메뉴 건너뛰기




Volumn 357, Issue 4, 2006, Pages 1089-1104

DNA topology and geometry in Flp and Cre recombination

Author keywords

DNA looping; DNA topology; Protein DNA interactions; Site specific recombination; Tangle analysis

Indexed keywords

CRE RECOMBINASE; INTEGRASE; PLASMID DNA; RECOMBINASE;

EID: 33644832221     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.01.037     Document Type: Article
Times cited : (49)

References (56)
  • 1
    • 22444435143 scopus 로고    scopus 로고
    • Strategies for the use of site-specific recombinases in genome engineering
    • J.R. Jones, K.D. Shelton, and M.A. Magnuson Strategies for the use of site-specific recombinases in genome engineering Methods Mol. Med. 103 2005 245 257
    • (2005) Methods Mol. Med. , vol.103 , pp. 245-257
    • Jones, J.R.1    Shelton, K.D.2    Magnuson, M.A.3
  • 2
    • 0022669622 scopus 로고
    • The integrase family of site-specific recombinases: Regional similarities and global diversity
    • P. Argos, A. Landy, K. Abremski, J.B. Egan, E. Haggard-Ljungquist, and R.H. Hoess The integrase family of site-specific recombinases: regional similarities and global diversity EMBO J. 5 1986 433 440
    • (1986) EMBO J. , vol.5 , pp. 433-440
    • Argos, P.1    Landy, A.2    Abremski, K.3    Egan, J.B.4    Haggard-Ljungquist, E.5    Hoess, R.H.6
  • 3
    • 0022497169 scopus 로고
    • Site-specific recombination promotes plasmid amplification in yeast
    • F.C. Volkert, and J.R. Broach Site-specific recombination promotes plasmid amplification in yeast Cell 46 1986 541 550
    • (1986) Cell , vol.46 , pp. 541-550
    • Volkert, F.C.1    Broach, J.R.2
  • 4
    • 0022388399 scopus 로고
    • Determination of DNA sequences essential for FLP-mediated recombination by a novel method
    • R.M. Gronostajski, and P.D. Sadowski Determination of DNA sequences essential for FLP-mediated recombination by a novel method J. Biol. Chem. 260 1985 12320 12327
    • (1985) J. Biol. Chem. , vol.260 , pp. 12320-12327
    • Gronostajski, R.M.1    Sadowski, P.D.2
  • 5
    • 0022399815 scopus 로고
    • Two-micrometer circle site-specific recombination: The minimal substrate and the possible role of flanking sequences
    • M. Jayaram Two-micrometer circle site-specific recombination: the minimal substrate and the possible role of flanking sequences Proc. Natl Acad. Sci. USA 82 1985 5875 5879
    • (1985) Proc. Natl Acad. Sci. USA , vol.82 , pp. 5875-5879
    • Jayaram, M.1
  • 6
    • 0024292652 scopus 로고
    • DNA recognition by the FLP recombinase of the yeast 2 mu plasmid. a mutational analysis of the FLP binding site
    • J.F. Senecoff, P.J. Rossmeissl, and M.M. Cox DNA recognition by the FLP recombinase of the yeast 2 mu plasmid. A mutational analysis of the FLP binding site J. Mol. Biol. 201 1988 405 421
    • (1988) J. Mol. Biol. , vol.201 , pp. 405-421
    • Senecoff, J.F.1    Rossmeissl, P.J.2    Cox, M.M.3
  • 7
    • 0022111794 scopus 로고
    • The stereostructure of knots and catenanes produced by phage lambda integrative recombination: Implications for mechanism and DNA structure
    • S.J. Spengler, A. Stasiak, and N.R. Cozzarelli The stereostructure of knots and catenanes produced by phage lambda integrative recombination: implications for mechanism and DNA structure Cell 42 1985 325 334
    • (1985) Cell , vol.42 , pp. 325-334
    • Spengler, S.J.1    Stasiak, A.2    Cozzarelli, N.R.3
  • 8
    • 4444363103 scopus 로고    scopus 로고
    • Analysis of DNA knots and catenanes by agarose-gel electrophoresis
    • S.D. Levene, and H. Tsen Analysis of DNA knots and catenanes by agarose-gel electrophoresis Methods Mol. Biol. 94 1999 75 85
    • (1999) Methods Mol. Biol. , vol.94 , pp. 75-85
    • Levene, S.D.1    Tsen, H.2
  • 12
    • 0022000777 scopus 로고
    • Recombination site selection by Tn3 resolvase: Topological tests of a tracking mechanism
    • H.W. Benjamin, M.M. Matzuk, M.A. Krasnow, and N.R. Cozzarelli Recombination site selection by Tn3 resolvase: topological tests of a tracking mechanism Cell 40 1985 147 158
    • (1985) Cell , vol.40 , pp. 147-158
    • Benjamin, H.W.1    Matzuk, M.M.2    Krasnow, M.A.3    Cozzarelli, N.R.4
  • 13
  • 14
    • 0024364817 scopus 로고
    • Site-specific recombination by Tn3 resolvase: Topological changes in the forward and reverse reactions
    • W.M. Stark, D.J. Sherratt, and M.R. Boocock Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions Cell 58 1989 779 790
    • (1989) Cell , vol.58 , pp. 779-790
    • Stark, W.M.1    Sherratt, D.J.2    Boocock, M.R.3
  • 15
    • 0025214694 scopus 로고
    • Geometric arrangements of Tn3 resolvase sites
    • H.W. Benjamin, and N.R. Cozzarelli Geometric arrangements of Tn3 resolvase sites J. Biol. Chem. 265 1990 6441 6447
    • (1990) J. Biol. Chem. , vol.265 , pp. 6441-6447
    • Benjamin, H.W.1    Cozzarelli, N.R.2
  • 16
    • 0024024317 scopus 로고
    • Isolation and characterization of the Tn3 resolvase synaptic intermediate
    • H.W. Benjamin, and N.R. Cozzarelli Isolation and characterization of the Tn3 resolvase synaptic intermediate EMBO J. 7 1988 1897 1905
    • (1988) EMBO J. , vol.7 , pp. 1897-1905
    • Benjamin, H.W.1    Cozzarelli, N.R.2
  • 17
    • 0023046599 scopus 로고
    • The role of the loxP spacer region in P1 site-specific recombination
    • R.H. Hoess, A. Wierzbicki, and K. Abremski The role of the loxP spacer region in P1 site-specific recombination Nucl. Acids Res 14 1986 2287 2300
    • (1986) Nucl. Acids Res , vol.14 , pp. 2287-2300
    • Hoess, R.H.1    Wierzbicki, A.2    Abremski, K.3
  • 18
    • 0002625615 scopus 로고
    • DNA inversion in the 2 μm plasmid of saccharomyces cerevisiae
    • D.E. Berg M.M. Howe American Society for Microbiology Washington, DC
    • M.M. Cox DNA inversion in the 2 μm plasmid of saccharomyces cerevisiae D.E. Berg M.M. Howe Mobile DNA 1989 American Society for Microbiology Washington, DC 661 670
    • (1989) Mobile DNA , pp. 661-670
    • Cox, M.M.1
  • 19
    • 0033637213 scopus 로고    scopus 로고
    • Crystal structure of a Flp recombinase-Holliday junction complex: Assembly of an active oligomer by helix swapping
    • Y. Chen, U. Narendra, L.E. Iype, M.M. Cox, and P.A. Rice Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping Mol. Cell. 6 2000 885 897
    • (2000) Mol. Cell. , vol.6 , pp. 885-897
    • Chen, Y.1    Narendra, U.2    Iype, L.E.3    Cox, M.M.4    Rice, P.A.5
  • 20
    • 0035850784 scopus 로고    scopus 로고
    • Quasi-equivalence in site-specific recombinase structure and function: Crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction
    • K.C. Woods, S.S. Martin, V.C. Chu, and E.P. Baldwin Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction J. Mol. Biol. 313 2001 49 69
    • (2001) J. Mol. Biol. , vol.313 , pp. 49-69
    • Woods, K.C.1    Martin, S.S.2    Chu, V.C.3    Baldwin, E.P.4
  • 21
    • 0036304839 scopus 로고    scopus 로고
    • The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex
    • S.S. Martin, E. Pulido, V.C. Chu, T.S. Lechner, and E.P. Baldwin The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex J. Mol. Biol. 319 2002 107 127
    • (2002) J. Mol. Biol. , vol.319 , pp. 107-127
    • Martin, S.S.1    Pulido, E.2    Chu, V.C.3    Lechner, T.S.4    Baldwin, E.P.5
  • 22
    • 0037436326 scopus 로고    scopus 로고
    • Structural plasticity of the Flp-Holliday junction complex
    • A.B. Conway, Y. Chen, and P.A. Rice Structural plasticity of the Flp-Holliday junction complex J. Mol. Biol. 326 2003 425 434
    • (2003) J. Mol. Biol. , vol.326 , pp. 425-434
    • Conway, A.B.1    Chen, Y.2    Rice, P.A.3
  • 23
    • 0344012172 scopus 로고    scopus 로고
    • Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation
    • E. Ennifar, J.E. Meyer, F. Buchholz, A.F. Stewart, and D. Suck Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation Nucl. Acids Res. 31 2003 5449 5460
    • (2003) Nucl. Acids Res. , vol.31 , pp. 5449-5460
    • Ennifar, E.1    Meyer, J.E.2    Buchholz, F.3    Stewart, A.F.4    Suck, D.5
  • 25
    • 0026639433 scopus 로고
    • Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction
    • R.M. Clegg, A.I. Murchie, A. Zechel, C. Carlberg, S. Diekmann, and D.M. Lilley Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction Biochemistry 31 1992 4846 4856
    • (1992) Biochemistry , vol.31 , pp. 4846-4856
    • Clegg, R.M.1    Murchie, A.I.2    Zechel, A.3    Carlberg, C.4    Diekmann, S.5    Lilley, D.M.6
  • 26
    • 0033636685 scopus 로고    scopus 로고
    • Structures of helical junctions in nucleic acids
    • D.M. Lilley Structures of helical junctions in nucleic acids Quart. Rev. Biophys. 33 2000 109 159
    • (2000) Quart. Rev. Biophys. , vol.33 , pp. 109-159
    • Lilley, D.M.1
  • 27
    • 0034635961 scopus 로고    scopus 로고
    • The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
    • B.F. Eichman, J.M. Vargason, B.H. Mooers, and P.S. Ho The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions Proc. Natl Acad. Sci. USA 97 2000 3971 3976
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 3971-3976
    • Eichman, B.F.1    Vargason, J.M.2    Mooers, B.H.3    Ho, P.S.4
  • 28
    • 0036076678 scopus 로고    scopus 로고
    • The inherent properties of DNA four-way junctions: Comparing the crystal structures of holliday junctions
    • B.F. Eichman, M. Ortiz-Lombardia, J. Aymami, M. Coll, and P.S. Ho The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions J. Mol. Biol. 320 2002 1037 1051
    • (2002) J. Mol. Biol. , vol.320 , pp. 1037-1051
    • Eichman, B.F.1    Ortiz-Lombardia, M.2    Aymami, J.3    Coll, M.4    Ho, P.S.5
  • 29
    • 0020397021 scopus 로고
    • Site-specific DNA condensation and pairing mediated by the int protein of bacteriophage lambda
    • M. Better, C. Lu, R.C. Williams, and H. Echols Site-specific DNA condensation and pairing mediated by the int protein of bacteriophage lambda Proc. Natl Acad. Sci. USA 79 1982 5837 5841
    • (1982) Proc. Natl Acad. Sci. USA , vol.79 , pp. 5837-5841
    • Better, M.1    Lu, C.2    Williams, R.C.3    Echols, H.4
  • 30
    • 15244360525 scopus 로고    scopus 로고
    • Architecture of recombination intermediates visualized by in-gel FRET of lambda integrase-Holliday junction-arm DNA complexes
    • M. Radman-Livaja, T. Biswas, D. Mierke, and A. Landy Architecture of recombination intermediates visualized by in-gel FRET of lambda integrase-Holliday junction-arm DNA complexes Proc. Natl Acad. Sci. USA 102 2005 3913 3920
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 3913-3920
    • Radman-Livaja, M.1    Biswas, T.2    Mierke, D.3    Landy, A.4
  • 32
    • 0025642871 scopus 로고
    • FLP protein of 2 μ circle plasmid of yeast induces multiple bends in the FLP recognition target site
    • C.J. Schwartz, and P.D. Sadowski FLP protein of 2 μ circle plasmid of yeast induces multiple bends in the FLP recognition target site J. Mol. Biol. 216 1990 289 298
    • (1990) J. Mol. Biol. , vol.216 , pp. 289-298
    • Schwartz, C.J.1    Sadowski, P.D.2
  • 33
    • 0029127499 scopus 로고
    • The role of DNA bending in Flp-mediated site-specific recombination
    • K.H. Luetke, and P.D. Sadowski The role of DNA bending in Flp-mediated site-specific recombination J. Mol. Biol. 251 1995 493 506
    • (1995) J. Mol. Biol. , vol.251 , pp. 493-506
    • Luetke, K.H.1    Sadowski, P.D.2
  • 34
    • 0029094283 scopus 로고
    • Chemical probe and missing nucleoside analysis of Flp recombinase bound to the recombination target sequence
    • A.S. Kimball, M.L. Kimball, M. Jayaram, and T.D. Tullius Chemical probe and missing nucleoside analysis of Flp recombinase bound to the recombination target sequence Nucl. Acids Res. 23 1995 3009 3017
    • (1995) Nucl. Acids Res. , vol.23 , pp. 3009-3017
    • Kimball, A.S.1    Kimball, M.L.2    Jayaram, M.3    Tullius, T.D.4
  • 35
    • 21344466779 scopus 로고    scopus 로고
    • A structural basis for allosteric control of DNA recombination by lambda integrase
    • T. Biswas, H. Aihara, M. Radman-Livaja, D. Filman, A. Landy, and T. Ellenberger A structural basis for allosteric control of DNA recombination by lambda integrase Nature 435 2005 1059 1066
    • (2005) Nature , vol.435 , pp. 1059-1066
    • Biswas, T.1    Aihara, H.2    Radman-Livaja, M.3    Filman, D.4    Landy, A.5    Ellenberger, T.6
  • 38
    • 0030596081 scopus 로고    scopus 로고
    • Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis
    • C. Rivetti, M. Guthold, and C. Bustamante Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis J. Mol. Biol. 264 1996 919 932
    • (1996) J. Mol. Biol. , vol.264 , pp. 919-932
    • Rivetti, C.1    Guthold, M.2    Bustamante, C.3
  • 39
    • 15244361577 scopus 로고    scopus 로고
    • DNA structure and dynamics: An atomic force microscopy study
    • Y.L. Lyubchenko DNA structure and dynamics: an atomic force microscopy study Cell Biochem. Biophys. 41 2004 75 98
    • (2004) Cell Biochem. Biophys. , vol.41 , pp. 75-98
    • Lyubchenko, Y.L.1
  • 40
    • 0033548163 scopus 로고    scopus 로고
    • DNA-sequence asymmetry directs the alignment of recombination sites in the FLP synaptic complex
    • K.E. Huffman, and S.D. Levene DNA-sequence asymmetry directs the alignment of recombination sites in the FLP synaptic complex J. Mol. Biol. 286 1999 1 13
    • (1999) J. Mol. Biol. , vol.286 , pp. 1-13
    • Huffman, K.E.1    Levene, S.D.2
  • 41
    • 0037123778 scopus 로고    scopus 로고
    • Path of DNA within the Mu transpososome. Transposase interactions bridging two Mu ends and the enhancer trap five DNA supercoils
    • S. Pathania, M. Jayaram, and R.M. Harshey Path of DNA within the Mu transpososome. Transposase interactions bridging two Mu ends and the enhancer trap five DNA supercoils Cell 109 2002 425 436
    • (2002) Cell , vol.109 , pp. 425-436
    • Pathania, S.1    Jayaram, M.2    Harshey, R.M.3
  • 42
    • 84972274704 scopus 로고
    • A calculus for rational tangles: Applications to DNA recombination
    • C. Ernst, and D.W. Sumners A calculus for rational tangles: applications to DNA recombination Math. Proc. Cambridge Philos. Soc. 108 1990 489 515
    • (1990) Math. Proc. Cambridge Philos. Soc. , vol.108 , pp. 489-515
    • Ernst, C.1    Sumners, D.W.2
  • 43
    • 12544251405 scopus 로고    scopus 로고
    • Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway
    • M. Vazquez, S.D. Colloms, and D.W. Sumners Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway J. Mol. Biol. 346 2005 493 504
    • (2005) J. Mol. Biol. , vol.346 , pp. 493-504
    • Vazquez, M.1    Colloms, S.D.2    Sumners, D.W.3
  • 45
    • 0001931601 scopus 로고
    • Möbius energy of knots and unknots
    • M.H. Freedman, Z.-X. He, and Z. Wang Möbius energy of knots and unknots Ann. Math. 139 1994 1 50
    • (1994) Ann. Math. , vol.139 , pp. 1-50
    • Freedman, M.H.1    He, Z.-X.2    Wang, Z.3
  • 46
    • 1642334642 scopus 로고    scopus 로고
    • Quantization of energy and writhe in self-repelling knots
    • P. Hoidn, R.B. Kusner, and A. Stasiak Quantization of energy and writhe in self-repelling knots New J. Phys. 4 2002 20.1-20.11
    • (2002) New J. Phys. , vol.4
    • Hoidn, P.1    Kusner, R.B.2    Stasiak, A.3
  • 49
    • 0037974405 scopus 로고    scopus 로고
    • Entropy loss in long-distance DNA looping
    • A. Hanke, and R. Metzler Entropy loss in long-distance DNA looping Biophys. J. 85 2003 167 173
    • (2003) Biophys. J. , vol.85 , pp. 167-173
    • Hanke, A.1    Metzler, R.2
  • 51
    • 0033594916 scopus 로고    scopus 로고
    • Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse
    • F. Guo, D.N. Gopaul, and G.D. Van Duyne Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse Proc. Natl Acad. Sci. USA 96 1999 7143 7148
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 7143-7148
    • Guo, F.1    Gopaul, D.N.2    Van Duyne, G.D.3
  • 52
    • 0024509548 scopus 로고
    • FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending
    • C.J. Schwartz, and P.D. Sadowski FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending J. Mol. Biol. 205 1989 647 658
    • (1989) J. Mol. Biol. , vol.205 , pp. 647-658
    • Schwartz, C.J.1    Sadowski, P.D.2
  • 53
    • 13544266569 scopus 로고    scopus 로고
    • Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
    • J. Yu, T. Ha, and K. Schulten Conformational model of the Holliday junction transition deduced from molecular dynamics simulations Nucl. Acids Res. 32 2004 6683 6695
    • (2004) Nucl. Acids Res. , vol.32 , pp. 6683-6695
    • Yu, J.1    Ha, T.2    Schulten, K.3
  • 54
    • 0034685618 scopus 로고    scopus 로고
    • Geometry of site alignment during int family recombination: Antiparallel synapsis by the Flp recombinase
    • I. Grainge, D. Buck, and M. Jayaram Geometry of site alignment during int family recombination: antiparallel synapsis by the Flp recombinase J. Mol. Biol. 298 2000 749 764
    • (2000) J. Mol. Biol. , vol.298 , pp. 749-764
    • Grainge, I.1    Buck, D.2    Jayaram, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.