메뉴 건너뛰기




Volumn 269, Issue 24, 2002, Pages 5993-5999

Dynamic mechanism of nick recognition by DNA ligase

Author keywords

A form DNA; A B form DNA hybrid; B A DNA helix transition; DNA ligase; Nick recognition; Protein DNA interactions

Indexed keywords

CURVED DNA; DNA; DNA HYBRID; DOUBLE STRANDED DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

EID: 0036451168     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.03309.x     Document Type: Review
Times cited : (33)

References (88)
  • 1
    • 0016273515 scopus 로고
    • DNA ligase: Structure, mechanism, and function
    • Lehman, I.R. (1974) DNA ligase: Structure, mechanism, and function. Science 186, 790-797.
    • (1974) Science , vol.186 , pp. 790-797
    • Lehman, I.R.1
  • 2
    • 0037127211 scopus 로고    scopus 로고
    • Mechanism underlying replication protein A stimulation of DNA Ligase I
    • Ranalli, T.A., DeMott, M.S. & Bambara, R.A. (2002) Mechanism underlying replication protein A stimulation of DNA Ligase I. J. Biol. Chem. 277, 1719-1727.
    • (2002) J. Biol. Chem. , vol.277 , pp. 1719-1727
    • Ranalli, T.A.1    DeMott, M.S.2    Bambara, R.A.3
  • 3
    • 0032486375 scopus 로고    scopus 로고
    • DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair
    • Mossi, R., Ferrari, E. & Hubscher, U. (1998) DNA ligase I selectively affects DNA synthesis by DNA polymerases delta and epsilon suggesting differential functions in DNA replication and repair. J. Biol. Chem. 273, 14322-14330.
    • (1998) J. Biol. Chem. , vol.273 , pp. 14322-14330
    • Mossi, R.1    Ferrari, E.2    Hubscher, U.3
  • 4
    • 0031972353 scopus 로고    scopus 로고
    • Structure and function of mammalian DNA ligases
    • Tomkinson, A.E. & Mackey, Z.B. (1998) Structure and function of mammalian DNA ligases. Mutation Res. 407, 1-9.
    • (1998) Mutation Res. , vol.407 , pp. 1-9
    • Tomkinson, A.E.1    Mackey, Z.B.2
  • 5
    • 0032126647 scopus 로고    scopus 로고
    • DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: Identification of a common targeting mechanism for the assembly of replication factories
    • Montecucco, A., Rossi, R., Levin, D.S., Gary, R., Park, M.S., Motycka, T.A., Ciarrocchi, G., Villa, A., Biamonti, G. & Tomkinson, A.E. (1998) DNA ligase I is recruited to sites of DNA replication by an interaction with proliferating cell nuclear antigen: Identification of a common targeting mechanism for the assembly of replication factories. EMBO J. 17, 3786-3795.
    • (1998) EMBO J. , vol.17 , pp. 3786-3795
    • Montecucco, A.1    Rossi, R.2    Levin, D.S.3    Gary, R.4    Park, M.S.5    Motycka, T.A.6    Ciarrocchi, G.7    Villa, A.8    Biamonti, G.9    Tomkinson, A.E.10
  • 6
    • 0033569841 scopus 로고    scopus 로고
    • Delayed DNA joining at 3′ mismatches by human DNA ligases
    • Bhagwat, A.S., Sanderson, R.J. & Lindahl, T. (1999) Delayed DNA joining at 3′ mismatches by human DNA ligases. Nucleic Acids Res. 27, 4028-4033.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4028-4033
    • Bhagwat, A.S.1    Sanderson, R.J.2    Lindahl, T.3
  • 7
    • 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
  • 8
    • 0342350255 scopus 로고    scopus 로고
    • Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair
    • Levin, D.S., McKenna, A.E., Motycka, T.A., Matsumoto, Y. & Tomkinson, A.E. (2000) Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr. Biol. 10, 919-922.
    • (2000) Curr. Biol. , vol.10 , pp. 919-922
    • Levin, D.S.1    McKenna, A.E.2    Motycka, T.A.3    Matsumoto, Y.4    Tomkinson, A.E.5
  • 10
    • 0032185230 scopus 로고    scopus 로고
    • DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes
    • Grawunder, U., Zimmer, D., Fugmann, S., Schwarz, K. & Lieber, M.R. (1998) DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes. Mol. Cell 2, 477-484.
    • (1998) Mol. Cell , vol.2 , pp. 477-484
    • Grawunder, U.1    Zimmer, D.2    Fugmann, S.3    Schwarz, K.4    Lieber, M.R.5
  • 11
    • 0035903103 scopus 로고    scopus 로고
    • Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radio-sensitivity
    • Riballo, E., Doherty, A.J., Dai, Y., StiN, T., Oettinger, M.A., Jeggo, P.A. & Kysela, B. (2001) Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radio-sensitivity. J. Biol. Chem. 276, 31124-31132.
    • (2001) J. Biol. Chem. , vol.276 , pp. 31124-31132
    • Riballo, E.1    Doherty, A.J.2    Dai, Y.3    Stiff, T.4    Oettinger, M.A.5    Jeggo, P.A.6    Kysela, B.7
  • 12
    • 0035834067 scopus 로고    scopus 로고
    • DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair
    • Adachi, N., Ishino, T., Ishii, Y., Takeda, S. & Koyama, H. (2001) DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair. Proc. Natl. Acad. Sci. USA 98, 12109-12113.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 12109-12113
    • Adachi, N.1    Ishino, T.2    Ishii, Y.3    Takeda, S.4    Koyama, H.5
  • 13
    • 0029166107 scopus 로고
    • Mammalian DNA ligase III: Molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination
    • Chen, J., Tomkinson, A.E., Ramos, W., Mackey, Z.B., Dane-hower, S., Walter, C.A., Schultz, R.A., Besterman, J.M. & Husain, I. (1995) Mammalian DNA ligase III: Molecular cloning, chromosomal localization, and expression in spermatocytes undergoing meiotic recombination. Mol. Cell Biol. 15, 5412-5422.
    • (1995) Mol. Cell Biol. , vol.15 , pp. 5412-5422
    • Chen, J.1    Tomkinson, A.E.2    Ramos, W.3    Mackey, Z.B.4    Danehower, S.5    Walter, C.A.6    Schultz, R.A.7    Besterman, J.M.8    Husain, I.9
  • 14
    • 0035818603 scopus 로고    scopus 로고
    • Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends
    • Jones, J.M. & Gellert, M. (2001) Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends. Proc. Natl. Acad. Sci. USA 98, 12926-12931.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 12926-12931
    • Jones, J.M.1    Gellert, M.2
  • 16
    • 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
  • 17
    • 0029938467 scopus 로고    scopus 로고
    • Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7
    • Subramanya, H.S., Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615.
    • (1996) Cell , vol.85 , pp. 607-615
    • Subramanya, H.S.1    Doherty, A.J.2    Ashford, S.R.3    Wigley, D.B.4
  • 18
    • 0029969958 scopus 로고    scopus 로고
    • Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization
    • Doherty, A.J., Ashford, S.R., Subramanya, H.S. & Wigley, D.B. (1996) Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization. J. Biol. Chem. 271, 11083-11089.
    • (1996) J. Biol. Chem. , vol.271 , pp. 11083-11089
    • Doherty, A.J.1    Ashford, S.R.2    Subramanya, H.S.3    Wigley, D.B.4
  • 19
    • 0033634655 scopus 로고    scopus 로고
    • Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining
    • Odell, M., Sriskanda, V., Shuman, S. & Nikolov, D.B. (2000) Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol. Cell 6, 1183-1193.
    • (2000) Mol. Cell , vol.6 , pp. 1183-1193
    • Odell, M.1    Sriskanda, V.2    Shuman, S.3    Nikolov, D.B.4
  • 23
    • 0035965270 scopus 로고    scopus 로고
    • +-dependent DNA ligase encoded by a eukaryotic virus
    • Sriskanda, V., Moyer, R.W. & Shuman, S. (2001) NAD(+)-dependent DNA ligase encoded by a eukaryotic virus. J. Biol. Chem. 276, 36100-36109.
    • (2001) J. Biol. Chem. , vol.276 , pp. 36100-36109
    • Sriskanda, V.1    Moyer, R.W.2    Shuman, S.3
  • 24
    • 0034734323 scopus 로고    scopus 로고
    • DNA ligases in the repair and replication of DNA
    • Timson, D.J., Singleton, M.R. & Wigley, D.B. (2000) DNA ligases in the repair and replication of DNA. Mutation Res. 460, 301-318.
    • (2000) Mutation Res. , vol.460 , pp. 301-318
    • Timson, D.J.1    Singleton, M.R.2    Wigley, D.B.3
  • 25
    • 0034635347 scopus 로고    scopus 로고
    • Nick recognition by DNA ligases
    • Doherty, A.J. & DaNorn, 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
  • 26
    • 0037155931 scopus 로고    scopus 로고
    • Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase
    • Sriskanda, V. & Shuman, S. (2002) Role of nucleotidyl transferase motif V in strand joining by Chlorella virus DNA ligase. J. Biol. Chem. 277, 9661-9667.
    • (2002) J. Biol. Chem. , vol.277 , pp. 9661-9667
    • Sriskanda, V.1    Shuman, S.2
  • 27
    • 0030585422 scopus 로고    scopus 로고
    • Closing the gap on DNA ligase
    • Shuman, S. (1996) Closing the gap on DNA ligase. Structure 4, 653-656.
    • (1996) Structure , vol.4 , pp. 653-656
    • Shuman, S.1
  • 28
    • 0031090688 scopus 로고    scopus 로고
    • Common fold, common function, common origin?
    • Suck, D. (1997) Common fold, common function, common origin? Nat. Struct. Biol. 4, 161-165.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 161-165
    • Suck, D.1
  • 29
    • 0027479161 scopus 로고
    • OB (oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
    • Murzin, A.G. (1993) OB (oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences. EMBO J. 12, 861-867.
    • (1993) EMBO J. , vol.12 , pp. 861-867
    • Murzin, A.G.1
  • 30
    • 0038228666 scopus 로고    scopus 로고
    • X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes
    • Hakansson, K., Doherty, A.J., Shuman, S. & Wigley, D.B. (1997) X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89, 545-553.
    • (1997) Cell , vol.89 , pp. 545-553
    • Hakansson, K.1    Doherty, A.J.2    Shuman, S.3    Wigley, D.B.4
  • 31
    • 0029906410 scopus 로고    scopus 로고
    • Characterization of proteolytic fragments of bacteriophage T7 DNA ligase
    • Doherty, A.J., Ashford, S.R. & Wigley, D.B. (1996) Characterization of proteolytic fragments of bacteriophage T7 DNA ligase. Nucleic Acids Res. 24, 2281-2287.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 2281-2287
    • Doherty, A.J.1    Ashford, S.R.2    Wigley, D.B.3
  • 32
    • 0033553405 scopus 로고    scopus 로고
    • Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA
    • Odell, M. & Shuman, S. (1999) Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. J. Biol. Chem. 274, 14032-14039.
    • (1999) J. Biol. Chem. , vol.274 , pp. 14032-14039
    • Odell, M.1    Shuman, S.2
  • 33
    • 0033534370 scopus 로고    scopus 로고
    • Functional domains of an ATP-dependent DNA ligase
    • Doherty, A.J. & Wigley, D.B. (1999) Functional domains of an ATP-dependent DNA ligase. J. Mol. Biol. 285, 63-71.
    • (1999) J. Mol. Biol. , vol.285 , pp. 63-71
    • Doherty, A.J.1    Wigley, D.B.2
  • 34
    • 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
  • 35
    • 0033581011 scopus 로고    scopus 로고
    • DNA polymerases: Structural diversity and common mechanisms
    • Steitz, T.A. (1999) DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem. 274, 17395-17398.
    • (1999) J. Biol Chem. , vol.274 , pp. 17395-17398
    • Steitz, T.A.1
  • 36
    • 0028881713 scopus 로고
    • Polymerase structures and function: Variations on a theme?
    • Joyce, C.M. & Steitz, T.A. (1995) Polymerase structures and function: Variations on a theme? J. Bacteriol. 177, 6321-6329.
    • (1995) J. Bacteriol. , vol.177 , pp. 6321-6329
    • Joyce, C.M.1    Steitz, T.A.2
  • 37
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a pol alpha family DNA polymerase
    • Franklin, M.C., Wang, J. & Steitz, T.A. (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105, 657-667.
    • (2001) Cell , vol.105 , pp. 657-667
    • Franklin, M.C.1    Wang, J.2    Steitz, T.A.3
  • 39
    • 0030930760 scopus 로고    scopus 로고
    • Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
    • Sawaya, M.R., Prasad, R., Wilson, S.H., Kraut, J. & Pelletier, H. (1997) Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: Evidence for an induced fit mechanism. Biochemistry 36, 11205-11215.
    • (1997) Biochemistry , vol.36 , pp. 11205-11215
    • Sawaya, M.R.1    Prasad, R.2    Wilson, S.H.3    Kraut, J.4    Pelletier, H.5
  • 40
    • 0028049441 scopus 로고
    • Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP
    • Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
    • (1994) Science , vol.264 , pp. 1891-1903
    • Pelletier, H.1    Sawaya, M.R.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 41
    • 0032535528 scopus 로고    scopus 로고
    • Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
    • Li, Y., Korolev, S. & Waksman, G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation. EMBO J. 17, 7514-7525.
    • (1998) EMBO J. , vol.17 , pp. 7514-7525
    • Li, Y.1    Korolev, S.2    Waksman, G.3
  • 42
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu, X.J., Shakked, Z. & Olson, W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300, 819-840.
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.J.1    Shakked, Z.2    Olson, W.K.3
  • 43
    • 0032518524 scopus 로고    scopus 로고
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    • Kiefer, J.R., Mao, C., Braman, J.C. & Beese, L.S. (1998) Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304-307.
    • (1998) Nature , vol.391 , pp. 304-307
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 44
    • 0030586279 scopus 로고    scopus 로고
    • A model for DNA polymerase translocation: Worm-like movement of DNA within the binding cleft
    • WlassoN, W.A., Dymshits, G.M. & Lavrik, O.I. (1996) A model for DNA polymerase translocation: Worm-like movement of DNA within the binding cleft. FEBS Lett. 390, 6-9.
    • (1996) FEBS Lett. , vol.390 , pp. 6-9
    • Wlassoff, W.A.1    Dymshits, G.M.2    Lavrik, O.I.3
  • 45
    • 0027231782 scopus 로고
    • Structure of DNA polymerase I Klenow fragment bound to duplex DNA
    • Beese, L.S., Derbyshire, V. & Steitz, T.A. (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science 260, 352-355.
    • (1993) Science , vol.260 , pp. 352-355
    • Beese, L.S.1    Derbyshire, V.2    Steitz, T.A.3
  • 46
    • 0027244844 scopus 로고
    • Evidence of DNA bending in transcription complexes imaged by scanning force microscopy
    • Rees, W.A., Keller, R.W., Vesenka, J.P., Yang, G. & Bustamante, C. (1993) Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science 260, 1646-1649.
    • (1993) Science , vol.260 , pp. 1646-1649
    • Rees, W.A.1    Keller, R.W.2    Vesenka, J.P.3    Yang, G.4    Bustamante, C.5
  • 47
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution
    • Doublie, S., Tabor, S., Long, A.M., Richardson, C.C. & Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391, 251-258.
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 48
    • 0034214208 scopus 로고    scopus 로고
    • Characterization of the 'helix clamp' motif of HIV-1 reverse transcriptase using MALDI-TOF MS and surface plasmon resonance
    • Lin, S., Long, S., Ramirez, S.M., Cotter, R.J. & Woods, A.S. (2000) Characterization of the 'helix clamp' motif of HIV-1 reverse transcriptase using MALDI-TOF MS and surface plasmon resonance. Anal. Chem. 72, 2635-2640.
    • (2000) Anal. Chem. , vol.72 , pp. 2635-2640
    • Lin, S.1    Long, S.2    Ramirez, S.M.3    Cotter, R.J.4    Woods, A.S.5
  • 49
    • 0018397705 scopus 로고
    • Bent DNA: Visualization of a base-paired and stacked A-B conformational junction
    • Selsing, E., Wells, R.D., Alden, C.J. & Arnott, S. (1979) Bent DNA: Visualization of a base-paired and stacked A-B conformational junction. J. Biol. Chem. 254, 5417-5422.
    • (1979) J. Biol. Chem. , vol.254 , pp. 5417-5422
    • Selsing, E.1    Wells, R.D.2    Alden, C.J.3    Arnott, S.4
  • 50
    • 0027935377 scopus 로고
    • The solution structure of the r (gcg) d (TATACCC): D (GGGTA-TACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction
    • Salazar, M., FedoroN, O., Zhu, L. & Reid, B.R. (1994) The solution structure of the r (gcg) d (TATACCC): D (GGGTA-TACGC) Okazaki fragment contains two distinct duplex morphologies connected by a junction. J. Mol. Biol. 241, 440-455.
    • (1994) J. Mol. Biol. , vol.241 , pp. 440-455
    • Salazar, M.1    Fedoroff, O.2    Zhu, L.3    Reid, B.R.4
  • 53
    • 0034671291 scopus 로고    scopus 로고
    • DNA structure: What's in charge?
    • McConnell, K.J. & Beveridge, D.L. (2000) DNA structure: What's in charge? J. Mol. Biol. 304, 803-820.
    • (2000) J. Mol. Biol. , vol.304 , pp. 803-820
    • McConnell, K.J.1    Beveridge, D.L.2
  • 54
    • 0021770861 scopus 로고
    • A base-centred explanation of the B-to-A transition in DNA
    • Calladine, C.R. & Drew, H.R. (1984) A base-centred explanation of the B-to-A transition in DNA. J. Mol. Biol. 178, 773-782.
    • (1984) J. Mol. Biol. , vol.178 , pp. 773-782
    • Calladine, C.R.1    Drew, H.R.2
  • 55
    • 0031722426 scopus 로고    scopus 로고
    • An analysis of the relationship between hydration and protein-DNA interactions
    • Woda, J., Schneider, B., Patel, K., Mistry, K. & Berman, H.M. (1998) An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75, 2170-2177.
    • (1998) Biophys. J. , vol.75 , pp. 2170-2177
    • Woda, J.1    Schneider, B.2    Patel, K.3    Mistry, K.4    Berman, H.M.5
  • 56
    • 0000127073 scopus 로고
    • Sequence-specific recognition of double helical nucleic acids by proteins
    • Seeman, N.C., Rosenberg, J.M. & Rich, A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73, 804-808.
    • (1976) Proc. Natl. Acad. Sci. USA , vol.73 , pp. 804-808
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 57
    • 0000619168 scopus 로고
    • Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity
    • Petruska, J., Sowers, L.C. & Goodman, M.F. (1986) Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity. Proc. Natl. Acad. Sci. USA 83, 1559-1562.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 1559-1562
    • Petruska, J.1    Sowers, L.C.2    Goodman, M.F.3
  • 58
    • 0023056536 scopus 로고
    • Salt induced B-A transition of poly (dG) poly (dC) and the stabilization of A form by its methylation
    • Nishimura, Y., Torigoe, C. & Tsuboi, M. (1986) Salt induced B-A transition of poly (dG) poly (dC) and the stabilization of A form by its methylation. Nucleic Acids Res. 14, 2737-2748.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 2737-2748
    • Nishimura, Y.1    Torigoe, C.2    Tsuboi, M.3
  • 60
    • 0028241531 scopus 로고
    • Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes
    • Nekludova, L. & Pabo, C.O. (1994) Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. Proc. Natl. Acad. Sci. USA 91, 6948-6952.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 6948-6952
    • Nekludova, L.1    Pabo, C.O.2
  • 61
    • 0028315988 scopus 로고
    • Determinants of repressor/operator recognition from the structure of the trp operator binding site
    • Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A. & Sigler, P.B. (1994) Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature 368, 469-473.
    • (1994) Nature , vol.368 , pp. 469-473
    • Shakked, Z.1    Guzikevich-Guerstein, G.2    Frolow, F.3    Rabinovich, D.4    Joachimiak, A.5    Sigler, P.B.6
  • 62
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson, W.K., Gorin, A.A., Lu, X.J., Hock, L.M. & Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA 95, 11163-11168.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 63
    • 0034326316 scopus 로고    scopus 로고
    • B-form to A-form conversion by a 3′-terminal ribose: Crystal structure of the chimera d (CCACTAGTG) r (G)
    • Wahl, M.C. & Sundaralingam, M. (2000) B-form to A-form conversion by a 3′-terminal ribose: Crystal structure of the chimera d (CCACTAGTG) r (G). Nucleic Acids Res. 28, 4356-4363.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4356-4363
    • Wahl, M.C.1    Sundaralingam, M.2
  • 64
    • 0028618356 scopus 로고
    • Crystal structure of the highly distorted chimeric decamer r (C) d (CGGCGCCG) r (G) spermine complex-spermine binding to phosphate only and minor groove tertiary base-pairing
    • Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994) Crystal structure of the highly distorted chimeric decamer r (C) d (CGGCGCCG) r (G) spermine complex-spermine binding to phosphate only and minor groove tertiary base-pairing. Nucleic Acids Res. 22, 5466-5476.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5466-5476
    • Ban, C.1    Ramakrishnan, B.2    Sundaralingam, M.3
  • 65
    • 0028350664 scopus 로고
    • A single 2′-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d (CCGGC) r (G) d (CCGG) with a novel intermolecular G-C base-paired quadruplet
    • Ban, C., Ramakrishnan, B. & Sundaralingam, M. (1994) A single 2′-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d (CCGGC) r (G) d (CCGG) with a novel intermolecular G-C base-paired quadruplet. J. Mol. Biol. 236, 275-285.
    • (1994) J. Mol. Biol. , vol.236 , pp. 275-285
    • Ban, C.1    Ramakrishnan, B.2    Sundaralingam, M.3
  • 67
    • 33947547892 scopus 로고
    • Molecular architecture and biological reactions
    • Pauling, L. (1946) Molecular architecture and biological reactions. Chem. Engng. News 24, 1375-1377.
    • (1946) Chem. Engng. News , vol.24 , pp. 1375-1377
    • Pauling, L.1
  • 68
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland, D.E.J. (1958) Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44, 98-104.
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland, D.E.J.1
  • 70
    • 0032518177 scopus 로고    scopus 로고
    • Chlorella virus DNA ligase: Nick recognition and mutational analysis
    • Sriskanda, V. & Shuman, S. (1998) Chlorella virus DNA ligase: Nick recognition and mutational analysis. Nucleic Acids Res. 26, 525-531.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 525-531
    • Sriskanda, V.1    Shuman, S.2
  • 71
    • 0031858138 scopus 로고    scopus 로고
    • Apparent pore size of polyacrylamide gels: Comparison of gels cast and run in Tris-acetate-EDTA and Tris-borate-EDTA buNers
    • Stellwagen, N.C. (1998) Apparent pore size of polyacrylamide gels: Comparison of gels cast and run in Tris-acetate-EDTA and Tris-borate-EDTA buNers. Electrophoresis 19, 1542-1547.
    • (1998) Electrophoresis , vol.19 , pp. 1542-1547
    • Stellwagen, N.C.1
  • 72
    • 0022970697 scopus 로고
    • DNA ligase from Drosophila melanogaster embryos. Purification and physical characterization
    • Rabin, B.A., Hawley, R.S. & Chase, J.W. (1986) DNA ligase from Drosophila melanogaster embryos. Purification and physical characterization. J. Biol. Chem. 261, 10637-10645.
    • (1986) J. Biol. Chem. , vol.261 , pp. 10637-10645
    • Rabin, B.A.1    Hawley, R.S.2    Chase, J.W.3
  • 73
    • 0034653795 scopus 로고    scopus 로고
    • +-dependent DNA ligase from the hyperthermophile Aquifex aeolicus
    • +-dependent DNA ligase from the hyperthermophile Aquifex aeolicus. Nucleic Acids Res. 28, 1447-1454.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1447-1454
    • Tong, J.1    Barany, F.2    Cao, W.3
  • 74
    • 0033527667 scopus 로고    scopus 로고
    • DNA structure and polymerase fidelity
    • Timsit, Y. (1999) DNA structure and polymerase fidelity. J. Mol. Biol. 293, 835-853.
    • (1999) J. Mol. Biol. , vol.293 , pp. 835-853
    • Timsit, Y.1
  • 75
    • 0023708040 scopus 로고
    • Water: An integral part of nucleic acid structure
    • Westhof, E. (1988) Water: An integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem. 17, 125-144.
    • (1988) Annu. Rev. Biophys. Biophys. Chem. , vol.17 , pp. 125-144
    • Westhof, E.1
  • 76
    • 0003890119 scopus 로고
    • W.H. Freeman, New York, USA
    • Kornberg, A. & Baker, T.A. (1992) In DNA Replication, pp. 307-322. W.H. Freeman, New York, USA.
    • (1992) DNA Replication , pp. 307-322
    • Kornberg, A.1    Baker, T.A.2
  • 77
    • 0030929525 scopus 로고    scopus 로고
    • Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing
    • Rumbaugh, J.A., Murante, R.S., Shi, S. & Bambara, R.A. (1997) Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing. J. Biol. Chem. 272, 22591-22599.
    • (1997) J. Biol. Chem. , vol.272 , pp. 22591-22599
    • Rumbaugh, J.A.1    Murante, R.S.2    Shi, S.3    Bambara, R.A.4
  • 78
    • 0030767872 scopus 로고    scopus 로고
    • Ligation of RNA-containing duplexes by Vaccinia DNA ligase
    • Sekiguchi, J. & Shuman, S. (1997) Ligation of RNA-containing duplexes by Vaccinia DNA ligase. Biochemistry 36, 9073-9079.
    • (1997) Biochemistry , vol.36 , pp. 9073-9079
    • Sekiguchi, J.1    Shuman, S.2
  • 79
    • 0032145356 scopus 로고    scopus 로고
    • Specificity and fidelity of strand joining by Chlorella virus DNA ligase
    • Sriskanda, V. & Shuman, S. (1998) Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res. 26, 3536-3541.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3536-3541
    • Sriskanda, V.1    Shuman, S.2
  • 80
    • 0029950158 scopus 로고    scopus 로고
    • Characterization of DNA ligase from the fungus Coprinus cinereus
    • Matsuda, S., Sakaguchi, K., Tsukada, K. & Teraoka, H. (1996) Characterization of DNA ligase from the fungus Coprinus cinereus. Eur. J. Biochem. 237, 691-697.
    • (1996) Eur. J. Biochem. , vol.237 , pp. 691-697
    • Matsuda, S.1    Sakaguchi, K.2    Tsukada, K.3    Teraoka, H.4
  • 81
    • 0029817836 scopus 로고    scopus 로고
    • DNA ligase IV from HeLa cell nuclei
    • Robins, P. & Lindahl, T. (1996) DNA ligase IV from HeLa cell nuclei. J. Biol. Chem. 271, 24257-24261.
    • (1996) J. Biol. Chem. , vol.271 , pp. 24257-24261
    • Robins, P.1    Lindahl, T.2
  • 83
    • 0016304026 scopus 로고
    • Structures for the polynucleotide complexes poly (dA) with poly (dT) and poly (dT) with poly (dA) with poly (dT)
    • Arnott, S. & Selsing, E. (1974) Structures for the polynucleotide complexes poly (dA) with poly (dT) and poly (dT) with poly (dA) with poly (dT). J. Mol. Biol. 88, 509-521.
    • (1974) J. Mol. Biol. , vol.88 , pp. 509-521
    • Arnott, S.1    Selsing, E.2
  • 84
    • 0026722438 scopus 로고
    • A-DNA in solution as studied by diverse approaches
    • Ivanov, V.I. & Krylov, D. (1992) A-DNA in solution as studied by diverse approaches. Methods Enzymol. 211, 111-127.
    • (1992) Methods Enzymol. , vol.211 , pp. 111-127
    • Ivanov, V.I.1    Krylov, D.2
  • 85
    • 0035193091 scopus 로고    scopus 로고
    • Sequence-dependent B-A transition in DNA evaluated with dimeric and trimeric scales
    • Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L. & Zhurkin, V.B. (2001) Sequence-dependent B-A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 81, 3409-3421.
    • (2001) Biophys. J. , vol.81 , pp. 3409-3421
    • Tolstorukov, M.Y.1    Ivanov, V.I.2    Malenkov, G.G.3    Jernigan, R.L.4    Zhurkin, V.B.5
  • 86
    • 0027190862 scopus 로고
    • The DNA strand in DNA. RNA hybrid duplexes is neither B-form nor A-form in solution
    • Salazar, M., Fedoroff, O.Y., Miller, J.M., Ribeiro, N.S. & Reid, B.R. (1993) The DNA strand in DNA. RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry 32, 4207-4215.
    • (1993) Biochemistry , vol.32 , pp. 4207-4215
    • Salazar, M.1    Fedoroff, O.Y.2    Miller, J.M.3    Ribeiro, N.S.4    Reid, B.R.5
  • 87
    • 0034615785 scopus 로고    scopus 로고
    • An A-type double helix of DNA having B-type puckering of the deoxyribose rings
    • Trantirek, L., Stefl, R., Vorlickova, M., Koca, J., Sklenar, V. & Kypr, J. (2000) An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J. Mol. Biol. 297, 907-922.
    • (2000) J. Mol. Biol. , vol.297 , pp. 907-922
    • Trantirek, L.1    Stefl, R.2    Vorlickova, M.3    Koca, J.4    Sklenar, V.5    Kypr, J.6
  • 88
    • 0029375390 scopus 로고
    • Crystal structures of B-form DNA-RNA chimers complexed with distamycin
    • Chen, X., Ramakrishnan, B. & Sundaralingam, M. (1995) Crystal structures of B-form DNA-RNA chimers complexed with distamycin. Nat. Struct. Biol. 2, 733-735.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 733-735
    • Chen, X.1    Ramakrishnan, B.2    Sundaralingam, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.