Plasmids

Marcelo E. Tolmasky; Luis A. Actis; Timothy J. Welch; Jorge H. Crosa

doi:10.1128/9781555817497.ch30

Chapter 30 : Plasmids

Authors: Marcelo E. Tolmasky, Luis A. Actis, Timothy J. Welch, Jorge H. Crosa

Content Type: Reference

Publication Year: 2007

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817497

Chapter DOI: 10.1128/9781555817497.ch30

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Plasmids, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap30-1.gif /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap30-2.gif

Abstract:

The elimination (curing) of a genetic trait by treating the bacterial population with chemical or physical curing agents such as acridine dyes, ethidium bromide, sodium dodecyl sulfate (SDS), antibiotics, high temperature, or electroporation indicates that the expression of that genetic trait is linked to the presence of a plasmid. This chapter deals with the isolation, purification, and characterization of bacterial plasmids and also provides some information concerning the novel application of plasmid biology in gene therapy. The chapter provides a representative rather than comprehensive account of techniques and references concerning the biology of plasmids and their use as tools in molecular biology and pharmacology. The lysostaphin and lysozyme method was adapted in large scale isolation methods. The cold alkaline pH method is a scaled-down version of the one described in large scale that has been used to prepare Escherichia coli and Vibrio anguillarum plasmids. The acid phenol method is based on the addition of an acid phenol extraction to the cold alkaline lysis preparation of DNA and has been used very successfully. The boiling method described here is the original method of Holmes and Quigley, used effectively for screening of high-copy-number plasmids. The protocols to isolate linear plasmids involve cell lysis, in some cases followed by CsCl-ethidium chloride gradient purification, and the separation of the linear plasmid from the chromosomal DNA by either sucrose gradient or agarose gel electrophoresis.

Citation: Tolmasky M, Actis L, Welch T, Crosa J. 2007. Plasmids, p 709-734. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch30

Highlighted Text: Show | Hide

Full text loading...

Figures

Plasmids

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817497.chap30-1,webId=/content/author/10.1128/9781555817497.chap30-1,properties={foaf_givenname=Marcelo E., foaf_name=Marcelo E. Tolmasky, foaf_surname=Tolmasky}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817497.chap30-2,webId=/content/author/10.1128/9781555817497.chap30-2,properties={foaf_givenname=Luis A., foaf_name=Luis A. Actis, foaf_surname=Actis}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817497.chap30-3,webId=/content/author/10.1128/9781555817497.chap30-3,properties={foaf_givenname=Timothy J., foaf_name=Timothy J. Welch, foaf_surname=Welch}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817497.chap30-4,webId=/content/author/10.1128/9781555817497.chap30-4,properties={foaf_givenname=Jorge H., foaf_name=Jorge H. Crosa, foaf_surname=Crosa}]]

/content/10.1128/9781555817497.chap30.fig30-1

FIGURE 1

Determination of plasmid copy number. A plasmid-containing bacterial strain was grown in a minimal salts medium plus Casamino Acids and glucose. Labeling and lysis were carried out, and the lysate was centrifuged in the CsClethidium bromide gradient. Seven-drop fractions were collected on microtiter trays and assayed for radioactivity.

10.1128/9781555817497/fig30-1_thmb.gif

10.1128/9781555817497/fig30-1.gif

FIGURE 1

References

/content/book/10.1128/9781555817497.chap30

1. Abai, A. M.,, P. M. Hobart,, and K. M. Barnhart. 1999. Insulin delivery with plasmid DNA. Hum. Gene Ther. 10: 2637– 2649.

2. Actis, L. A.,, M. E. Tolmasky,, and J. H. Crosa. 1999. Bacterial plasmids: replication of extrachromosomal genetic elements encoding resistance to antimicrobial compounds. Front. Biosci. 4: D43– D62.

3. Actis, L. A.,, M. E. Tolmasky,, L. Crosa,, and J. H. Crosa. 1993. Effect of iron-limiting conditions on growth of clinical isolates of Acinetobacter baumannii. J. Clin. Microbiol. 31: 2812– 2815.

4. Alter, D. C.,, and K. N. Subramanian. 1989. A one step, quick step, mini prep. BioTechniques 7: 456– 458.

5. Anderson, D. G.,, and L. L. McKay. 1983. Simple and rapid method for isolating large plasmid DNA from lactic streptococci. Appl. Environ. Microbiol. 46: 549– 552.

6. Banfalvi, Z.,, E. Kondorosi,, and A. Kondorosi. 1985. Rhizobium meliloti carries two megaplasmids. Plasmid 13: 129– 138.

7. Barbour, A. G.,, and C. F. Garon. 1987. Linear plasmids of the bacterium Borrelia burgdorferi have covalently closed ends. Science 237: 409– 411.

8. Barnett, M. J.,, R. F. Fisher,, T. Jones,, C. Komp,, A. P. Abola,, F. Barloy-Hubler,, L. Bowser,, D. Capela,, F. Galibert,, J. Gouzy,, M. Gurjal,, A. Hong,, L. Huizar,, R. W. Hyman,, D. Kahn,, M. L. Kahn,, S. Kalman,, D. H. Keating,, C. Palm,, M. C. Peck,, R. Surzycki,, D. H. Wells,, K. C. Yeh,, R. W. Davis,, N. A. Federspiel,, and S. R. Long. 2001. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmids. Proc. Natl. Acad. Sci. USA 98: 9883– 9888.

9. Barre, F. X.,, M. Aroyo,, S. D. Colloms,, A. Helfrich,, F. Cornet,, and D. J. Sherratt. 2000. FtsK functions in the processing of a Holliday junction intermediate during bacterial chromosome segregation. Genes Dev. 14: 2976– 2988.

10. Barth, P. L.,, L. Tobin,, and G. Sharpe,. 1981. Development of broad host-range plasmid vectors, p. 439– 448. In S. B. Levy,, R. C. Clowes,, and E. L. Koenig (ed.), Molecular Biology, Pathogenicity, and Ecology of Bacterial Plasmids. Plenum Press, New York, NY.

11. Berfer, A.,, and A. Kimmel. 1987. Guide to Molecular Cloning Techniques, vol. 152. Academic Press, San Diego, CA.

12. Bhattacharyya, A.,, and D. H. Figurski. 2001. A small protein-protein interaction domain common to KlcB and global regulators KorA and TrbA of promiscuous IncP plasmids. J. Mol. Biol. 310: 51– 67.

13. Birnboim, H. C.,, and J. Doly. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7: 1513– 1523.

14. Boyd, E. F.,, and D. L. Hartl. 1998. Salmonella virulence plasmid. Modular acquisition of the spv virulence region by an F-plasmid in Salmonella enterica subspecies I and insertion into the chromosome of subspecies II, IIIa, IV and VII isolates. Genetics 149: 1183– 1190.

15. Brown, M. D.,, A. G. Schatzlein,, and I. F. Uchegbu. 2001. Gene delivery with synthetic (non viral) carriers. Int. J. Pharm. 229: 1– 21.

16. Brunk, C. F.,, C. K. Jones,, and T. W. James. 1979. Assay for nanogram quantities of DNA in cellular homogenates. Anal. Biochem. 92: 497– 500.

17. Burkardt, B.,, D. Schillik,, and A. Puhler. 1987. Physical characterization of Rhizobium meliloti megaplasmids. Plasmid 17: 13– 25.

18. Campeau, P.,, P. Chapdelaine,, S. Seigneurin-Venin,, B. Massie,, and J. P. Tremblay. 2001. Transfection of large plasmids in primary human myoblasts. Gene Ther. 8: 1387– 1394.

19. Caplen, N.,, E. Alton,, P. Middelton,, J. Dorin,, B. Stevenson,, X. Gao,, S. Durham,, P. Jeffrey,, M. Hodson,, C. Coutelle,, L. Huang,, D. Porteus,, R. Williamson,, and D. Geddes. 1995. A phase trial of liposome mediated CFTR gene transfer to the nasal epithelia of patients with cystic fibrosis. Nat. Med. 1: 39– 46.

20. Carle, G. F.,, and M. V. Olson. 1985. An electrophoretic karyotype for yeast. Proc. Natl. Acad. Sci. USA 82: 3756– 3760.

21. Chakrabarty, A. M. 1992. Microorganisms having multiple compatible degradative energy-generating plasmids and preparation thereof. Biotechnology 24: 535– 545.

22. Chakrabarty, A. M. 1976. Plasmids in Pseudomonas. Annu. Rev. Genet. 10: 7– 30.

23. Chassy, B. M.,, and A. Giuffrida. 1980. Method for the lysis of gram-positive, asporogenous bacteria with lysozyme. Appl. Environ. Microbiol. 39: 153– 158.

24. Chattoraj, D. K. 2000. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37: 467– 476.

25. Choate, K. A.,, and P. A. Khavari. 1997. Direct cutaneous gene delivery in a human genetic skin disease. Hum. Gene Ther. 8: 1659– 1665.

26. Clark, P. R.,, A. T. Stopeck,, M. Ferrari,, S. E. Parker,, and E. M. Hersh. 2000. Studies of direct intratumoral gene transfer using cationic lipid-complexed plasmid DNA. Cancer Gene Ther. 7: 853– 860.

27. Clayton, D. A.,, R. W. Davis,, and J. Vinograd. 1970. Homology and structural relationships between the dimeric and monomeric circular forms of mitochondrial DNA from human leukemic leukocytes. J. Mol. Biol. 47: 137– 153.

28. Clewell, D. B.,, and D. R. Helinski. 1969. Supercoiled circular DNA-protein complex in Escherichia coli: purification and induced conversion to an open circular DNA form. Proc. Natl. Acad. Sci. USA 62: 1159– 1166.

29. Clowes, R. C. 1972. Molecular structure of bacterial plasmids. Bacteriol. Rev. 36: 361– 405.

30. Courvalin, P.,, S. Goussard,, and C. Grillot-Courvalin. 1995. Gene transfer from bacteria to mammalian cells. C. R. Acad. Sci. III 318: 1207– 1212.

31. Couturier, M.,, F. Bex,, P. L. Bergquist,, and W. K. Maas. 1988. Identification and classification of bacterial plasmids. Microbiol. Rev. 52: 375– 395.

32. Crosa, J. H. 1997. Signal transduction and transcriptional and posttranscriptional control of iron-regulated genes in bacteria. Microbiol. Mol. Biol. Rev. 61: 319– 336.

33. Crosa, J. H.,, D. J. Brenner,, and S. Falkow. 1973. Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J. Bacteriol. 115: 904– 911.

34. Crosa, J. H.,, L. K. Luttropp,, F. Heffron,, and S. Falkow. 1975. Two replication initiation sites on R-plasmid DNA. Mol. Gen. Genet. 140: 39– 50.

35. Crystal, R. 1995. Transfer of genes to humans: early lessons and obstacles to success. Science 270: 404.

36. Currier, T. C.,, and E. W. Nester. 1976. Isolation of covalently closed circular DNA of high molecular weight from bacteria. Anal. Biochem. 76: 431– 441.

37. Davey, R. B.,, P. I. Bird,, S. M. Nikoletti,, J. Praszkier,, and J. Pittard. 1984. The use of mini-Gal plasmids for rapid incompatibility grouping of conjugative R plasmids. Plasmid 11: 234– 242.

38. del Solar, G.,, J. C. Alonso,, M. Espinosa,, and R. Diaz- Orejas. 1996. Broad-host-range plasmid replication: an open question. Mol. Microbiol. 21: 661– 666.

39. del Solar, G.,, and M. Espinosa. 2000. Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37: 492– 500.

40. Densmore, C. L.,, E. S. Kleinerman,, A. Gautam,, S. F. Jia,, B. Xu,, L. L. Worth,, J. C. Waldrep,, Y. K. Fung,, A. T’Ang,, and V. Knight. 2001. Growth suppression of established human osteosarcoma lung metastases in mice by aerosol gene therapy with PEI-p53 complexes. Cancer Gene Ther. 8: 619– 627.

41. Dotto, G. P.,, V. Enea,, and N. D. Zinder. 1981. Functional analysis of bacteriophage f1 intergenic region. Virology 114: 463– 473.

42. Dunny, G. M.,, D. A. Krug,, C. L. Pan,, and R. A. Ledford. 1988. Identification of cell wall antigens associated with a large conjugative plasmid encoding phage resistance and lactose fermentation ability in lactic streptococci. Biochimie 70: 443– 450.

43. Eckhardt, T. 1978. A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid 1: 584– 588.

44. Estruch, E. J.,, S. L. Hart,, C. Kinnon,, and B. G. Winchester. 2001. Non-viral, integrin-mediated gene transfer into fibroblasts from patients with lysosomal storage diseases. J. Gene Med. 3: 488– 497.

45. Farhood, H.,, X. Gao,, K. Son,, Y. Y. Yang,, J. S. Lazo,, L. Huang,, J. Barsoum,, R. Bottega,, and R. M. Epand. 1994. Cationic liposomes for direct gene transfer in therapy of cancer and other diseases. Ann. N. Y. Acad. Sci. 716:23- 34, 34– 35.

46. Felgner, J. H.,, R. Kumar,, C. N. Sridhar,, C. J. Wheeler,, Y. J. Tsai,, R. Border,, P. Ramsey,, M. Martin,, and P. L. Felgner. 1994. Enhanced gene delivery and mechanism studies with a novel series of cationic lipid formulations. J. Biol. Chem. 269: 2550– 2561.

47. Figurski, D. H.,, and D. R. Helinski. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. USA 76: 1648– 1652.

48. Finan, T. M.,, S. Weidner,, K. Wong,, J. Buhrmester,, P. Chain,, F. J. Vorholter,, I. Hernandez-Lucas,, A. Becker,, A. Cowie,, J. Gouzy,, B. Golding,, and A. Puhler. 2001. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl. Acad. Sci. USA 98: 9889– 9894.

49. Finkelstein, M.,, and T. H. Rownd. 1978. A rapid method for extracting DNA from agarose gels. Plasmid 1: 557– 562.

50. Gerdes, K.,, J. Moller-Jensen,, and R. Bugge Jensen. 2000. Plasmid and chromosome partitioning: surprises from phylogeny. Mol. Microbiol. 37: 455– 466.

51. Gershon, H.,, R. Ghirlando,, S. B. Guttman,, and A. Minsky. 1993. Mode of formation and structural features of DNA-cationic liposome complexes used for transfection. Biochemistry 32: 7143– 7151.

52. Gordon, G. S.,, D. Sitnikov,, C. D. Webb,, A. Teleman,, A. Straight,, R. Losick,, A. W. Murray,, and A. Wright. 1997. Chromosome and low copy plasmid segregation in E. coli: visual evidence for distinct mechanisms. Cell 90: 1113– 1121.

53. Gordon, G. S.,, and A. Wright. 2000. DNA segregation in bacteria. Annu. Rev. Microbiol. 54: 681– 708.

54. Gottschalk, S.,, J. T. Sparrow,, J. Hauer,, M. P. Mims,, F. E. Leland,, S. L. Woo,, and L. C. Smith. 1996. A novel DNA-peptide complex for efficient gene transfer and expression in mammalian cells. Gene Ther. 3: 48– 57.

55. Grillot-Courvalin, C.,, S. Goussard,, and P. Courvalin. 1999. Bacteria as gene delivery vectors for mammalian cells. Curr. Opin. Biotechnol. 10: 477– 481.

56. Gruss, A.,, and S. D. Ehrlich. 1989. The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol. Rev. 53: 231– 241.

57. Guerry, P.,, D. J. LeBlanc,, and S. Falkow. 1973. General method for the isolation of plasmid deoxyribonucleic acid. J. Bacteriol. 116: 1064– 1066.

58. Hansen, J. B.,, and R. H. Olsen. 1978. Isolation of large bacterial plasmids and characterization of the P2 incompatibility group plasmids pMG1 and pMG5. J. Bacteriol. 135: 227– 238.

59. Hardy, D. A.,, J. I. Bell,, E. O. Long,, T. Lindsten,, and H. O. McDevitt. 1986. Mapping of the class II region of the human major histocompatibility complex by pulsedfield gel electrophoresis. Nature 323: 453– 455.

60. Hardy, K. G. (ed.). 1993. Plasmids: a Practical Approach, 2nd ed. IRL Press at Oxford University Press, Oxford, United Kingdom.

61. Haro, M. A.,, and V. de Lorenzo. 2001. Metabolic engineering of bacteria for environmental applications: construction of Pseudomonas strains for biodegradation of 2- chlorotoluene. J. Biotechnol. 85: 103– 113.

62. Hartstein, A. I.,, A. L. Rashad,, J. M. Liebler,, L. A. Actis,, J. Freeman,, J. W. Rourke, Jr.,, T. B. Stibolt,, M. E. Tolmasky,, G. R. Ellis,, and J. H. Crosa. 1988. Multiple intensive care unit outbreak of Acinetobacter calcoaceticus subspecies anitratus respiratory infection and colonization associated with contaminated, reusable ventilator circuits and resuscitation bags. Am. J. Med. 85: 624– 631.

63. Heery, D. M.,, R. Powell,, F. Gannon,, and L. K. Dunican. 1989. Curing of a plasmid from E. coli using high-voltage electroporation. Nucleic Acids Res. 17: 10131.

64. Helinski, D.,, A. Toukdarian,, and R. Novick,. 1996. Replication control and other stable maintenance mechanisms of plasmids, p. 2295– 2234. In F. Neidhart,, R. Curtis III,, J. Ingraham,, C. Lin,, K. Low,, B. Magasanik,, W. Reznikoff,, M. Riley,, M. Schaechter,, and H. Umbarger (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 2. ASM Press, Washington, DC.

65. Helinski, D. R. 1973. Plasmid determined resistance to antibiotics: molecular properties of R factors. Annu. Rev. Microbiol. 27: 437– 470.

66. Hiraga, S. 2000. Dynamic localization of bacterial and plasmid chromosomes. Annu. Rev. Genet. 34: 21– 59.

67. Hirochika, H.,, and K. Sakaguchi. 1982. Analysis of linear plasmids isolated from Streptomyces: association of protein with the ends of the plasmid DNA. Plasmid 7: 59– 65.

68. Hirota, Y. 1956. Artificial elimination of the F factor in Bact. coli K-12. Nature ( London) 178: 92.

69. Hirt, B. 1967. Selective extraction of polyoma DNA from infected mouse cell cultures. J. Mol. Biol. 26: 365– 369.

70. Holmes, D. S.,, and M. Quigley. 1981. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114: 193– 197.

71. Hull, R. A.,, R. E. Gill,, P. Hsu,, B. H. Minshew,, and S. Falkow. 1981. Construction and expression of recombinant plasmids encoding type 1 or D-mannose-resistant pili from a urinary tract infection Escherichia coli isolate. Infect. Immun. 33: 933– 938.

72. Ingmer, H.,, C. Miller,, and S. N. Cohen. 2001. The RepA protein of plasmid pSC101 controls Escherichia coli cell division through the SOS response. Mol. Microbiol. 42: 519– 526.

73. Kado, C. I.,, and S. T. Liu. 1981. Rapid procedure for detection and isolation of large and small plasmids. J. Bacteriol. 145: 1365– 1373.

74. Kawakami, M.,, and O. Landman. 1965. Experiments concerning the curing and intracellular site of episomes. Biochem. Biophys. Res. Commun. 18: 716– 724.

75. Khan, S. A. 2000. Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37: 477– 484.

76. Kim, A. Y.,, A. A. Vertes,, and H. P. Blaschek. 1990. Isolation of a single-stranded plasmid from Clostridium acetobutylicum NCIB 6444. Appl. Environ. Microbiol. 56: 1725– 1728.

77. Klavinskis, L. S.,, C. Barnfield,, L. Gao,, and S. Parker. 1999. Intranasal immunization with plasmid DNA-lipid complexes elicits mucosal immunity in the female genital and rectal tracts. J. Immunol. 162: 254– 262.

78. Klavinskis, L. S.,, L. Gao,, C. Barnfield,, T. Lehner,, and S. Parker. 1997. Mucosal immunization with DNAliposome complexes. Vaccine 15: 818– 820.

79. Krum, J. G.,, and S. A. Ensign. 2001. Evidence that a linear megaplasmid encodes enzymes of aliphatic alkene and epoxide metabolism and coenzyme M (2-mercaptoethanesulfonate) biosynthesis in Xanthobacter strain Py2. J. Bacteriol. 183: 2172– 2177.

80. Kumar, M.,, A. K. Behera,, J. Hu,, R. F. Lockey,, and S. S. Mohapatra. 2001. IFN-gamma and IL-12 plasmid DNAs as vaccine adjuvant in a murine model of grass allergy. J. Allergy Clin. Immunol. 108: 402– 408.

81. Kupersztoch, Y. M.,, and D. R. Helinski. 1973. A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor R6K in Escherichia coli. Biochem. Biophys. Res. Commun. 54: 1451– 1459.

82. Kupersztoch-Portnoy, Y. M.,, M. A. Lovett,, and D. R. Helinski. 1974. Strand and site specificity of the relaxation event for the relaxation complex of the antibiotic resistance plasmid R6K. Biochemistry 13: 5484– 5490.

83. Lai, E.,, B. W. Birren,, S. M. Clark,, M. I. Simon,, and L. Hood. 1989. Pulsed field gel electrophoresis. BioTechniques 7: 34– 42.

84. Leifert, J. A.,, J. A. Lindencrona,, J. Charo,, and J. L. Whitton. 2001. Enhancing T cell activation and antiviral protection by introducing the HIV-1 protein transduction domain into a DNA vaccine. Hum. Gene Ther. 12: 1881– 1892.

85. Lev, Z. 1987. A procedure for large-scale isolation of RNA-free plasmid and phage DNA without the use of RNase. Anal. Biochem. 160: 332– 336.

86. Lev, Z.,, and O. Seveg. 1986. The RNA transcripts of Drosophila melanogaster src are differentially regulated during development. Biochim. Biophys. Acta 867: 144– 151.

87. Levy, M. S.,, P. Lotfian,, R. O’Kennedy,, M. Y. Lo-Yim,, and P. A. Shamlou. 2000. Quantitation of supercoiled circular content in plasmid DNA solutions using a fluorescence- based method. Nucleic Acids Res. 28: E57.

88. Lyon, B. R.,, J. W. May,, and R. A. Skurray. 1983. Analysis of plasmids in nosocomial strains of multipleantibiotic- resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 23: 817– 826.

89. Maas, R. 2001. Change of plasmid DNA structure, hypermethylation, and Lon-proteolysis as steps in a replicative cascade. Cell 105: 945– 955.

90. Macrina, F. L.,, D. J. Kopecko,, K. R. Jones,, D. J. Ayers,, and S. M. McCowen. 1978. A multiple plasmid-containing Escherichia coli strain: convenient source of size reference plasmid molecules. Plasmid 1: 417– 420.

91. Manis, J. J.,, and H. J. Whitfield. 1977. Physical characterization of a plasmid cointegrate containing an F’his gnd element and the Salmonella typhimurium LT2 cryptic plasmid. J. Bacteriol. 129: 1601– 1606.

92. McClung, J. K.,, and R. A. Gonzales. 1989. Purification of plasmid DNA by fast protein liquid chromatography on superose 6 preparative grade. Anal. Biochem. 177: 378– 382.

93. McConaughy, B. L.,, C. D. Laird,, and B. J. McCarthy. 1969. Nucleic acid reassociation in formamide. Biochemistry 8: 3289– 3295.

94. Middaugh, C.,, R. Evans,, D. Montgomery,, and D. Casimiro. 1998. Analysis of plasmid DNA from a pharmaceutical perspective. J. Pharm. Sci. 87: 130– 146.

95. Miller, J. F.,, W. J. Dower,, and L. S. Tompkins. 1988. High-voltage electroporation of bacteria: genetic transformation of Campylobacter jejuni with plasmid DNA. Proc. Natl. Acad. Sci. USA 85: 856– 860.

96. Myers, J. A.,, D. Sanchez,, L. P. Elwell,, and S. Falkow. 1976. Simple agarose gel electrophoretic method for the identification and characterization of plasmid deoxyribonucleic acid. J. Bacteriol. 127: 1529– 1537.

97. Nabel, G.,, E. Nabel,, Z. Yang,, B. Fox,, G. Plautz,, X. Gao,, L. Huang,, S. Shu,, D. Gordon,, and A. Chang. 1993. Direct gene transfer with DNA-liposome complexes in melanoma: expression, biologic activity, and lack of toxicity in humans. Proc. Natl. Acad. Sci. USA 90: 11307– 11311.

98. Niki, H.,, and S. Hiraga. 1998. Polar localization of the replication origin and terminus in Escherichia coli nucleoids during chromosome partitioning. Genes Dev. 12: 1036– 1045.

99. Niki, H.,, and S. Hiraga. 1997. Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli. Cell 90: 951– 957.

100. Niki, H.,, and S. Hiraga. 1999. Subcellular localization of plasmids containing the oriC region of the Escherichia coli chromosome, with or without the sopABC partitioning system. Mol. Microbiol. 34: 498– 503.

101. Novick, R. P. 1987. Plasmid incompatibility. Microbiol. Rev. 51: 381– 395.

102. Palchaudhuri, S. 1977. Molecular characterization of hydrocarbon degradative plasmids in Pseudomonas putida. Biochem. Biophys. Res. Commun. 77: 518– 525.

103. Patton, C. M.,, I. K. Wachsmuth,, G. M. Evins,, J. A. Kiehlbauch,, B. D. Plikaytis,, N. Troup,, L. Tompkins,, and H. Lior. 1991. Evaluation of 10 methods to distinguish epidemic-associated Campylobacter strains. J. Clin. Microbiol. 29: 680– 688.

104. Patton, J. 1998. Breathing life into protein drugs. Nat. Biotechnol. 16: 141– 143.

105. Perez-Casal, J. F.,, and J. H. Crosa. 1987. Novel incompatibility and partition loci for the REPI replication region of plasmid ColV-K30. J. Bacteriol. 169: 5078– 5086.

106. Perng, G. C.,, and R. B. LeFebvre. 1990. Expression of antigens from chromosomal and linear plasmid DNA of Borrelia coriaceae. Infect. Immun. 58: 1744– 1748.

107. Pogliano, J.,, T. Q. Ho,, Z. Zhong,, and D. R. Helinski. 2001. Multicopy plasmids are clustered and localized in Escherichia coli. Proc. Natl. Acad. Sci. USA 98: 4486– 4491.

108. Radloff, R.,, W. Bauer,, and J. Vinograd. 1967. A dyebuoyant- density method for the detection and isolation of closed circular duplex DNA: the closed circular DNA in HeLa cells. Proc. Natl. Acad. Sci. USA 57: 1514– 1521.

109. Recchia, G. D.,, M. Aroyo,, D. Wolf,, G. Blakely,, and D. J. Sherratt. 1999. FtsK-dependent and -independent pathways of Xer site-specific recombination. EMBO J. 18: 5724– 5734.

110. Reddy, B. A.,, P. M. Billingsley,, and L. Etkin. 1990. A quick protocol for plasmid DNA analysis. BioTechniques 9: 716– 718.

111. Robinett, C.,, A. Straight,, G. Li,, C. Willhelm,, G. Sudlow,, A. Murray,, and A. Belmont. 1996. In vivo localization of DNA sequences and visualization of largescale chromatin organization using lac operator-repressor recognition. J. Cell Biol. 135: 1685– 1700.

112. Saha, B.,, D. Saha,, S. Niyogi,, and M. Bal. 1989. A new method of plasmid DNA preparation by sucrose-mediated detergent lysis from Escherichia coli (gram-negative) and Staphylococcus aureus (gram-positive). Anal. Biochem. 176: 344– 349.

113. Sakaguchi, K.,, H. Hirochika,, and N. Gunge. 1985. Linear plasmids with terminal inverted repeats obtained from Streptomyces rochei and Kluyveromyces lactis. Basic Life Sci. 30: 433– 451.

114. Sambrook, J.,, and D. W. Russell. 2001. Molecular Cloning. A Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

115. Schatzlein, A. G. 2001. Non-viral vectors in cancer gene therapy: principles and progress. Anticancer Drugs 12: 275– 304.

116. Schmidt, T.,, K. Friehs,, M. Schleef,, C. Voss,, and E. Flaschel. 1999. Quantitative analysis of plasmid forms by agarose and capillary gel electrophoresis. Anal. Biochem. 274: 235– 240.

117. Schwartz, D. C.,, and C. R. Cantor. 1984. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37: 67– 75.

118. Sedegah, M.,, R. Hedstrom,, P. Hobart,, and S. L. Hoffman. 1994. Protection against malaria by immunization with plasmid DNA encoding circumsporozoite protein. Proc. Natl. Acad. Sci. USA 91: 9866– 9870.

119. Sedegah, M.,, W. Weiss,, J. B. Sacci, Jr.,, Y. Charoenvit,, R. Hedstrom,, K. Gowda,, V. F. Majam,, J. Tine,, S. Kumar,, P. Hobart,, and S. L. Hoffman. 2000. Improving protective immunity induced by DNA-based immunization: priming with antigen and GM-CSF-encoding plasmid DNA and boosting with antigen-expressing recombinant poxvirus. J. Immunol. 164: 5905– 5912.

120. Serghini, M. A.,, C. Ritzenthaler,, and L. Pinck. 1989. A rapid and efficient ‘miniprep’ for isolation of plasmid DNA. Nucleic Acids Res. 17: 3604.

121. Service, R. F. 1997. Drug delivery takes a deep breath. Science 277: 1199– 1200.

122. Sharp, P. A.,, M. T. Hsu,, E. Otsubo,, and N. Davidson. 1972. Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli. I. Structure of F-prime factors. J. Mol. Biol. 71: 471– 497.

123. Shi, W.,, J. Liu,, Y. Huang,, and L. Qiao. 2001. Papillomavirus pseudovirus: a novel vaccine to induce mucosal and systemic cytotoxic T-lymphocyte responses. J. Virol. 75: 10139– 10148.

124. Shields, M.,, B. Kline,, and J. Tam. 1986. A rapid method for the quantitative measurement of gene dosage: mini-F plasmid concentration as a function of cell growth rate. J. Microbiol. Methods 6: 33– 46.

125. Simske, J. S.,, and S. Scherer. 1989. Pulsed-field gel electrophoresis of circular DNA. Nucleic Acids Res. 17: 4359– 4365.

126. Singer, V. L.,, L. J. Jones,, S. T. Yue,, and R. P. Haugland. 1997. Characterization of Pico Green reagent and development of a fluorescence-based solution assay for doublestranded DNA quantitation. Anal. Biochem. 249: 228– 238.

127. Skurray, R. A.,, H. Nagaishi,, and A. J. Clark. 1976. Molecular cloning of DNA from F sex factor of Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 73: 64– 68.

128. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98: 503– 517.

129. Stirling, C. J.,, G. Stewart,, and D. J. Sherratt. 1988. Multicopy plasmid stability in Escherichia coli requires host-encoded functions that lead to plasmid site-specific recombination. Mol. Gen. Genet. 214: 80– 84.

130. Stopeck, A. T.,, E. M. Hersh,, J. L. Brailey,, P. R. Clark,, J. Norman,, and S. E. Parker. 1998. Transfection of primary tumor cells and tumor cell lines with plasmid DNA/lipid complexes. Cancer Gene Ther. 5: 119– 126.

131. Straight, A.,, A. Belmont,, C. Robinett,, and A. Murray. 1996. GFP tagging of budding yeast chromosomes reveals that protein-protein interactions can mediate sister chromatid cohesion. Curr. Biol. 6: 1599– 1608.

132. Summers, D. K. 1996. The Biology of Plasmids. Blackwell Science Ltd., Oxford, United Kingdom.

133. Summers, D. K.,, and D. J. Sherratt. 1988. Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site. EMBO J. 7: 851– 858.

134. te Riele, H.,, B. Michel,, and S. D. Ehrlich. 1986. Singlestranded plasmid DNA in Bacillus subtilis and Staphylococcus aureus. Proc. Natl. Acad. Sci. USA 83: 2541– 2545.

135. Thomas, C. M. 2000. Paradigms of plasmid organization. Mol. Microbiol. 37: 485– 491.

136. Thomas, C. M.,, C. A. Smith,, V. Shingler,, M. A. Cross,, A. A. Hussain,, and M. Pinkney. 1985. Regulation of replication and maintenance functions of broad hostrange plasmid RK2. Basic Life Sci. 30: 261– 276.

137. Tolmasky, M. E.,, L. Actis,, and J. H. Crosa,. 1999. Plasmid DNA replication, p. 2004– 2019. In M. Flickinger, and S. Drew (ed.), Bioprocess Technology: Fermentation, Biocatalysis, and Bioseparation. John Wiley & Sons, Inc., New York, NY.

138. Tolmasky, M. E.,, L. A. Actis,, and J. H. Crosa,. 1993. Virulence plasmids, p. 95– 118. In K. Hardy (ed.), Plasmids: a Practical Approach, 2nd ed. IRL Press at Oxford University Press, Oxford, United Kingdom.

139. Tolmasky, M. E.,, L. A. Actis,, A. E. Toranzo,, J. L. Barja,, and J. H. Crosa. 1985. Plasmids mediating iron uptake in Vibrio anguillarum strains isolated from turbot in Spain. J. Gen. Microbiol. 131: 1989– 1997.

140. Tolmasky, M. E.,, S. Colloms,, G. Blakely,, and D. J. Sherratt. 2000. Stability by multimer resolution of pJHCMW1 is due to the Tn 1331 resolvase and not to the Escherichia coli Xer system. Microbiology 146: 581– 589.

141. Tolmasky, M. E.,, R. J. Staneloni,, and L. F. Leloir. 1982. Lipid-bound saccharides in Rhizobium meliloti. J. Biol. Chem. 257: 6751– 6767.

142. Tservistas, M.,, M. Levy,, M. Lo-Yin,, R. O’Kennedy,, P. York,, G. Humphrey,, and M. Hoare. 2001. The formation of plasmid DNA loaded pharmaceutical powders using supercritical fluids technology. Biotechnol. Bioeng. 72: 12– 18.

143. Tservistas, M.,, T. Scheper,, and R. Freitag,. 1999. Supercritical fluid extraction (SFE)—novel strategies in the processing of biomaterials, p. 106– 113. In S. Grabley, and R. Thiericke (ed.), Drug Discovery from Nature. Springer Verlag, Berlin, Germany.

144. Vahlsing, H. L.,, M. A. Yankauckas,, M. Sawdey,, S. H. Gromkowski,, and M. Manthorpe. 1994. Immunization with plasmid DNA using a pneumatic gun. J. Immunol. Methods 175: 11– 22.

145. Van Larebeke, N.,, G. Engler,, M. Holsters,, S. Van den Elsacker,, I. Zaenen,, R. A. Schilperoort,, and J. Schell. 1974. Large plasmid in Agrobacterium tumefaciens essential for crown gall-inducing ability. Nature 252: 169– 170.

146. Vitzthum, F.,, G. Geiger,, H. Bisswanger,, H. Brunner,, and J. Bernhagen. 1999. A quantitative fluorescencebased microplate assay for the determination of doublestranded DNA using SYBR Green I and a standard ultraviolet transilluminator gel imaging system. Anal. Biochem. 276: 59– 64.

147. Wang, R.,, D. Doolan,, T. Le,, R. Hedstrom,, K. Coonan,, Y. Charoenvit,, T. Jones,, P. Hobart,, M. Margalith,, J. Ng,, W. Weiss,, M. Sedegah,, C. de Taisne,, J. Norman,, and S. Hoffman. 1998. Induction of antigen-specific cytotoxic T lymphocytes in humans by malaria DNA vaccine. Science 282: 476– 480.

148. Waters, V. 2001. Conjugation between bacterial and mammalian cells. Nat. Genet. 29: 375– 376.

149. Watson, B.,, T. C. Currier,, M. P. Gordon,, M. D. Chilton,, and E. W. Nester. 1975. Plasmid required for virulence of Agrobacterium tumefaciens. J. Bacteriol. 123: 255– 264.

150. Wegrzyn, G.,, P. Neubauer,, S. Krueger,, M. Hecker,, and K. Taylor. 1991. Stringent control of replication of plasmids derived from coliphage lambda. Mol. Gen. Genet. 225: 94– 98.

151. Weickert, M.,, and G. Chambliss. 1989. Acid-phenol minipreps make excellent sequencing templates. U.S. Biochemical Corp. Editorial Comments 16: 5– 6.

152. Weiss, W. R.,, K. J. Ishii,, R. C. Hedstrom,, M. Sedegah,, M. Ichino,, K. Barnhart,, D. M. Klinman,, and S. L. Hoffman. 1998. A plasmid encoding murine granulocytemacrophage colony-stimulating factor increases protection conferred by a malaria DNA vaccine. J. Immunol. 161: 2325– 2332.

153. Weitao, T.,, S. Dasgupta,, and K. Nordstrom. 2000. Plasmid R1 is present as clusters in the cells of Escherichia coli. Plasmid 43: 200– 204.

154. Weitao, T.,, S. Dasgupta,, and K. Nordstrom. 2000. Role of the mukB gene in chromosome and plasmid partition in Escherichia coli. Mol. Microbiol. 38: 392– 400.

155. Whisenant, E. C.,, B. K. Rasheed,, and Y. M. Bhatnagar. 1988. Plasmid purification using high-performance gel filtration chromatography. Nucleic Acids Res. 16: 5202.

156. White, F. F.,, and E. W. Nester. 1980. Hairy root: plasmid encodes virulence traits in Agrobacterium rhizogenes. J. Bacteriol. 141: 1134– 1141.

157. Woloj, M.,, M. E. Tolmasky,, M. C. Roberts,, and J. H. Crosa. 1986. Plasmid-encoded amikacin resistance in multiresistant strains of Klebsiella pneumoniae isolated from neonates with meningitis. Antimicrob. Agents Chemother. 29: 315– 319.

158. Yarmolinsky, M. B. 2000. A pot-pourri of plasmid paradoxes: effects of a second copy. Mol. Microbiol. 38: 1– 7.

159. Zasloff, M.,, G. D. Ginder,, and G. Felsenfeld. 1978. A new method for the purification and identification of covalently closed circular DNA molecules. Nucleic Acids Res. 5: 1139– 1152.

160. Zhang, Y. P.,, D. L. Reimer,, G. Zhang,, P. H. Lee,, and M. B. Bally. 1997. Self-assembling DNA-lipid particles for gene transfer. Pharm. Res. 14: 190– 196.

161. Ziai, M. R.,, C. V. Hamby,, R. Reddy,, K. Hayashibe,, and S. Ferrone. 1989. Rapid purification of plasmid DNA following acid precipitation of bacterial proteins. Bio- Techniques 7: 147.

Tables

Plasmids

/content/10.1128/9781555817497.chap30.tab30-1

TABLE 1

Composition of commonly used reagents

10.1128/9781555817497/tab30-1_thmb.gif

10.1128/9781555817497/tab30-1.gif

TABLE 1

Composition of commonly used reagents

/content/10.1128/9781555817497.chap30.tab30-2

TABLE 2

Determination of homology between heterologous plasmids by use of single-strand-specific endonuclease

a The count-per-minute values were obtained by subtracting a background of 20 cpm. +, positive strand; ‒, negative strand.

b Values in this column were obtained by subtracting the value in sample 2 from the respective values in samples 3, 4, and 5 and then normalizing to the corrected value in sample 3.

10.1128/9781555817497/tab30-2_thmb.gif

10.1128/9781555817497/tab30-2.gif

TABLE 2

Determination of homology between heterologous plasmids by use of single-strand-specific endonuclease

a The count-per-minute values were obtained by subtracting a background of 20 cpm. +, positive strand; ‒, negative strand.

b Values in this column were obtained by subtracting the value in sample 2 from the respective values in samples 3, 4, and 5 and then normalizing to the corrected value in sample 3.