메뉴 건너뛰기




Volumn 270, Issue 21, 2003, Pages 4315-4325

Kinetics and thermodynamics of nick sealing by T4 DNA ligase

Author keywords

DNA ligase; End joining; Kinetics; Mechanism of action; Mismatching nick

Indexed keywords

ADENOSINE PHOSPHATE; MAGNESIUM ION; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

EID: 0242299593     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2003.03824.x     Document Type: Article
Times cited : (52)

References (40)
  • 1
    • 0016273515 scopus 로고
    • DNA ligase: Structure, mechanism, function
    • Lehman, I.R. (1974) DNA ligase: structure, mechanism, function. Science 186, 790-797.
    • (1974) Science , vol.186 , pp. 790-797
    • Lehman, I.R.1
  • 2
    • 0018266028 scopus 로고
    • T4 polynucleotide ligase catalyzed joining on triple-stranded nucleic acids
    • Raae, A.J. & Kleppe, K. (1978) T4 polynucleotide ligase catalyzed joining on triple-stranded nucleic acids. Biochemistry 17, 2939-2942.
    • (1978) Biochemistry , vol.17 , pp. 2939-2942
    • Raae, A.J.1    Kleppe, K.2
  • 3
    • 0020480166 scopus 로고
    • Sealing of gaps in duplex DNA by T4 DNA ligase
    • Nilsson, S.V. & Magnusson, G. (1982) Sealing of gaps in duplex DNA by T4 DNA ligase. Nucleic Acids Res. 10, 1425-1437.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 1425-1437
    • Nilsson, S.V.1    Magnusson, G.2
  • 4
    • 0032478802 scopus 로고    scopus 로고
    • The action of DNA ligase at abasic sites in DNA
    • Bogenhagen, D.F. & Pinz, K.G. (1998) The action of DNA ligase at abasic sites in DNA. J. Biol. Chem. 273, 7888-7893.
    • (1998) J. Biol. Chem. , vol.273 , pp. 7888-7893
    • Bogenhagen, D.F.1    Pinz, K.G.2
  • 5
    • 0030873236 scopus 로고    scopus 로고
    • Functional characterization of the T4 DNA ligase: A new insight into the mechanism of action
    • Rossi, R., Montecucco, A., Ciarrocchi, G. & Biamonti, G. (1997) Functional characterization of the T4 DNA ligase: a new insight into the mechanism of action. Nucleic Acids Res. 25, 2106-2113.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2106-2113
    • Rossi, R.1    Montecucco, A.2    Ciarrocchi, G.3    Biamonti, G.4
  • 6
    • 0014409781 scopus 로고
    • Enzymatic breakage and joining of deoxyribonucleic acid. VI. Further purification and properties of polynucleotide ligase from Escherichia coli infected with bacteriophage T4
    • Weiss, B., Jacquemin-Sablon, A., Live, T.R., Fareed, G.C. & Richardson, C.C. (1968) Enzymatic breakage and joining of deoxyribonucleic acid. VI. Further purification and properties of polynucleotide ligase from Escherichia coli infected with bacteriophage T4. J. Biol. Chem. 243, 4543-4555.
    • (1968) J. Biol. Chem. , vol.243 , pp. 4543-4555
    • Weiss, B.1    Jacquemin-Sablon, A.2    Live, T.R.3    Fareed, G.C.4    Richardson, C.C.5
  • 7
    • 0014409837 scopus 로고
    • Ezymatic breakage and joining of deoxyribonucleic acid. VII. Properties of the enzyme-adenylate intermediate in the polynucleotide ligase reaction
    • Weiss, B., Thompson, A. & Richardson, C.C. (1968) Ezymatic breakage and joining of deoxyribonucleic acid. VII. Properties of the enzyme-adenylate intermediate in the polynucleotide ligase reaction. J. Biol. Chem. 243, 4556-4563.
    • (1968) J. Biol. Chem. , vol.243 , pp. 4556-4563
    • Weiss, B.1    Thompson, A.2    Richardson, C.C.3
  • 8
    • 0015134265 scopus 로고
    • Structure of the DNA ligase-adenylate intermediate: Lysine (ε-amino)-linked adenosine monophosphoramidate
    • Gumport R.I. & Lehman, I.R. (1971) Structure of the DNA ligase-adenylate intermediate: lysine (ε-amino)-linked adenosine monophosphoramidate. Proc. Natl Acad. Sci. USA 68, 2559-2563.
    • (1971) Proc. Natl Acad. Sci. USA , vol.68 , pp. 2559-2563
    • Gumport, R.I.1    Lehman, I.R.2
  • 9
    • 0015239823 scopus 로고
    • Enzymatic breakage and joining of deoxyribonucleic acid. IX. Synthesis and properties of the deoxyribonucleic acid adenylate in the phage T4 ligase reaction
    • Harvey, C.L., Gabriel, T.F., Wilt, E.M. & Richardson, C.C. (1971) Enzymatic breakage and joining of deoxyribonucleic acid. IX. Synthesis and properties of the deoxyribonucleic acid adenylate in the phage T4 ligase reaction. J. Biol. Chem. 246, 4523-4530.
    • (1971) J. Biol. Chem. , vol.246 , pp. 4523-4530
    • Harvey, C.L.1    Gabriel, T.F.2    Wilt, E.M.3    Richardson, C.C.4
  • 10
    • 0016766914 scopus 로고
    • Kinetics and effect of salts and polyamines on T4 polynucleotide ligase
    • Raae, A.J., Kleppe, R.K. & Kleppe, K. (1975) Kinetics and effect of salts and polyamines on T4 polynucleotide ligase. Eur J. Biochem. 60, 437-443.
    • (1975) Eur. J. Biochem. , vol.60 , pp. 437-443
    • Raae, A.J.1    Kleppe, R.K.2    Kleppe, K.3
  • 11
    • 0027318626 scopus 로고
    • Unexpected substrate specificity of T4 DNA ligase revealed by in vitro selection
    • Harada, K. & Orgel, L.E. (1993) Unexpected substrate specificity of T4 DNA ligase revealed by in vitro selection. Nucleic Acids Res. 21, 2287-2291.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2287-2291
    • Harada, K.1    Orgel, L.E.2
  • 12
    • 0024559478 scopus 로고
    • Specificity of the nick-closing activity of bacteriophage T4 DNA ligase
    • Wu, D.Y. & Wallace, R.B. (1989) Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene 76, 245-254.
    • (1989) Gene , vol.76 , pp. 245-254
    • Wu, D.Y.1    Wallace, R.B.2
  • 13
    • 0030738913 scopus 로고    scopus 로고
    • Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases
    • Pritchard, C.E. & Southern, E.M. (1997) Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases. Nucleic Acids Res. 25, 3403-3407.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3403-3407
    • Pritchard, C.E.1    Southern, E.M.2
  • 14
    • 0035125009 scopus 로고    scopus 로고
    • Joining of short DNA oligonucleotides with base pair mismatches by T4 DNA Ligase
    • Cherepanov, A., Yildirim, E. & de Vries, S. (2001) Joining of short DNA oligonucleotides with base pair mismatches by T4 DNA Ligase. J. Biochem. (Tokyo). 129, 61-68.
    • (2001) J. Biochem. (Tokyo) , vol.129 , pp. 61-68
    • Cherepanov, A.1    Yildirim, E.2    De Vries, S.3
  • 15
    • 0037563785 scopus 로고    scopus 로고
    • Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions
    • Alexander, R.C., Johnson, A.K., Thorpe, J.A., Gevedon, T. & Testa, S.M. (2003) Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions. Nucleic Acids Res. 31, 3208-3216.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3208-3216
    • Alexander, R.C.1    Johnson, A.K.2    Thorpe, J.A.3    Gevedon, T.4    Testa, S.M.5
  • 16
    • 85044703958 scopus 로고    scopus 로고
    • Interaction of short oligonucleotide derivatives with nucleic acids. VI. Discrimination of mismatch-containing complexes upon ligation of a short oligonucleotide tandem on DNA template
    • Pyshnyi, D.V., Krivenko, A.A., Lokhov, S.G., Ivanova, E.M., Dymshits, G.M. & Zarytova, V.F. (1998) Interaction of short oligonucleotide derivatives with nucleic acids. VI. Discrimination of mismatch-containing complexes upon ligation of a short oligonucleotide tandem on DNA template. Bioorg. Khim. 24, 32-37.
    • (1998) Bioorg. Khim. , vol.24 , pp. 32-37
    • Pyshnyi, D.V.1    Krivenko, A.A.2    Lokhov, S.G.3    Ivanova, E.M.4    Dymshits, G.M.5    Zarytova, V.F.6
  • 17
    • 85044702149 scopus 로고    scopus 로고
    • Interaction of short oligonucleotide derivatives with nucleic acids. V. Ligation of short oligonucleotides in tandem on a complementary DNA template
    • Pyshnyi, D.V., Krivenko, A.A., Lokhov, S.G., Ivanova, E.M., Dymshits, G.M. & Zarytova, V.F. (1998) Interaction of short oligonucleotide derivatives with nucleic acids. V. Ligation of short oligonucleotides in tandem on a complementary DNA template. Bioorg. Khim. 24, 25-31.
    • (1998) Bioorg. Khim. , vol.24 , pp. 25-31
    • Pyshnyi, D.V.1    Krivenko, A.A.2    Lokhov, S.G.3    Ivanova, E.M.4    Dymshits, G.M.5    Zarytova, V.F.6
  • 18
    • 0033605569 scopus 로고    scopus 로고
    • Standard free energy for the hydrolysis of adenylylated T4 DNA ligase and the apparent pKa of lysine 159
    • Arabshahi, A. & Frey, P.A. (1999) Standard free energy for the hydrolysis of adenylylated T4 DNA ligase and the apparent pKa of lysine 159. J. Biol. Chem. 274, 8586-8588.
    • (1999) J. Biol. Chem. , vol.274 , pp. 8586-8588
    • Arabshahi, A.1    Frey, P.A.2
  • 20
    • 0033796867 scopus 로고    scopus 로고
    • Synthesis of dinucleoside polyphosphates catalyzed by firefly luciferase and several ligases
    • Sillero, A. & Sillero, M.A. (2000) Synthesis of dinucleoside polyphosphates catalyzed by firefly luciferase and several ligases. Pharmacol. Ther. 87, 91-102.
    • (2000) Pharmacol. Ther. , vol.87 , pp. 91-102
    • Sillero, A.1    Sillero, M.A.2
  • 21
    • 0035204634 scopus 로고    scopus 로고
    • Binding of nucleotides by T4 DNA ligase and RNA ligase: Optical absorbance and fluorescence studies
    • Cherepanov, A.V. & de Vries, S. (2001) Binding of nucleotides by T4 DNA ligase and RNA ligase: optical absorbance and fluorescence studies. Biophys. J. 81, 3545-3559.
    • (2001) Biophys. J. , vol.81 , pp. 3545-3559
    • Cherepanov, A.V.1    De Vries, S.2
  • 22
    • 0036451168 scopus 로고    scopus 로고
    • Dynamic mechanism of nick recognition by DNA ligase
    • Cherepanov, A.V. & de Vries, S. (2002) Dynamic mechanism of nick recognition by DNA ligase. Eur. J. Biochem. 269, 5993-5999.
    • (2002) Eur. J. Biochem. , vol.269 , pp. 5993-5999
    • Cherepanov, A.V.1    De Vries, S.2
  • 23
    • 0036330503 scopus 로고    scopus 로고
    • Scanning mutagenesis using T4 DNA ligase and short degenerate DNA oligonucleotides containing tri-nucleotide mismatches
    • Cherepanov, A.V. & de Vries, S. (2002) Scanning mutagenesis using T4 DNA ligase and short degenerate DNA oligonucleotides containing tri-nucleotide mismatches. J. Biochem. (Tokyo) 132, 143-147.
    • (2002) J. Biochem. (Tokyo) , vol.132 , pp. 143-147
    • Cherepanov, A.V.1    De Vries, S.2
  • 24
    • 0037126846 scopus 로고    scopus 로고
    • 2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases
    • 2+-dependent nucleotidyl transfer catalyzed by T4 DNA and RNA ligases. J. Biol. Chem. 277, 1695-1704.
    • (2002) J. Biol. Chem. , vol.277 , pp. 1695-1704
    • Cherepanov, A.V.1    De Vries, S.2
  • 25
    • 0015408606 scopus 로고
    • Purification and properties of bacteriophage T4-induced RNA ligase
    • Silber, R., Malathi, V.G. & Hurwitz, J. (1972) Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl Acad. Sci. USA 69, 3009-3013.
    • (1972) Proc. Natl Acad. Sci. USA , vol.69 , pp. 3009-3013
    • Silber, R.1    Malathi, V.G.2    Hurwitz, J.3
  • 26
    • 0034635347 scopus 로고    scopus 로고
    • Nick recognition by DNA ligases
    • Doherty, A.J. & Dafforn, T.R. (2000) Nick recognition by DNA ligases. J. Mol. Biol. 296, 43-56.
    • (2000) J. Mol. Biol. , vol.296 , pp. 43-56
    • Doherty, A.J.1    Dafforn, T.R.2
  • 27
    • 0034327406 scopus 로고    scopus 로고
    • Structural and mechanistic conservation in DNA ligases
    • Doherty, A.J. & Suh, S.W. (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res. 28, 4051-4058.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4051-4058
    • Doherty, A.J.1    Suh, S.W.2
  • 28
    • 0003320265 scopus 로고    scopus 로고
    • Structure and mechanism in protein science
    • W.H. Freeman, New York
    • Fersht, A. (1999) Structure and mechanism in protein science. In A Guide to Enzyme Catalysis and Protein Folding, p. 3. W.H. Freeman, New York.
    • (1999) A Guide to Enzyme Catalysis and Protein Folding , pp. 3
    • Fersht, A.1
  • 29
    • 0022422692 scopus 로고
    • Influence of monovalent cations on the activity of T4 DNA ligase in the presence of polyethylene glycol
    • Hayashi, K., Nakazawa, M., Ishizaki, Y. & Obayashi, A. (1985) Influence of monovalent cations on the activity of T4 DNA ligase in the presence of polyethylene glycol. Nucleic Acids Res. 13, 3261-3271.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 3261-3271
    • Hayashi, K.1    Nakazawa, M.2    Ishizaki, Y.3    Obayashi, A.4
  • 30
    • 0033080784 scopus 로고    scopus 로고
    • Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D
    • Tong, J., Cao, W. & Barany, F. (1999) Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D. Nucleic Acids Res. 27, 788-794.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 788-794
    • Tong, J.1    Cao, W.2    Barany, F.3
  • 31
    • 0035378247 scopus 로고    scopus 로고
    • Molecular cloning and characterization of thermostable DNA ligase from Aquifex pyrophilus, a hyperthermophilic bacterium
    • Lim, J.H., Choi, J., Han, S.J., Kim, S.H., Hwang, H.Z., Jin, D.K., Ahn, B.Y. & Han, Y.S. (2001) Molecular cloning and characterization of thermostable DNA ligase from Aquifex pyrophilus, a hyperthermophilic bacterium. Extremophiles 5, 161-168.
    • (2001) Extremophiles , vol.5 , pp. 161-168
    • Lim, J.H.1    Choi, J.2    Han, S.J.3    Kim, S.H.4    Hwang, H.Z.5    Jin, D.K.6    Ahn, B.Y.7    Han, Y.S.8
  • 32
    • 0017134355 scopus 로고
    • Transcriptional control of T4 coliphage-specific genes 30, 42, 43, RIIA, RIIB, and e
    • Witmer, H., Baros, A., Forbes, J., Padnos, D., Maricondia, W. & Weiner, M. (1976) Transcriptional control of T4 coliphage-specific genes 30, 42, 43, RIIA, RIIB, and e. J. Gen. Virol. 31, 289-302.
    • (1976) J. Gen. Virol. , vol.31 , pp. 289-302
    • Witmer, H.1    Baros, A.2    Forbes, J.3    Padnos, D.4    Maricondia, W.5    Weiner, M.6
  • 33
    • 0028143584 scopus 로고
    • Physiological concentrations of purines and pyrimidines
    • Traut, T.W. (1994) Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 140, 1-22.
    • (1994) Mol. Cell. Biochem. , vol.140 , pp. 1-22
    • Traut, T.W.1
  • 35
    • 0029056990 scopus 로고
    • RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases
    • Shuman, S. & Schwer, B. (1995) RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Mol. Microbiol. 17, 405-410.
    • (1995) Mol. Microbiol. , vol.17 , pp. 405-410
    • Shuman, S.1    Schwer, B.2
  • 36
    • 0032077454 scopus 로고    scopus 로고
    • Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme
    • Schwer, B., Mao, X. & Shuman, S. (1998) Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme. Nucleic Acids Res. 26, 2050-2057.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 2050-2057
    • Schwer, B.1    Mao, X.2    Shuman, S.3
  • 37
    • 0017224213 scopus 로고
    • Capping of eucaryotic mRNAs
    • Shatkin, A.J. (1976) Capping of eucaryotic mRNAs. Cell 9, 645-653.
    • (1976) Cell , vol.9 , pp. 645-653
    • Shatkin, A.J.1
  • 39
    • 0001569132 scopus 로고
    • Determination of the interaction of deoxyribonucleate and magnesium ions by means of a metal ion indicator
    • Shack, J. & Bynum, B.S. (1959) Determination of the interaction of deoxyribonucleate and magnesium ions by means of a metal ion indicator. Nature (London) 184, 635-636.
    • (1959) Nature (London) , vol.184 , pp. 635-636
    • Shack, J.1    Bynum, B.S.2
  • 40
    • 0242309051 scopus 로고
    • Studies on the structure of nucleic acids. V. On the mechanism of metal enzyme interactions
    • Cavalieri, L.F. (1951) Studies on the structure of nucleic acids. V. On the mechanism of metal enzyme interactions. J. Am. Chem. Soc. 74, 1242-1247.
    • (1951) J. Am. Chem. Soc. , vol.74 , pp. 1242-1247
    • Cavalieri, L.F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.