Similarity Analysis of DNAs

John L. Johnson; William B. Whitman

doi:10.1128/9781555817497.ch26

Chapter 26 : Similarity Analysis of DNAs

Authors: John L. Johnson, William B. Whitman

Content Type: Reference

Publication Year: 2007

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817497

Chapter DOI: 10.1128/9781555817497.ch26

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Abstract:

In contrast to gram-negative bacteria, nearly all gram-positive bacteria must be digested with a lytic enzyme before they can be lysed by a detergent. In addition to lysozyme, which is the enzyme most commonly used, several other enzymes are available. These include N-acetylmuramidase, which is isolated from Streptomyces globisporus and also cleaves the muramic acid backbone; lysostaphin, an endopeptidase that is isolated from Staphylococcus sp. strain K-6-WI and is specific for the cross-linking peptides of other staphylococci. There are two approaches available for disrupting recalcitrant bacteria. The first involves making the cells susceptible to one or more lytic enzymes by growing them in the presence of wall-component analogs or antibiotics, and the second involves the use of any of several physical methods for cell disruption. The moles percent G+C content of DNA can be estimated by several different methods. The methods described in this chapter use thermal denaturation, high-performance liquid chromatography (HPLC), or dye-binding fluorimetry. Bacteriologists have been criticized for being a bit sloppy in doing and reporting DNA reassociation experiments, compared with those researchers working with eucaryotes. Although some of this criticism is justified, there are additional reasons for greater variability in bacterial DNA experiments. First, the sheer number of bacteriology laboratories involved in performing DNA reassociation experiments has contributed to the variability of results. Second, the hydroxylapatite (HA) procedure has been used for most eucaryotic studies, whereas all of the procedures discussed in the chapter have been used extensively by bacteriologists.

Citation: Johnson J, Whitman W. 2007. Similarity Analysis of DNAs, p 624-652. 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.ch26

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Similarity Analysis of DNAs

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FIGURE 1

Spooling DNA onto a glass rod during precipitation by ethanol. Photo by D. Arbour.

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FIGURE 1

Spooling DNA onto a glass rod during precipitation by ethanol. Photo by D. Arbour.

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FIGURE 2

Hyperchromic shift tracings for two samples of DNA in an automatic recording spectrophotometer. The points at which any vertical line crosses the absorbance and temperature curves give values for these two parameters at a given time. The inflection points are estimated at one-half of the hyperchromatic shift, and the temperature at that time is the melting temperature (T m ).

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FIGURE 2

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FIGURE 3

Separation of deoxynucleosides from the ribonucleosides by HPLC for determination of the moles percent G+C. (A) Separation of ribonucleosides from deoxyribonucleosides at 24°C in 12% methanol on a C18 reverse-phase column. The nucleosides were obtained from enzymatic degradation of Methanococcus voltae nucleic acid. (B) Separation of nucleosides under the optimal conditions for resolution of deoxyguanosine (dG) and thymidine (dT), which were 38°C and 12% methanol for this particular column. Under these conditions, guanosine (G) and 5-methyldeoxycytidine (mC) elute as minor peaks just prior to dG and deoxycytidine (dC) and uridine (U) are not resolved. The nucleoside mixture was prepared from standards. (C) Separation of nucleosides from the nucleotide monophosphates. The chromatography was performed as for panel B. The nucleoside mixture contained 2% of the nucleotide monophosphates. Under these conditions, the nucleotides appear as minor peaks near the nucleosides. Possible products of incomplete degradation, the nucleotides can interfer with the determination of dG and dT. Abbreviations: A, adenosine; dA, deoxyadenosine; dAMP, deoxyadenosine monophosphate; C, cytidine; dC, deoxycytidine; mC, 5-methyldeoxycytidine; G, guanosine; dG, deoxyguanosine; dGMP, deoxyguanosine monophosphate; dT, thymidine; U, uridine; X, unidentified compound. From reference 79 .

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FIGURE 3

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FIGURE 4

Specialized equipment for DNA reassociation experiments. (A) Stainless-steel holder for vials, used during incubation in a water bath. (B) Plexiglas rack for setting up experiments. (C) Plexiglas washing chamber for membrane filters. (D) Autoinjection tubes used for iodinating nucleic acids. (E) Polyethylene tubes (0.2 ml) for use in reassociation experiments.

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FIGURE 4

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FIGURE 5

Plexiglas filtration devices for immobilizing DNA on membranes.

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FIGURE 5

Plexiglas filtration devices for immobilizing DNA on membranes.

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FIGURE 6

Diagram of apparatus for testing the thermostability of hybrid duplexes. A piece of 7-mm-diameter glass tubing (A) is sealed with a rubber plug (C), which is made from a rubber stopper by use of a cork borer. Membrane filters (E) and Teflon washers (F) are impaled on an insect pin (D) close to the head of the pin. The pointed end of the pin is inserted into the rubber plug. This assembly is placed into a 13- by 100-mm glass test tube (B) containing 1.2 ml of 0.5× SSC. The test tube is then placed in a heated-water bath.

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FIGURE 6

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FIGURE 8

Scheme for performing free-solution DNA reassociation experiments, assayed either by the HA or S1 nuclease procedure. TCA, trichloroacetic acid.

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FIGURE 8

Scheme for performing free-solution DNA reassociation experiments, assayed either by the HA or S1 nuclease procedure. TCA, trichloroacetic acid.

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FIGURE 7

Tube rack for thermal stability experiments. This rack fits into the opening of a circulating-water bath. The small amount of exposed surface area cuts down on evaporation.

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FIGURE 7

Tube rack for thermal stability experiments. This rack fits into the opening of a circulating-water bath. The small amount of exposed surface area cuts down on evaporation.

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FIGURE 9

Thermal stability profiles obtained with the hypothetical HA procedure data in Table 2 . Symbols: ∇, percent counts per minute eluted at each temperature for heterologous duplexes; ▴, sum of percent counts per minute eluted at each temperature for heterologous duplexes; ×, percent counts per minute eluted at each temperature for homologous duplexes; +, sum of percent counts per minute eluted at each temperature for homologous duplexes.

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FIGURE 9

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FIGURE 10

Generalized C 0 t plot. At C 0 t values of less than or equal to a, 1/(1 + C 0 t) values are 0.9 or greater. At C 0 t values equal to or greater than b, 1/(1 + C 0 t) values are less than 0.1.

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FIGURE 10

Generalized C 0 t plot. At C 0 t values of less than or equal to a, 1/(1 + C 0 t) values are 0.9 or greater. At C 0 t values equal to or greater than b, 1/(1 + C 0 t) values are less than 0.1.

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FIGURE 11

Scheme for performing membrane DNA reassociation experiments by using either the direct-binding or competition procedure.

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FIGURE 11

Scheme for performing membrane DNA reassociation experiments by using either the direct-binding or competition procedure.

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FIGURE 12

Apparatus for counting radioactivity on membrane filters. A, scintillation vial; B, insect pin; C, nonaqueous- based cocktail; D, duplicate filters impaled on pin.

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FIGURE 12

Apparatus for counting radioactivity on membrane filters. A, scintillation vial; B, insect pin; C, nonaqueous- based cocktail; D, duplicate filters impaled on pin.

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FIGURE 13

Comparison of S1 and HA reassociation methods at different temperatures. Symbols: ▄, S1 method, 75°C; *, HA method, 75°C; +, S1 method, 60°C; □, HA method, 60°C.

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FIGURE 13

Comparison of S1 and HA reassociation methods at different temperatures. Symbols: ▄, S1 method, 75°C; *, HA method, 75°C; +, S1 method, 60°C; □, HA method, 60°C.

References

/content/book/10.1128/9781555817497.chap26

1. Hills, D. M.,, and C. Moritz (ed.). 1990. Molecular Systematics. Sinauer Associates, Inc., Sunderland, MA. Although this useful book emphasizes the systematics of eucaryotic organisms, many of the techniques are directly applicable to bacteria..

2. Johnson, J. L., 1985. Determination of DNA base composition, p. 1– 31. In G. Gottschalk (ed.), Methods in Microbiology, vol. 18. Academic Press, Ltd., London, United Kingdom. Review of the determination of moles percent G+C of DNA preparations.

3. Johnson, J. L., 1989. Nucleic acid hybridization: principles and techniques, p. 3– 31. In B. Swaminathan, and G. Prakash (ed.), Nucleic Acids and Monoclonal Antibody Probes. Marcel Dekker, Inc., New York, NY. Reviews reassociation and hybridization kinetics, effects of experimental variables, duplex and hybrid specificities, and techniques.

4. Sambrook, J.,, E. F. Fritsch,, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. This large manual (it is published as three sequential books) includes protocols for nearly all molecular biology techniques.

5. Stackbrandt, E.,, and M. Goodfellow (ed.). 1991. Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons Ltd., Chichester, England. Provides an extensive range of molecular methods for studying bacterial classification by the techniques of molecular biology.

6. Wetmur, J. G. 1976. Hybridization and renaturation kinetics of nucleic acids. Annu. Rev. Biophys. Bioeng. 5: 337– 361. This review deals primarily with free-solution reassociation kinetics.

7. Alwine, J. C.,, D. J. Kemp,, and G. R. Stark. 1977. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc. Natl. Acad. Sci. USA 74: 5350– 5354.

8. Bacon, M. F. 1965. Analysis of DNA preparations by a variation of the cysteine-sulfuric acid test. Anal. Biochem. 13: 223– 228.

9. Beji, A.,, D. Izard,, F. Gavini,, H. Leclere,, M. Leseine- Delstanche,, and J. Krembel. 1987. A rapid chemical procedure for isolation and purification of chromosomal DNA from Gram-negative bacilli. Anal. Biochem. 162: 18– 23.

10. Bouvet, P. J. M.,, and P. A. D. Grimont. 1986. Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffi. Int. J. Syst. Bacteriol. 36: 228– 240.

11. Brenner, D. J.,, G. R. Fanning,, A. V. Rake,, and K. E. Johnson. 1969. Batch procedure for thermal elution of DNA from hydroxyapatite. Anal. Biochem. 28: 447– 459.

12. Bresser, J.,, J. Doering,, and D. Gillespie. 1983. Quickblot: selective mRNA or DNA immobilization from whole cells. DNA 2: 243– 253.

13. Britten, R. J.,, D. E. Graham,, and B. R. Neufeld. 1974. Analysis of repeated DNA sequences by reassociation. Methods Enzymol. 24E: 363– 406.

14. Britten, R. J.,, and D. E. Kohne. 1968. Repeated sequences in DNA. Science 161: 529– 540.

15. Britten, R. J.,, M. Pavich,, and J. Smith. 1969. A new method for DNA purification. Carnegie Inst. Wash. Year Book 68: 400– 402.

16. Burton, K. 1968. Determination of DNA concentration with diphenylamine. Methods Enzymol. 12B: 163– 166.

17. 17 Byvoet, P. 1966. Determination of nucleic acids with concentrated H2SO4. II. Simultaneous determination of riboand deoxyribonucleic acid. Anal. Biochem. 15: 31– 39.

18. Caccone, A.,, R. DeSalle,, and J. R. Powell. 1988. Calibration of the change in thermal stability of DNA duplexes and degree of base pair mismatch. J. Mol. Evol. 27: 212– 216.

19. Cannon, G.,, S. Heinhorst,, and A. Weissbach. 1985. Quantitative molecular hybridization on nylon membranes. Anal. Biochem. 149: 229– 237.

20. Cesarone, C. F.,, C. Bolognesi,, and L. Santi. 1979. Improved microfluorometric DNA determination in biological material using 33258 Hoechst. Anal. Biochem. 100: 188– 197.

21. Chan, H. C.,, W. T. Ruyechan,, and J. G. Wetmur. 1976. In vitro iodination of low complexity nucleic acids without chain scission. Biochemistry 15: 5487– 5490.

22. Chassy, B. M.,, and A. Giuffrida. 1980. A method for improved lysis of some gram-positive asporogenous bacteria with lysozyme. Appl. Environ. Microbiol. 39: 153– 158.

23. Colwell, R. R.,, R. Johnson,, L. Wan,, T. E. Lovelace,, and D. J. Brenner. 1974. Numerical taxonomy and deoxyribonucleic acid reassociation in the taxonomy of some gram-negative fermentative bacteria. Int. J. Syst. Bacteriol. 24: 422– 433.

24. Commerford, S. L. 1971. Iodination of nucleic acids in vitro. Biochemistry 10: 1993– 1999.

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

26. Cummins, C. S.,, and J. L. Johnson. 1971. Taxonomy of the clostridia: wall composition and DNA homologies in Clostridium butyricum and other butyric acid-producing clostridia. J. Gen. Microbiol. 67: 33– 46.

27. DeLey, J.,, H. Cattoir,, and A. Reynaerts. 1970. The quantitative measurement of DNA hybridization from renaturation rates. Eur. J. Biochem. 12: 133– 142.

28. Denhardt, D. T. 1966. A membrane-filter technique for the detection of complementary DNA. Biochem. Biophys. Res. Commun. 23: 641– 646.

29. Downs, T. R.,, and W. W. Wilfinger. 1983. Fluorometric quantification of DNA in cells and tissue. Anal. Biochem. 131: 538– 547.

30. Ezaki, T.,, Y. Hashimoto,, N. Takeuchi,, H. Yamamoto,, S. Liu,, H. Miura,, K. Matsui,, and E. Yabuuchi. 1988. Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells . J. Clin. Microbiol. 26: 1708– 1713.

31. Ezaki, T.,, N. Takeuchi,, S. Liu,, A. Kai,, H. Yamamoto,, and E. Yabuuchi. 1988. Small-scale DNA preparation for rapid genetic identification of Campylobacter species with radioisotope. Microbiol. Immunol. 32: 141– 150.

32. Ezaki, T.,, Y. Hashimoto,, and E. Yabuuchi. 1989. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybrization in microdilution wells as an alternative to membrane filter hybrization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int. J. Syst. Bacteriol. 39: 224– 229.

33. Feinberg, A. P.,, and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132: 6– 13.

34. Feinberg, A. P.,, and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 137: 266– 267. (Addendum.)

35. Ferragut, C.,, and H. Leclerc. 1976. Etude comparative des methodes de détermination du Tm de L’ADN bactérien. Ann. Microbiol. (Inst. Pasteur) 127A: 223– 235.

36. Forster, A. C.,, J. L. McInnes,, D. C. Skingle,, and R. H. Symons. 1985. Non-radioactive hybridization probes prepared by the chemical labeling of DNA and RNA with a novel reagent, photobiotin. Nucleic Acids Res. 13: 745– 762.

37. Giles, K. W.,, and A. Meyers. 1965. An improved diphenylamine method for estimation of deoxyribonucleic acid. Nature ( London) 206: 93.

38. Gillespie, D.,, and S. Spiegelman. 1966. A quantitative assay for DNA hybrids with DNA immobilized on a membrane. J. Mol. Biol. 12: 829– 842.

39. Gold, D. V.,, and D. Shochat. 1980. A rapid colorimetric assay for the estimation of microgram quantities of DNA. Anal. Biochem. 105: 121– 125.

40. Grimont, P. A. D.,, M. Y. Popoff,, F. Grimont,, C. Coyault,, and M. Lemelin. 1980. Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr. Microbiol. 4: 325– 330.

41. Hartford, T.,, and P. H. A. Sneath. 1988. Distortion of taxonomic structure from DNA relationships due to different choice of reference strains. Syst. Appl. Microbiol. 10: 241– 250.

42. Hill, B. T.,, and S. Whatley. 1975. A simple, rapid microassay for DNA. FEBS Lett. 56: 20– 23.

43. Holdeman, L. V.,, E. P. Cato,, and W. E. C. Moore. 1977. Anaerobe Laboratory Manual, 4th ed. Virginia Polytechnic Institute and State University, Blacksburg.

44. Horinouchi, S.,, T. Uozumi,, T. Beppu,, and K. Arima. 1977. A new isolation method of plasmid deoxyribonucleic acid from Staphylococcus aureus using a lytic enzyme of Achromobacter lyticus. Agric. Biol. Chem. 41: 2487– 2489.

45. Hoyer, B. H.,, B. J. McCarthy,, and E. T. Bolton. 1964. A molecular approach in the systematics of higher organisms. Science 144: 959– 967.

46. Huss, V. A. R.,, H. Festl,, and K. H. Schleifer. 1983. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst. Appl. Microbiol. 4: 184– 192.

47. Johnson, D. A.,, J. W. Gautsch,, J. R. Sportsman,, and J. H. Elder. 1984. Improved technique utilizing nonfat dry milk for analysis of proteins and nucleic acids transferred to nitrocellulose. Gene Anal. Tech. 1: 3– 8.

48. Johnson, J. L. 1973. Use of nucleic acid homologies in the taxonomy of anaerobic bacteria. Int. J. Syst. Bacteriol. 23: 308– 315.

49. Johnson, J. L. 1978. Taxonomy of the bacteroides. I. Deoxyribonucleic acid homologies among Bacteroides fragilis and other saccharolytic Bacteroides species. Int. J. Syst. Bacteriol. 28: 245– 256.

50. Johnson, J. L., 1981. Genetic characterization, p. 450– 472. In P. Gerhardt,, R. G. E. Murray,, R. N. Costilow,, E. W. Nester,, W. A. Wood,, N. R. Krieg,, and G. B. Phillips (ed.), Manual of Methods for General Bacteriology. American Society for Microbiology, Washington, DC..

51. Johnson, J. L., 1985. DNA reassociation and RNA hybridization of bacterial nucleic acids, p. 33– 74. In G. Gottschalk (ed.), Methods in Microbiology, vol. 18. Academic Press, Ltd., London, United Kingdom.

52. Johnson, J. L.,, L. V. H. Moore,, B. Kaneko,, and W. E. C. Moore. 1990. Actinomyces georgiae sp. nov., Actinomyces gerencseriae sp. nov., designation of two genospecies of Actinomyces naeslundii, and inclusion of A. naeslundii serotypes II and III and Actinomyces viscosus serotype II in A. naeslundii genospecies 2. Int. J. Syst. Bacteriol. 40: 273– 286.

53. Jones, A. S. 1953. The isolation of bacterial nucleic acids using cetyltrimethylammonium bromide (CETAVLON). Biochim. Biophys. Acta 10: 607– 612.

54. Jones, D.,, and P. H. A. Sneath. 1970. Genetic transfer and bacterial taxonomy. Bacteriol. Rev. 34: 40– 81.

55. Kane, M. D.,, A. Brauman,, and J. A. Breznak. 1991. Clostridium mayombei sp. nov., an H2/CO2 acetogenic bacterium from the gut of the African soil-feeding termite, Cubitermes speciosus. Arch. Microbiol. 156: 99– 104.

56. Kapuciski, J.,, and B. Skoczylas. 1977. Simple and rapid fluorometric method for DNA microassay. Anal. Biochem. 83: 252– 257.

57. Karsten, U.,, and A. Wollenberger. 1977. Improvements in the ethidium bromide method for direct fluorometric estimation of DNA and RNA in cell and tissue homogenates. Anal. Biochem. 77: 464– 470.

58. Keswani, J.,, and W. B. Whitman. 2001. Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int. J. Syst. Evol. Microbiol. 51: 667– 678.

59. Kirby, K. S. 1957. A new method for the isolation of deoxyribonucleic acids: evidence on the nature of bonds between deoxyribonucleic acid and protein. Biochem. J. 66: 495– 504.

60. Kirby, K. S.,, E. Fox-Carter,, and M. Guest. 1967. Isolation of deoxyribonucleic acid and ribosomal ribonucleic acid from bacteria. Biochem. J. 104: 258– 262.

61. Ko, C. Y.,, J. L. Johnson,, L. B. Barnett,, H. M. McNair,, and J. R. Vercellotti. 1977. A sensitive estimation of the percentage of guanine plus cytosine in deoxyribonucleic acid by high performance liquid chromatography. Anal. Biochem. 80: 183– 192.

62. Labarca, C.,, and K. Paigen. 1980. A simple, rapid, and sensitive DNA assay procedure. Anal. Biochem. 102: 344– 352.

63. Lachance, M. A. 1980. A simple method for determination of deoxyribonucleic acid relatedness by thermal elution in hydroxyapatite microcolumns. Int. J. Syst. Bacteriol. 30: 433– 436.

64. Langer, P. R.,, A. A. Waldrop,, and D. C. Ward. 1981. Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA 78: 6633– 6637.

65. Leary, J. J.,, D. J. Brigati,, and D. C. Ward. 1983. Rapid and sensitive colorimetric method for visualizing biotinlabeled DNA probes hybridized to DNA or RNA immobilized on nitrocellulose: bio-blots. Proc. Natl. Acad. Sci. USA 80: 4045– 4049.

66. Leary, J. J.,, and J. L. Ruth,. 1989. Nonradioactive labeling of nucleic acid probes, p. 33– 57. In B. Swaminathan, and G. Prakash (ed.), Nucleic Acids and Monoclonal Antibody Probes. Marcel Dekker, Inc., New York, NY.

67. Legros, M.,, and A. Kepes. 1985. One-step fluorometric microassay of DNA in procaryotes. Anal. Biochem. 147: 497– 502.

68. Le Pecq, J.-B.,, and C. Paoletti. 1966. A new fluorometric method for RNA and DNA determination. Anal. Biochem. 17: 100– 107.

69. Lutz, L. H.,, and A. A. Yayanos. 1985. Spectrofluorometric determination of bacterial DNA base composition. Anal. Biochem. 144: 1– 5.

70. Mackey, B. M.,, C. A. Miles,, S. E. Parsons,, and D. A. Seymour. 1991. Thermal denaturation of whole cells and cell components of Escherichia coli examined by differential scanning calorimetry. J. Gen. Microbiol. 137: 2361– 2374.

71. Mackey, B. M.,, S. E. Parsons,, C. A. Miles,, and R. J. Owen. 1988. The relationship between the base composition of bacterial DNA and its intracellular melting temperature as determined by differential scanning calorimetry. J. Gen. Microbiol. 134: 1185– 1195.

72. Mandel, M.,, L. Igambi,, J. Bergendahl,, M. L. Dodson, Jr.,, and E. Schelgen. 1970. Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J. Bacteriol. 101: 333– 338.

73. Markov, G. G.,, and I. G. Ivanov. 1974. Hydroxyapatite column chromatography in procedures for isolation of purified DNA. Anal. Biochem. 59: 555– 563.

74. Marmur, J. 1961. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J. Mol. Biol. 3: 208– 218.

75. Marmur, J.,, and P. Doty. 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109– 118.

76. McConaughy, B. L.,, C. D. Laird,, and B. J. McCarthy. 1969. Nucleic acid reassociation in formamide. Biochemistry 8: 3289– 3294.

77. McIntyre, P.,, and G. R. Stark. 1988. A quantitative method for analyzing specific DNA sequences directly from whole cells. Anal. Biochem. 174: 209– 214.

78. Mesbah, M.,, U. Premachandran,, and W. B. Whitman. 1989. Precise measurement of G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39: 159– 167.

79. Mesbah, M.,, and W. B. Whitman. 1989. Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J. Chromatogr. 479: 297– 306.

80. Murray, M. G.,, and W. F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321– 4325.

81. Orosz, J. M.,, and J. G. Wetmur. 1974. In vitro iodination of DNA. Maximizing iodination while minimizing degradation; use of buoyant density shifts for DNA-DNA hybrid isolation. Biochemistry 13: 5467– 5473.

82. Paul, J. H.,, and B. Myers. 1982. Fluorometric determination of DNA in aquatic microorganisms by use of Hoechst 33258. Appl. Environ. Microbiol. 43: 1393– 1399.

83.Perkin-Elmer Corporation. 1986. Fluorometric Determination of DNA Concentration Biotechnology, Technical Report 1-913A (September). Perkin-Elmer Corp., Norwalk, CT.

84. Pollard-Knight, D.,, C. A. Read,, M. J. Downs,, L. A. Howard,, M. R. Leadbetter,, S. A. Pheby,, E. McNaughton,, A. Syms,, and M. A. W. Brady. 1990. Nonradioactive nucleic acid detection by enhanced chemiluminescence using probes directly labeled with horseradish peroxidase. Anal. Biochem. 185: 84– 89.

85. Renz, M.,, and C. Kurz. 1984. A colorimetric method for DNA hybridization. Nucleic Acids Res. 12: 3435– 3444.

86. Rigby, P. W.,, J. M. Dieckmann,, C. Rhodes,, and P. Berg. 1977. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J. Mol. Biol. 113: 237– 251.

87. Sanders, C. A.,, D. M. Yajko,, W. Hyun,, R. G. Langlois,, P. S. Nassos,, M. J. Fulwyler,, and W. K. Hadley. 1990. Determination of guanine-plus-cytosine content of bacterial DNA by dual-laser flow cytometry. J. Gen. Microbiol. 136: 359– 365.

88. Schindler, C. A.,, and V. T. Schuhardt. 1964. Lysostaphin: a new bacteriolytic agent for the Staphylococcus. Proc. Natl. Acad. Sci. USA 51: 414– 421.

89. Schwinghammer, E. A. 1980. A method for improved lysis of some Gram-negative bacteria. FEMS Microbiol. Lett. 7: 157– 162.

90. Seed, B. 1982. Attachment of nucleic acids to nitrocellulose and diazonium-substituted supports. Genet. Eng. 4: 91– 102.

91. Seidler, R. J.,, and M. Mandel. 1971. Quantitative aspects of deoxyribonucleic acid renaturation: base composition, state of chromosome replication, and polynucleotide homologies. J. Bacteriol. 106: 608– 614.

92. Selin, Y. M.,, B. Harich,, and J. L. Johnson. 1983. Preparation of labeled nucleic acids (nick translation and iodination) for DNA homology and rRNA hybridization experiments. Curr. Microbiol. 8: 127– 132.

93. Setaro, F.,, and C. D. G. Morley. 1977. A rapid colorimetric assay for DNA. Anal. Biochem. 81: 467– 471.

94. Sibley, C. G.,, and J. E. Ahlquist,. 1981. The phylogeny and relationships of the ratite birds as indicated by DNADNA hybridization, p. 301– 335. In G. G. E. Scudder, and J. L. Reveal (ed.), Evolution Today. Proceedings of the Second International Congress of Systematic and Evolutionary Biology. Carnegie-Mellon University, Pittsburgh, PA.

95. Smith, M. J.,, R. J. Britten,, and E. H. Davidson. 1975. Studies on nucleic acid reassociation kinetics: reactivity of single-stranded tails in DNA-DNA renaturation. Proc. Natl. Acad. Sci. USA 72: 4805– 4809.

96. Sneath, P. H. A. 1989. Analysis and interpretation of sequence data for bacterial systematics: the view of a numerical taxonomist. Syst. Appl. Microbiol. 12: 15– 31.

97. Stackebrandt, E.,, W. Frederiksen,, G. M. Garrity,, P. A. D. Grimont,, P. Kämpfer,, M. C. J. Maiden,, X. Nesme,, R. Rosselló-Moro,, J. Swings,, H. G. Trüper,, L. Vauterin,, A. C. Ward,, and W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043– 1047.

98. Stackebrandt, E.,, and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846– 849.

99. Steiner, R. F.,, and H. Sternberg. 1979. The interaction of Hoechst 33258 with natural and biosynthetic nucleic acids. Arch. Biochem. Biophys. 197: 580– 588.

100. Sterzel, W.,, P. Bedford,, and G. Eisenbrand. 1985. Automated determination of DNA using the fluorochrome Hoechst 33258. Anal. Biochem. 147: 462– 467.

101. Takahashi, T.,, T. Mitsuda,, and K. Okuda. 1989. An alternative nonradioactive method for labeling DNA using biotin. Anal. Biochem. 179: 77– 85.

102. Tamaoka, J.,, and K. Komagata. 1984. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25: 125– 128.

103. Tereba, A.,, and B. J. McCarthy. 1973. Hybridization of 125I-labeled ribonucleic acid. Biochemistry 12: 4675– 4679.

104. Thompson, L. M., III, R. M. Smibert, J. L. Johnson, and N. R. Krieg. 1988. Phylogenetic study of the genus Campylobacter. Int. J. Syst. Bacteriol. 38: 190– 200.

105. Ullman, J. S.,, and B. J. McCarthy. 1973. Alkali deamination of cytosine residues in DNA Biochim. Biophys. Acta 294: 396– 404.

106. Ullman, J. S.,, and B. J. McCarthy. 1973. The relationship between mismatched base pairs and the thermal stability of DNA duplexes. Biochim. Biophys. Acta 294: 416– 424.

107. Van Dilla, M. A.,, R. G. Langlois,, D. Pinkel,, D. Yajko,, and W. K. Hadley. 1983. Bacterial characterization by flow cytometry. Science 220: 620– 622.

108. Warnaar, S. O.,, and J. A. Cohen. 1966. A quantitative assay for DNA-DNA hybrids using membrane filters. Biochem. Biophys. Res. Commun. 24: 554– 563.

109. Wayne, L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. I. Krichevsky,, L. H. Moore,, W. E. C. Moore,, R. G. E. Murray,, E. Stackebrandt,, M. P. Starr,, and H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463– 464.

110. Werman, S. D.,, M. S. Springer,, and R. J. Britten,. 1990. Nucleic acids I. DNA-DNA hybridization, p. 204– 249. In D. M. Hillis, and C. Moritz (ed.), Molecular Systematics. Sinauer Associates, Inc., Sunderland, MA.

111. Wetmur, J. G.,, and N. Davidson. 1968. Kinetics of renaturation of DNA. J. Mol. Biol. 31: 349– 370.

112. Wiener, S. L.,, M. Urievetzky,, S. Lendval,, S. Shafer,, and E. Meilman. 1976. The indole method for determination of DNA: conditions for maximal sensitivity. Anal. Biochem. 71: 579– 582.

113. Yamada, K.,, and K. Komagata. 1970. Taxonomic studies of coryneform bacteria. III. DNA base composition of coryneform bacteria. J. Gen. Appl. Microbiol. 16: 215– 224.

114. Yokogawa, K.,, S. Kawata,, and Y. Yoshimura. 1972. Bacteriolytic activity of enzymes derived from Streptomyces species. Agric. Biol. Chem. 36: 2055– 2065.

115. Yokogawa, K.,, S. Kawata,, and Y. Yoshimura. 1975. Purification and properties of lytic enzymes from Streptomyces globisporus 1829. Agric. Biol. Chem. 39: 1533– 1543.

116. Zolan, M. E.,, and P. J. Pukkila. 1986. Inheritance of DNA methylation in Coprinus cinereus. Mol. Cell. Biol. 6: 195– 200.

Tables

Similarity Analysis of DNAs

/content/10.1128/9781555817497.chap26.tab26-1

TABLE 1

Hypothetical examples of the calculations of percent similarity values in the free-solution method by the HA and S1 nuclease procedures

10.1128/9781555817497/tab26-1_thmb.gif

10.1128/9781555817497/tab26-1.gif

TABLE 1

Hypothetical examples of the calculations of percent similarity values in the free-solution method by the HA and S1 nuclease procedures

/content/10.1128/9781555817497.chap26.tab26-2

TABLE 2

Calculations for hypothetical data from HA thermal stability profile

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10.1128/9781555817497/tab26-2.gif

TABLE 2

Calculations for hypothetical data from HA thermal stability profile

/content/10.1128/9781555817497.chap26.tab26-3

TABLE 3

C0t values for various DNA concentrations and reassociation times

a Equivalents: 1 μg/110 μl = 9.1 μg/ml or 0.27 × 10−4 mol/liter; 5 μg/110 μl = 45 μg/ml or 1.37 × 10−4 mol/liter; 20 μg/110 μl = 182 μg/ml or 5.49 × 10−4 mol/liter; 30 μg/110 μl = 272 μg/ml or 8.24 x 10−4 mol/liter.

10.1128/9781555817497/tab26-3_thmb.gif

10.1128/9781555817497/tab26-3.gif

TABLE 3

C0t values for various DNA concentrations and reassociation times