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Chapter 26 : Similarity Analysis of DNAs

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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 -acetylmuramidase, which is isolated from and also cleaves the muramic acid backbone; lysostaphin, an endopeptidase that is isolated from 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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Image of FIGURE 1
FIGURE 1

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

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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Image of FIGURE 2
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 ( ).

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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Image of FIGURE 3
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 C reverse-phase column. The nucleosides were obtained from enzymatic degradation of 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 .

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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Image of FIGURE 4
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.

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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Image of FIGURE 5
FIGURE 5

Plexiglas filtration devices for immobilizing DNA on membranes.

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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Image of FIGURE 6
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.

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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Image of FIGURE 8
FIGURE 8

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

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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Image of FIGURE 7
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.

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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Image of FIGURE 9
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.

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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Image of FIGURE 10
FIGURE 10

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

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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Image of FIGURE 11
FIGURE 11

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

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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Image of FIGURE 12
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.

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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Image of FIGURE 13
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.

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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References

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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

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TABLE 1

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

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
Generic image for table
TABLE 2

Calculations for hypothetical data from HA thermal stability profile

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
Generic image for table
TABLE 3

0 values for various DNA concentrations and reassociation times

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

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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