstein-Barr virus origin of plasmid replication, oriP, contains both the initiation and termination sites of DNA replication. Cell 58 (1989) 527-535
20. Heck M.M.S., and Spradling A.C. Multiple replication origins are used during Drosophila chorion gene amplification. Journal of Cell Biology 110 (1990) 903-914
21. Hernández P., et al. Conserved features in the mode of replication of eukaryotic ribosomal RNA genes. EMBO Journal 12 (1993) 1475-1485
22. Higgins N.P., et al. A model for replication repair in mammalian cells. Journal of Molecular Biology 101 (1976) 417-425
23. Hill T.M., et al. The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication. Proceedings of the National Academy of Sciences of the United States of America 84 (1987) 1754-1758
24. Horiuchi T., and Hidaka M. Core sequence of two separable terminus sites of the R6K plasmid that exhibit polar inhibition of replication is a 20 bp inverted repeat. Cell 54 (1988) 515-523
25. Huberman J.A., et al. The in vivo replication origin of the yeast 2 mm plasmid. Cell 51 (1987) 473-481
26. Hyrien O., and Mechali M. Plasmid replication in Xenopus eggs and egg extracts-a 2D gel electrophoretic analysis. Nucleic Acids Research 20 (1992) 1463-1469
27. Hyrien O., and Mechali M. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO Journal 12 (1993) 4511-4520
28. Inselburg J. Replication of Colicin E1 plasmid DNA in minicells from a unique replication initiation site. Proceedings of the National Academy of Sciences of the United States of America 71 (1974) 2256-2259
29. Kalejta R.F., and Hamlin J.L. Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage. Molecular and Cellular Biology 16 (1996) 4915-4922
30. Kaplan D.L. The 3′-tail of a forked-duplex sterically determines whether one or two DNA strands pass through the central channel of a replication-fork helicase. Journal of Molecular Biology 301 (2000) 285-299
31. Khatri G.S., et al. The replication terminator protein of E. coli is a sequence-specific contra-helicase. Cell 59 (1989) 667-674
32. Krysan P.J., and Calos M.P. Replication initiates at multiple locations on an autonomously replicating plasmid in human cells. Molecular and Cellular Biology 11 (1991) 1464-1472
33. Lee C.H., et al. Unwinding of double-stranded DNA helix by dihydration. Proceedings of the National Academy of Sciences of the United States of America 78 (1981) 2838-2842
34. Linskens M.H.K., and Huberman J.A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Molecular and Cellular Biology 8 (1988) 4927-4935
35. Linskens M.H.K., and Huberman J.A. Ambiguities in results obtained with 2D gel replicon mapping techniques. Nucleic Acids Research 18 (1990) 647-652
36. Linskens M.H.K., and Huberman J.A. The two faces of eukaryotic DNA replication origins. Cell 62 (1990) 845-847
37. Little R.D., et al. Initiation and termination of DNA replication in human rRNA genes. Molecular and Cellular Biology 13 (1993) 6600-6613
38. Liu Y., and Botchan M. Replication of bovine papillomavirus type-1 DNA initiates within an E2-responsive enhancer element. Journal of Virology 64 (1990) 5903-5911
39. Long D.T., and Kreuzer K.N. Regression supports two mechanisms of fork processing in phage T4. Proceedings of the National Academy of Sciences of the United Stated of America 105 (2008) 6852-6857
40. Long D.T., and Kreuzer K.N. Fork regression is an active helicase-driven pathway in bacteriophage T4. EMBO Reports 10 (2009) 394-399
41. Lopes M., et al. The DNA replication checkpoint response stabilizes stalled replication forks. Nature 412 (2001) 557-561
42. Lucas I., et al. Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. Journal of Molecular Biology 296 (2000) 769-786
43. Lucas I., et al. Topoisomerase II can unlink replicating DNA by precatenane removal. EMBO Journal 20 (2001) 6509-6519
44. Mahbubani H.M., et al. DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. Nucleic Acids Research 20 (1992) 1457-1462
45. Marahrens Y., and Stillman B. Replicator dominance in a eukaryotic chromosome. EMBO Journal 13 (1994) 3395-3400
46. Marians K.J. Prokaryotic DNA replication. Annual Review of Biochemistry 61 (1992) 673-719
47. Martín-Parras L., et al. Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis. Journal of Molecular Biology 220 (1991) 843-853
48. Martín-Parras L., et al. Initiation of DNA replication in ColE1 plasmids containing multiple potential origins of replication. Journal of Biological Chemistry 267 (1992) 22496-22505
49. Martín-Parras L., et al. Topological complexity of different populations of pBR322 as visualized by two-dimensional agarose gel electrophoresis. Nucleic Acids Research 26 (1998) 3424-3432
50. Martínez-Robles M.L., et al. Interplay of DNA supercoiling and catenation during the segregation of sister duplexes. Nucleic Acids Research 37 (2009) 5126-5137
51. Nawotka K.A., and Huberman J.A. Two-dimensional gel electrophoretic method of mapping DNA replicons. Molecular and Cellular Biology 8 (1988) 1408-1413
52. Olavarrieta L., et al. DNA knotting caused by head-on collision of transcription and replication. Journal of Molecular Biology 322 (2002) 1-6
53. Olavarrieta L., et al. Knotting dynamics during DNA replication. Molecular Microbiology 46 (2002) 699-707
54. Olavarrieta L., et al. Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Research 30 (2002) 656-666
55. Oppenheim A. Separation of closed circular DNA from linear DNA by electrophoresis in two dimensions in agarose gels. Nucleic Acids Research 9 (1981) 6805-6812
56. Pomerantz R.T., and O'Donnell M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456 (2008) 762-766
57. Postow L., et al. Knot what we thought before: the twisted story of replication. Bioessays 21 (1999) 805-808
58. Postow L., et al. Positive torsional strain causes the formation of a four-way junction at replication forks. Journal of Biological Chemistry 276 (2001) 2790-2796
59. Sánchez-Gorostiaga A., et al. Transcription terminator factor reb1p causes two replication fork barriers at its cognate sites in fission yeast rDNA in vivo. Molecular and Cellular Biology 24 (2004) 398-406
60. Santamaría D., et al. DnaB helicase is unable to dissociate RNA-DNA hybrids-its implication in the polar pausing of replication forks at ColE1 origins. Journal of Biological Chemistry 273 (1998) 33386-33396
61. Santamaría D., et al. Premature termination of DNA replication in plasmids carrying two inversely oriented ColE1 origins. Journal of Molecular Biology 300 (2000) 75-82
62. Schvartzman J.B., et al. Evidence that replication initiates at only some of the potential origins in each oligomeric form of Bovine Papillomavirus Type 1 DNA. Molecular and Cellular Biology 10 (1990) 3078-3086
63. Schvartzman J.B., et al. The migration behaviour of DNA replicative intermediates containing an internal bubble analyzed by 2-dimensional agarose gel electrophoresis. Nucleic Acids Research 21 (1993) 5474-5479
64. Schvartzman J.B., and Stasiak A. A topological view of the replicon. EMBO Reports 5 (2004) 256-261
65. Sista P.R., et al. A host-encoded DNA-binding protein promotes termination of plasmid replication at a sequence-specific replication terminus. Proceedings of the National Academy of Sciences of the United States of America 86 (1989) 3026-3030
66. Sogo J.M., et al. Formation of knots in partially replicated DNA molecules. Journal of Molecular Biology 286 (1999) 637-643
67. Sundin O., and Varshavsky A. Terminal stages of SV40 DNA replication proceed via multiply intertwined catenated dimers. Cell 21 (1980) 103-114
68. Tomizawa J., et al. Replication of colicin E1 plasmid DNA in cell extracts origin and direction of replication. Proceedings of the National Academy of Sciences of the United States of America 71 (1974) 2260-2264
69. Vaughn J.P., et al. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell 61 (1990) 1075-1087
70. Viguera E., et al. The ColE1 unidirectional origin acts as a polar replication fork pausing site. Journal of Biological Chemistry 271 (1996) 22414-22421
71. Viguera E., et al. Visualisation of plasmid replication intermediates containing reversed forks. Nucleic Acids Research 28 (2000) 498-503
72. Waldeck W., et al. Origin of replication in episomal bovine papilloma virus type 1 DNA isolated from transformed cells. EMBO Journal 3 (1984) 2173-2178
73. Wang J.C., et al. DNA supercoiling and its effects on DNA structure and function. Cold Spring Harbor Symposium on Quantitative Biology 47 pt. 1 (1983) 85-91
74. Wiesendanger B., et al. Replication fork barriers in the Xenopus rDNA. Nucleic Acids Research 22 (1994) 5038-5046