916
Views
18
CrossRef citations to date
0
Altmetric
Review Article

DNA methyltransferases: Mechanistic models derived from kinetic analysis

&
Pages 97-193 | Received 27 Jun 2011, Accepted 02 Sep 2011, Published online: 20 Jan 2012

References

  • Abdurashitov MA, Kileva EV, Shinkarenko NM, Shevchenko AV, Dedkov VS, Degtyarev SKh. 1996. BstF5I, an unusual isoschizomer of FokI. Gene 172:49–51.
  • Adams GM, Blumenthal RM. 1997. The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine. Biochemistry 36:8284–8292.
  • Adams RL, Gardiner K, Rinaldi A, Bryans M, McGarvey M, Burdon RH. 1986. Mouse ascites DNA methylase: characterisation of size, proteolytic breakdown and nucleotide recognition. Biochim Biophys Acta 868:9–16.
  • Ahmad I, Rao DN. 1996. Chemistry and biology of DNA methyltransferases. Crit Rev Biochem Mol Biol 31:361–380.
  • Allan BW, Reich NO. 1996. Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35:14757–14762.
  • Allan BW, Beechem JM, Lindstrom WM, Reich NO. 1998. Direct real time observation of base flipping by the EcoRI DNA methyltransferase. J Biol Chem 273:2368–2373.
  • Allan BW, Reich NO, Beechem JM. 1999. Measurement of the absolute temporal coupling between DNA binding and base flipping. Biochemistry 38:5308–5314.
  • Allan BW, Garcia R, Maegley K, Mort J, Wong D, Lindstrom W, Beechem JM, Reich NO. 1999. DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity. J Biol Chem 274:19269–19275.
  • Bacolla A, Pradhan S, Roberts RJ, Wells RD. 1999. Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated dna. J Biol Chem 274:33011–33019.
  • Bacolla A, Pradhan S, Larson JE, Roberts RJ, Wells RD. 2001. Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence. J Biol Chem 276:18605–18613.
  • Bae SH, Cheong HK, Cheong C, Kang S, Hwang DS, Choi BS. 2003. Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition. J Biol Chem 278:45987–45993.
  • Barras F, Marinus MG. 1989. The great GATC: DNA methylation in E. coli. Trends Genet 5:139–143.
  • Berdis AJ, Lee I, Coward JK, Stephens C, Wright R, Shapiro L, Benkovic SJ. 1998. A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA. Proc Natl Acad Sci USA 95:2874–2879.
  • Berg OG, Winter RB, von Hippel PH. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20:6929–6948.
  • Bergerat A, Kriebardis A, Guschlbauer W. 1989. Preferential site-specific hemimethylation of GATC sites in pBR322 DNA by Dam methyltransferase from Escherichia coli. J Biol Chem 264:4064–4070.
  • Bergerat A, Guschlbauer W. 1990. The double role of methyl donor and allosteric effector of S-adenosyl-methionine for Dam methylase of E. coli. Nucleic Acids Res 18:4369–4375.
  • Bergerat A, Guschlbauer W, Fazakerley GV. 1991. Allosteric and catalytic binding of S-adenosylmethionine to Escherichia coli DNA adenine methyltransferase monitored by 3H NMR. Proc Natl Acad Sci USA 88:6394–6397.
  • Bestor TH. 2000. The DNA methyltransferases of mammals. Hum Mol Genet 9:2395–2402.
  • Bhattacharya SK, Dubey AK. 1999. Kinetic mechanism of cytosine DNA methyltransferase MspI. J Biol Chem 274:14743–14749.
  • Bheemanaik S, Chandrashekaran S, Nagaraja V, Rao DN. 2003. Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase. J Biol Chem 278:7863–7874.
  • Bheemanaik S, Reddy YV, Rao DN. 2006. Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J 399:177–190.
  • Bickle TA, Krüger DH. 1993. Biology of DNA restriction. Microbiol Rev 57:434–450.
  • Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453–1462.
  • Brennan CA, Van Cleve MD, Gumport RI. 1986. The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J Biol Chem 261:7279–7286.
  • Brooks JE, Nathan PD, Landry D, Sznyter LA, Waite-Rees P, Ives CL, Moran LS, Slatko BE, Benner JS. 1991. Characterization of the cloned BamHI restriction modification system: its nucleotide sequence, properties of the methylase, and expression in heterologous hosts. Nucleic Acids Res 19:841–850.
  • Bucci C, Lavitola A, Salvatore P, Del Giudice L, Massardo DR, Bruni CB, Alifano P. 1999. Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype. Mol Cell 3:435–445.
  • Buryanov YaI, Zinoviev VV, Vienozhinskis MT, Malygin EG, Nesterenko VF, Popov SG, Gorbunov YuA. 1984. Does the DNA methylase Eco dam pair nucleotide sequences to form site-specific duplexes? FEBS Lett 168:166–168.
  • Buryanov YaI, Zinoviev VV, Gorbunov YuA, Tuzikov FV, Rechkunova NI, Malygin EG, Bayev AA. 1988. Interaction of the EcoDam methyltransferase with synthetic oligodeoxyribo-nucleotides. Gene 74:67–69.
  • Cal S, Connolly BA. 1996. The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC. J Biol Chem 271:1008–1015.
  • Cal S, Connolly BA. 1997. DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides. J Biol Chem 272:490–496.
  • Cheng X, Kumar S, Posfai J, Pflugrath JW, Roberts RJ. 1993. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74:299–307.
  • Cleland WW. 1963. The kinetics of enzyme-catalyzed reactions with two or more substrates or products. III. Prediction of initial velocity and inhibition patterns by inspection. Biochim Biophys Acta 67:188–196.
  • Cleland WW. 1979. Substrate inhibition. Meth Enzymol 63:500–513.
  • Coffin SR, Reich NO. 2009. Escherichia coli DNA adenine methyltransferase: intrasite processivity and substrate-induced dimerization and activation. Biochemistry 48:7399–7410.
  • Coffin SR, Reich NO. 2008. Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences. J Biol Chem 283:20106–20116.
  • Cornish-Bowden A. 1976. Principles of enzyme kinetics. Butterworth. London.
  • Dong A, Zhou L, Zhang X, Stickel S, Roberts RJ, Cheng X. 2004. Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biol Chem 385:373–379.
  • Dryden DTF. 1999. Bacterial DNA Methyltransferases. In: Cheng X, Blumenthal RM (eds). S-Adenosylmethionine-dependent methyltransferases, structures and functions. Singapore: World Scientific Publishing, pp. 283–340.
  • Dugaiczyk A, Hedgpeth J, Boyer HW, Goodman HM. 1974. Physical identity of the SV40 deoxyribonucleic acid sequence recognized by the Eco RI restriction endonuclease and modification methylase. Biochemistry 13:503–512.
  • Ehbrecht HJ, Pingoud A, Urbanke C, Maass G, Gualerzi C. 1985. Linear diffusion of restriction endonucleases on DNA. J Biol Chem 260:6160–6166.
  • Ehrlich M, Wilson GG, Kuo KC, Gehrke CW. 1987. N4-methylcytosine as a minor base in bacterial DNA. J Bacteriol 169:939–943.
  • Engel JD, von Hippel PH. 1974. Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level. Biochemistry 13:4143–4158.
  • Engel JD, von Hippel PH. 1978. Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. J Biol Chem 253:927–934.
  • Evdokimov AA, Zinov’ev VV, Malygin EG. 2000. Effect of S-adenosyl-L-methionine and its analogs on site-specific binding DNA-(adenine-N6)-methyltransferase from T4 phage to the oligonucleotide substrate. Bioorg Khim 26:797–800.
  • Evdokimov AA. 2002. Study of the mechanism of site-specific action of bacteriophage T4 Dam DNA [N6-adenine]-methyltransferase. PhDThesis, State Research Center “Vector”. In Russian.
  • Evdokimov AA, Zinov’ev VV, Malygin EG. 2002. The kinetic mechanism of phage T4 DNA-[N6-adenine]-methyltransferase. Mol Biol (Mosk) 36:849–861.
  • Evdokimov AA, Zinoviev VV, Malygin EG, Schlagman SL, Hattman S. 2002a. Bacteriophage T4 Dam DNA-[N6-adenine]methyltransferase. Kinetic evidence for a catalytically essential conformational change in the ternary complex. J Biol Chem 277:279–286.
  • Evdokimov AA, Sclavi B, Zinoviev VV, Malygin EG, Hattman S, Buckle M. 2007. Study of bacteriophage T4-encoded Dam DNA (adenine-N6)-methyltransferase binding with substrates by rapid laser UV cross-linking. J Biol Chem 282:26067–26076.
  • Fatemi M, Hermann A, Pradhan S, Jeltsch A. 2001. The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. J Mol Biol 309:1189–1199.
  • Flynn J, Glickman JF, Reich NO. 1996. Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences. Biochemistry 35:7308–7315.
  • Flynn J, Reich N. 1998. Murine DNA (cytosine-5-)-methyltransferase: steady-state and substrate trapping analyses of the kinetic mechanism. Biochemistry 37:15162–15169.
  • Freese E. 1959. The specific mutagenic effect of base analogues on phage T4. J Mol Biol 1:87–105.
  • George J, Blakesley RW, Chirikjian JG. 1980. Sequence-specific endonuclease Bam HI. Effect of hydrophobic reagents on sequence recognition and catalysis. J Biol Chem 255:6521–6524.
  • Gong W, O’Gara M, Blumenthal RM, Cheng X. 1997. Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res 25:2702–2715.
  • Greene PH, Poonian MS, Nussbaum AL, Tobias L, Garfin DE, Boyer HW, Goodman HM. 1975. Restriction and modification of a self-complementary octanucleotide containing the EcoRI substrate. J Mol Biol 99:237–261.
  • Gowher H, Jeltsch A. 2000. Molecular enzymology of the EcoRV DNA-(Adenine-N (6))-methyltransferase: kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA. J Mol Biol 303:93–110.
  • Gromova ES, Oretskaya TS, Eritja R, Guschlbauer W. 1994. Kinetic studies of MvaI DNA methyltransferase interaction with modified oligonucleotide duplexes. Biochem Mol Biol Int 36:247–255.
  • Gromova ES, Khoroshaev AV. 2003. Prokaryotic DNA methyltransferases: the structure and the mechanism of interaction with DNA. Mol Biol (Mosk) 37:300–314.
  • Hale WB, van der Woude MW, Braaten BA, Low DA. 1998. Regulation of uropathogenic Escherichia coli adhesin expression by DNA methylation. Mol Genet Metab 65:191–196.
  • Handa V, Jeltsch A. 2005. Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome. J Mol Biol 348:1103–1112.
  • Hattman S. 1970. DNA methylation of T-even bacteriophages and of their nonglucosylated mutants: its role in P1-directed restriction. Virology 42:359–367.
  • Hattman S, Keister T, Gottehrer A. 1978. Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis. J Mol Biol 124:701–711.
  • Hattman S, van Ormondt H, de Waard A. 1978. Sequence specificity of the wild-type dam+) and mutant (damh) forms of bacteriophage T2 DNA adenine methylase. J Mol Biol 119:361–376.
  • Hattman S. 1981. DNA methylation. In: Boyer PD (ed). The Enzymes. New York: Academic Press, pp. 517–548.
  • Hattman S. 1983. DNA modification, methylation. In: Mathews CK, Kutter EM, Mosig G, Berget PB (eds). Bacteriophage T4. Washington: American Society for Microbiology, pp. 152–155.
  • Hattman S, Malygin EG. 2004. Bacteriophage T2Dam and T4Dam DNA-[N6-adenine]-methyltransferases. Prog Nucleic Acid Res Mol Biol 77:67–126.
  • Heithoff DM, Sinsheimer RL, Low DA, Mahan MJ. 1999. An essential role for DNA adenine methylation in bacterial virulence. Science 284:967–970.
  • Heitman J. 1993. On the origins, structures and functions of restriction-modification enzymes. Genet Eng (NY) 15:57–108.
  • Herman GE, Modrich P. 1982. Escherichia coli dam methylase. Physical and catalytic properties of the homogeneous enzyme. J Biol Chem 257:2605–2612.
  • Hermann A, Gowher H, Jeltsch A. 2004. Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61:2571–2587.
  • Holz B, Klimasauskas S, Serva S, Weinhold E. 1998. 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Res 26:1076–1083.
  • Hopkins BB, Reich NO. 2004. Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex. J Biol Chem 279:37049–37060.
  • Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X. 2005. Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell 121:349–361.
  • Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X. 2006. Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. J Mol Biol 358:559–570.
  • Ianulaitis AA, Stakenas PS, Piatrushite MP, Bitinaite IuB, Klimashauskas SI. 1984. Specificity of new restrictases and methylases. Unusual modification of cytosine at position 4. Mol Biol (Mosk) 18:115–129.
  • Javor GT. 1983. Depression of adenosylmethionine content of Escherichia coli by thioglycerol. Antimicrob Agents Chemother 24:860–867.
  • Jeltsch A, Friedrich T, Roth M. 1998. Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase. J Mol Biol 275:747–758.
  • Jeltsch A, Pingoud A. 1998. Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA. Biochemistry 37:2160–2169.
  • Jeltsch A, Christ F, Fatemi M, Roth M. 1999. On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4. J Biol Chem 274:19538–19544.
  • Jeltsch A, Roth M, Friedrich T. 1999. Mutational analysis of target base flipping by the EcoRV adenine-N6 DNA methyltransferase. J Mol Biol 285:1121–1130.
  • Jeltsch A. 2001. The cytosine N4-methyltransferase M.PvuII also modifies adenine residues. Biol Chem 382:707–710.
  • Jeltsch A. 2002. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem 3:274–293.
  • Jeltsch A. 2006. On the enzymatic properties of Dnmt1: specificity, processivity, mechanism of linear diffusion and allosteric regulation of the enzyme. Epigenetics 1:63–66.
  • Jurkowski TP, Anspach N, Kulishova L, Nellen W, Jeltsch A. 2007. The M.EcoRV DNA-(adenine N6)-methyltransferase uses DNA bending for recognition of an expanded EcoDam recognition site. J Biol Chem 282:36942–36952.
  • Kaszubska W, Webb HK, Gumport RI. 1992. Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli. Gene 118:5–11.
  • Klimasauskas S, Kumar S, Roberts RJ, Cheng X. 1994. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76:357–369.
  • Klimasauskas S, Roberts RJ. 1995. M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res 23:1388–1395.
  • Kossykh VG, Schlagman SL, Hattman S. 1993. Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding. Nucleic Acids Res 21:3563–3566.
  • Kossykh VG, Schlagman SL, Hattman S. 1993. Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding. Nucleic Acids Res 21:4659–4662.
  • Kossykh VG, Schlagman SL, Hattman S. 1995. Phage T4 DNA [N6-adenine]methyltransferase. Overexpression, purification, and characterization. J Biol Chem 270:14389–14393.
  • Kossykh VG, Schlagman SL, Hattman S. 1997. Comparative studies of the phage T2 and T4 DNA (N6-adenine)methyltransferases: amino acid changes that affect catalytic activity. J Bacteriol 179:3239–3243.
  • Kurganov BI. 1982. Allosteric enzymes: Kinetic behavior. Chichester: John Wiley & Sons.
  • Lehman IR, Pratt EA. 1960. On the structure of the glucosylated hydroxymethylcytosine nucleotides of coliphages T2, T4, and T6. J Biol Chem 235:3254–3259.
  • Lemon KP, Grossman AD. 1998. Localization of bacterial DNA polymerase: evidence for a factory model of replication. Science 282:1516–1519.
  • Lesser DR, Kurpiewski MR, Jen-Jacobson L. 1990. The energetic basis of specificity in the Eco RI endonuclease–DNA interaction. Science 250:776–786.
  • Lindstrom WM Jr, Flynn J, Reich NO. 2000. Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase. J Biol Chem 275:4912–4919.
  • Lindstrom WM Jr, Malygin EG, Ovechkina LG, Zinoviev VV, Reich NO. 2003. Functional analysis of BamHI DNA cytosine-N4 methyltransferase. J Mol Biol 325:711–720.
  • Malone T, Blumenthal RM, Cheng X. 1995. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253:618–632.
  • Malygin EG. 1977. Derivation of kinetic equations for steady-state enzyme reactions using multi-stage proportionate rates of enzyme form conversion. Biofizika 22:15–20.
  • Malygin EG. 1980. Specificity coefficient of alternative substrates in enzymic reaction. Biophysics, XXV, pp. 185–186. In Russian.
  • Malygin EG, Zinoviev VV. 1989. Studies on the role of symmetry in the specific recognition of natural and synthetic DNA by type II restriction and modification enzymes. Sov Sci Rev D Physiochem Biol 9:87–142.
  • Malygin EG, Petrov NA, Gorbunov YA, Kossykh VG, Hattman S. 1997. Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites. Nucleic Acids Res 25:4393–4399.
  • Malygin EG, Zinoviev VV, Petrov NA, Evdokimov AA, Jen-Jacobson L, Kossykh VG, Hattman S. 1999. Effect of base analog substitutions in the specific GATC site on binding and methylation of oligonucleotide duplexes by the bacteriophage T4 Dam DNA-[N6-adenine] methyltransferase. Nucleic Acids Res 27:1135–1144.
  • Malygin EG, Lindstrom WM Jr, Schlagman SL, Hattman S, Reich NO. 2000. Pre-steady state kinetics of bacteriophage T4 dam DNA-[N(6)-adenine] methyltransferase: interaction with native (GATC) or modified sites. Nucleic Acids Res 28:4207–4211.
  • Malygin EG, Ovechkina LG, Zinov’ev VV, Lindstrem UM, Reich NO. 2001. DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate binding properties. Mol Biol (Mosk) 35:42–51.
  • Malygin EG, Ovechkina LG, Evdokimov AA, Zinov’ev VV. 2001. Single turnover kinetics of phage T4 DNA-(N6-adenine)methyltransferase. Mol Biol (Mosk) 35:65–78.
  • Malygin EG, Lindstrom WM Jr, Zinoviev VV, Evdokimov AA, Schlagman SL, Reich NO, Hattman S. 2003. Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase): evidence for two distinct stages of methylation under single turnover conditions. J Biol Chem 278:41749–41755.
  • Malygin EG, Zinoviev VV, Evdokimov AA, Lindstrom WM Jr, Reich NO, Hattman S. 2003. DNA (cytosine-N4-)- and -(adenine-N6-)-methyltransferases have different kinetic mechanisms but the same reaction route. A comparison of M.BamHI and T4 Dam. J Biol Chem 278:15713–15719.
  • Malygin EG, Sclavi B, Zinoviev VV, Evdokimov AA, Hattman S, Buckle M. 2004. Bacteriophage T4Dam DNA-(adenine-N(6))-methyltransferase. Comparison of pre-steady state and single turnover methylation of 40-mer duplexes containing two (un)modified target sites. J Biol Chem 279:50012–50018.
  • Malygin EG, Hattman S. 2006. A probabilistic approach to compact steady-state kinetic equations for enzymic reactions. J Theor Biol 242:627–633.
  • Malygin EG, Evdokimov AA, Hattman S. 2009. Dimeric/oligomeric DNA methyltransferases: an unfinished story. Biol Chem 390:835–844.
  • Marinus MG. 1987. DNA methylation in Escherichia coli. Annu Rev Genet 21:113–131.
  • Marzabal S, DuBois S, Thielking V, Cano A, Eritja R, Guschlbauer W. 1995. Dam methylase from Escherichia coli: kinetic studies using modified DNA oligomers: hemimethylated substrates. Nucleic Acids Res 23:3648–3655.
  • Mashhoon N, Carroll M, Pruss C, Eberhard J, Ishikawa S, Estabrook RA, Reich N. 2004. Functional characterization of Escherichia coli DNA adenine methyltransferase, a novel target for antibiotics. J Biol Chem 279:52075–52081.
  • Merkiene E, Klimasauskas S. 2005. Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase. Nucleic Acids Res 33:307–315.
  • Nardone G, George J, Chirikjian JG. 1984. Sequence-specific BamHI methylase. Purification and characterization. J Biol Chem 259:10357–10362.
  • Nardone G, George J, Chirikjian JG. 1986. Differences in the kinetic properties of BamHI endonuclease and methylase with linear DNA substrates. J Biol Chem 261:12128–12133.
  • O’Gara M, Klimasauskas S, Roberts RJ, Cheng X. 1996. Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. J Mol Biol 261:634–645.
  • O’Gara M, Zhang X, Roberts RJ, Cheng X. 1999. Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. J Mol Biol 287:201–209.
  • Orsi BA, Tipton KF. 1979. Kinetic analysis of progress curves. Meth Enzymol 63:159–183.
  • Ovechkina LG, Zinov’ev VV, Gorbunov IuA, Malygin EG. 2000. Oligomerization of DNA-(adenine-N6)-methyltransferase from phage T4 and its effect on the catalytic characteristics of the enzyme. Bioorg Khim 26:940–943.
  • Peterson SN, Reich NO. 2006. GATC flanking sequences regulate Dam activity: evidence for how Dam specificity may influence pap expression. J Mol Biol 355:459–472.
  • Petrov NA, Gorbunov IuA, Malygin EG. 1997. Interaction between DNA-[N6-adenine]-methyltransferase from T4 phage and its substrates containing defective binding sites. Mol Biol (Mosk) 31:973–977.
  • Posnick LM, Samson LD. 1999. Influence of S-adenosylmethionine pool size on spontaneous mutation, dam methylation, and cell growth of Escherichia coli. J Bacteriol 181:6756–6762.
  • Powell LM, Connolly BA, Dryden DT. 1998. The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarisation and DNA footprinting. J Mol Biol 283:947–961.
  • Pradhan S, Talbot D, Sha M, Benner J, Hornstra L, Li E, Jaenisch R, Roberts RJ. 1997. Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase. Nucleic Acids Res 25:4666–4673.
  • Pradhan S, Bacolla A, Wells RD, Roberts RJ. 1999. Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation. J Biol Chem 274:33002–33010.
  • Pradhan S, Roberts RJ. 2000. Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain. EMBO J 19:2103–2114.
  • Quignard E, Fazakerley GV, Teoule R, Guy A, Guschlbauer W. 1985. Consequences of methylation on the amino group of adenine. A proton two-dimensional NMR study of d(GGATATCC) and d(GGm6ATATCC). Eur J Biochem 152:99–105.
  • Reich NO, Everett EA. 1990. Identification of peptides involved in S-adenosylmethionine binding in the EcoRI DNA methylase. Photoaffinity laveling with 8-azido-S-adenosylmethionine. J Biol Chem 265:8929–8934.
  • Reich NO, Mashhoon N. 1990. Inhibition of EcoRI DNA methylase with cofactor analogs. J Biol Chem 265:8966–8970.
  • Reich NO, Mashhoon N. 1991. Kinetic mechanism of the EcoRI DNA methyltransferase. Biochemistry 30:2933–2939.
  • Reich NO, Mashhoon N. 1993. Presteady state kinetics of an S-adenosylmethionine-dependent enzyme. Evidence for a unique binding orientation requirement for EcoRI DNA methyltransferase. J Biol Chem 268:9191–9193.
  • Rein T, Kobayashi T, Malott M, Leffak M, DePamphilis ML. 1999. DNA methylation at mammalian replication origins. J Biol Chem 274:25792–25800.
  • Reinisch KM, Chen L, Verdine GL, Lipscomb WN. 1995. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82:143–153.
  • Rose IA. 1980. The isotope trapping method: desorption rates of productive E.S complexes. Meth Enzymol 64:47–59.
  • Rubin RA, Modrich P. 1977. EcoRI methylase. Physical and catalytic properties of the homogeneous enzyme. J Biol Chem 252:7265–7272.
  • Rubin RA, Modrich P. 1978. Substrate dependence of the mechanism of EcoRI endonuclease. Nucleic Acids Res 5:2991–2997.
  • Scavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME. 2000. Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res 28:3950–3961.
  • Schermelleh L, Haemmer A, Spada F, Rösing N, Meilinger D, Rothbauer U, Cardoso MC, Leonhardt H. 2007. Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation. Nucleic Acids Res 35:4301–4312.
  • Schermelleh L, Spada F, Leonhardt H. 2008. Visualization and measurement of DNA methyltransferase activity in living cells. Curr Protoc Cell Biol Chapter 22:Unit 22.12.
  • Schlagman SL, Miner Z, Fehér Z, Hattman S. 1988. The DNA [adenine-N6]methyltransferase (Dam) of bacteriophage T4. Gene 73:517–530.
  • Seeman NC, Rosenberg JM, Rich A. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci USA 73:804–808.
  • Shier VK, Hancey CJ, Benkovic SJ. 2001. Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus. J Biol Chem 276:14744–14751.
  • Sternglanz H, Bugg CE. 1973. Conformations of N6-monosubstituted adenine derivatives. Crystal structure of N6-methyladenine. Biochim Biophys Acta 308:1–8.
  • Sternglanz H, Bugg CE. 1973. Conformation of N6-methyladenine, a base involved in DNA modification: restriction processes. Science 182:833–834.
  • Surby MA, Reich NO. 1996. Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: implications for the EcoRI restriction-modification system. Biochemistry 35:2201–2208.
  • Swaminathan CP, Sankpal UT, Rao DN, Surolia A. 2002. Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase. J Biol Chem 277:4042–4049.
  • Szczelkun MD, Connolly BA. 1995. Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acid and cofactor analogues. Biochemistry 34:10724–10733.
  • Szczelkun MD, Jones H, Connolly BA. 1995. Probing the protein-DNA interface of the EcoRV modification methyltransferase bound to its recognition sequence, GATATC. Biochemistry 34:10734–10743.
  • Szegedi SS, Reich NO, Gumport RI. 2000. Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase. Nucleic Acids Res 28:3962–3971.
  • Szilák L, Venetianer P, Kiss A. 1992. Purification and biochemical characterization of the EcaI DNA methyltransferase. Eur J Biochem 209:391–397.
  • Szilák L, Dér A, Deák F, Venetianer P. 1993. Kinetic characterization of the EcaI methyltransferase. Eur J Biochem 218:727–733.
  • Szybalski W, Kim SC, Hasan N, Podhajska AJ. 1991. Class-IIS restriction enzymes–a review. Gene 100:13–26.
  • Tao T, Walter J, Brennan KJ, Cotterman MM, Blumenthal RM. 1989. Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. Nucleic Acids Res 17:4161–4175.
  • Thielking V, Dubois S, Eritja R, Guschlbauer W. 1997. Dam methyltransferase from Escherichia coli: kinetic studies using modified DNA oligomers: nonmethylated substrates. Biol Chem 378:407–415.
  • Thomas CB, Gumport RI. 2006. Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase. Nucleic Acids Res 34:806–815.
  • Tuzikov FV, Tuzikova NA, Naumochkin AN, Zinov’ev VV, Malygin EG. 1997. Study of the equilibrium interaction of DAM-DNA-(N-adenine)-methyltransferase from phage T4 with substrates and ligands by fluorescence quenching. Mol Biol (Mosk) 31:86–90.
  • Urig S, Gowher H, Hermann A, Beck C, Fatemi M, Humeny A, Jeltsch A. 2002. The Escherichia coli dam DNA methyltransferase modifies DNA in a highly processive reaction. J Mol Biol 319:1085–1096.
  • Vanyushin BF. 2006. DNA methylation in plants. Curr Top Microbiol Immunol 301:67–122.
  • Varpholomeev SD, Gourevich KG. 1999. Biokinetika Prakticheski kours, Moscow: Fair-Press. In Russian.
  • Vertino PM. 1999. Eukaryotic DNA methyltransferases. In: Cheng X, Blumenthal RM (eds). Eukaryotic DNA methyltransferases. S-adenosylmethionine-dependent methyltransferases, structures and functions. Singapore: World Scientific Publishing, pp. 341–372.
  • Vertino PM, Sekowski JA, Coll JM, Applegren N, Han S, Hickey RJ, Malkas LH. 2002. DNMT1 is a component of a multiprotein DNA replication complex. Cell Cycle 1:416–423.
  • Vilkaitis G, Dong A, Weinhold E, Cheng X, Klimasauskas S. 2000. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J Biol Chem 275:38722–38730.
  • Vilkaitis G, Merkiene E, Serva S, Weinhold E, Klimasauskas S. 2001. The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of Hhai methyltransferase. J Biol Chem 276:20924–20934.
  • Wang MX, Church GM. 1992. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature 360:606–610.
  • Westley J. 1969. Enzymic catalysis. New York: Harper & Row.
  • Wilson GA, Young FE. 1975. Isolation of a sequence-specific endonuclease (BamI) from Bacillus amyloliquefaciens H. J Mol Biol 97:123–125.
  • Winter RB, Berg OG, von Hippel PH. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor–operator interaction: kinetic measurements and conclusions. Biochemistry 20:6961–6977.
  • Wright R, Stephens C, Shapiro L. 1997. The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus. J Bacteriol 179:5869–5877.
  • Wu JC, Santi DV. 1987. Kinetic and catalytic mechanism of HhaI methyltransferase. J Biol Chem 262:4778–4786.
  • Youngblood B, Reich NO. 2006. Conformational transitions as determinants of specificity for the DNA methyltransferase EcoRI. J Biol Chem 281:26821–26831.
  • Yang AS, Shen JC, Zingg JM, Mi S, Jones PA. 1995. HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. Nucleic Acids Res 23:1380–1387.
  • Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X. 2003. Structure of the bacteriophage T4 DNA adenine methyltransferase. Nat Struct Biol 10:849–855.
  • Zinoviev VV, Gorbunov JA, Baclanov MM, Popov SG, Malygin EG. 1983. Structure subtraction as an approach to investigation of the mechanism of restriction enzyme action. FEBS Lett 154:282–284.
  • Zinov’ev VV, Ovechkina LG, Malygin EG. 1996. Stoichiometry of phage T4 Dam-DNA-[N6-adenine]-methyltransferase binding with oligonucleotide substrates. Mol Biol (Mosk) 30:1203–1208.
  • Zinoviev VV, Evdokimov AA, Gorbunov YA, Malygin EG, Kossykh VG, Hattman S. 1998. Phage T4 DNA [N6-adenine] methyltransferase: kinetic studies using oligonucleotides containing native or modified recognition sites. Biol Chem 379:481–488.
  • Zinoviev VV, Evdokimov AA, Malygin EG, Schlagman SL, Hattman S. 2003. Bacteriophage T4 Dam DNA-(N6-adenine)-methyltransferase. Processivity and orientation to the methylation target. J Biol Chem 278:7829–7833.
  • Zinoviev VV, Yakishchik SI, Evdokimov AA, Malygin EG, Hattman S. 2004. Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases. Nucleic Acids Res 32:3930–3934.
  • Zinov’ev VV, Evdokimov AA, Hattman S, Malygin EG. 2004. Molecular enzymology of phage T4 Dam DNA-methyltransferase. Mol Biol (Mosk) 38:869–885.
  • Zinoviev VV, Evdokimov AA, Malygin EG, Sclavi B, Buckle M, Hattman S. 2007. Differential methylation kinetics of individual target site strands by T4Dam DNA methyltransferase. Biol Chem 388:1199–1207.
  • Zyskind JW, Smith DW. 1986. The bacterial origin of replication, oriC. Cell 46:489–490.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.