메뉴 건너뛰기




Volumn 86, Issue 5, 2004, Pages 3060-3069

Low-Resolution Reconstruction of a Synthetic DNA Holliday Junction

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM ION;

EID: 2142762521     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74355-6     Document Type: Article
Times cited : (20)

References (48)
  • 1
    • 0037215706 scopus 로고    scopus 로고
    • 19 Å solution structure of the filarial nematode immunomodulatory protein, ES-62
    • Ackerman, C., M. Harnett, W. Harnett, S. Kelly, D. Svergun, and O. Byron. 2003. 19 Å solution structure of the filarial nematode immunomodulatory protein, ES-62. Biophys. J. 84:489-500.
    • (2003) Biophys. J. , vol.84 , pp. 489-500
    • Ackerman, C.1    Harnett, M.2    Harnett, W.3    Kelly, S.4    Svergun, D.5    Byron, O.6
  • 2
    • 1542592156 scopus 로고
    • Occurrence of crossed strand-exchange forms in yeast DNA during meiosis
    • Bell, L., and B. Byers. 1979. Occurrence of crossed strand-exchange forms in yeast DNA during meiosis. Proc. Natl. Acad. Sci. USA. 76:3445-3449.
    • (1979) Proc. Natl. Acad. Sci. USA , vol.76 , pp. 3445-3449
    • Bell, L.1    Byers, B.2
  • 3
    • 0024584528 scopus 로고
    • Specific recognition of cruciform DNA by nuclear-protein HMGI
    • Bianchi, M., M. Beltrame, and G. Paonessa. 1989. Specific recognition of cruciform DNA by nuclear-protein HMGI. Science. 243:1056-1059.
    • (1989) Science , vol.243 , pp. 1056-1059
    • Bianchi, M.1    Beltrame, M.2    Paonessa, G.3
  • 4
    • 0024033744 scopus 로고
    • Data acquisition systems for linear and area x-ray detectors using delay-line readout
    • Boulin, C., R. Kempf, A. Gabriel, and M. Koch. 1988. Data acquisition systems for linear and area x-ray detectors using delay-line readout. Nucl. Instr. Meth. Phys. Res. 269:312-320.
    • (1988) Nucl. Instr. Meth. Phys. Res. , vol.269 , pp. 312-320
    • Boulin, C.1    Kempf, R.2    Gabriel, A.3    Koch, M.4
  • 6
    • 0034705330 scopus 로고    scopus 로고
    • Reconstruction of protein form with x-ray solution scattering and a genetic algorithm
    • Chacón, P., J. Diaz, F. Moran, and J. Andreu. 2000. Reconstruction of protein form with x-ray solution scattering and a genetic algorithm. J. Mol. Biol. 299:1289-1302.
    • (2000) J. Mol. Biol. , vol.299 , pp. 1289-1302
    • Chacón, P.1    Diaz, J.2    Moran, F.3    Andreu, J.4
  • 7
    • 0031807272 scopus 로고    scopus 로고
    • Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm
    • Chacón, P., F. Moran, J. Diaz, E. Pantos, and J. Andreu. 1998. Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm. Biophys. J. 74:2760-2775.
    • (1998) Biophys. J. , vol.74 , pp. 2760-2775
    • Chacón, P.1    Moran, F.2    Diaz, J.3    Pantos, E.4    Andreu, J.5
  • 8
    • 0032573536 scopus 로고    scopus 로고
    • A synthetic Holliday junction is sandwiched between two tetrameric Mycobacterium leprae RuvA structures in solution: New insights from neutron scattering contrast variation and modelling
    • Chamberlain, D., A. Keeley, M. Aslam, J. Arenas-Licea, T. Brown, I. Tsaneva, and S. Perkins. 1998. A synthetic Holliday junction is sandwiched between two tetrameric Mycobacterium leprae RuvA structures in solution: new insights from neutron scattering contrast variation and modelling. J. Mol. Biol. 284:385-400.
    • (1998) J. Mol. Biol. , vol.284 , pp. 385-400
    • Chamberlain, D.1    Keeley, A.2    Aslam, M.3    Arenas-Licea, J.4    Brown, T.5    Tsaneva, I.6    Perkins, S.7
  • 9
    • 0027976675 scopus 로고
    • The solution structure of the four-way DNA junction at low-salt conditions: A fluorescence resonance energy transfer analysis
    • Clegg, R., A. Murchie, and D. Lilley. 1994. The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis. Biophys. J. 66:99-109.
    • (1994) Biophys. J. , vol.66 , pp. 99-109
    • Clegg, R.1    Murchie, A.2    Lilley, D.3
  • 12
    • 0035798378 scopus 로고    scopus 로고
    • Distortion of DNA junctions imposed by the binding of resolving enzymes: A fluorescence study
    • Fogg, J., M. Kvaratskhelia, M. White, and D. Lilley. 2001. Distortion of DNA junctions imposed by the binding of resolving enzymes: a fluorescence study. J. Mol. Biol. 313:751-764.
    • (2001) J. Mol. Biol. , vol.313 , pp. 751-764
    • Fogg, J.1    Kvaratskhelia, M.2    White, M.3    Lilley, D.4
  • 13
    • 0034613196 scopus 로고    scopus 로고
    • Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron x-ray solution scattering
    • Funari, S., G. Rapp, M. Perbandt, K. Dierks, M. Vallazza, C. Betzel, V. Erdmann, and D. Svergun. 2000. Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron x-ray solution scattering. J. Biol. Chem. 274:31283-31288.
    • (2000) J. Biol. Chem. , vol.274 , pp. 31283-31288
    • Funari, S.1    Rapp, G.2    Perbandt, M.3    Dierks, K.4    Vallazza, M.5    Betzel, C.6    Erdmann, V.7    Svergun, D.8
  • 14
    • 0023057852 scopus 로고
    • Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate
    • Furlong, J., and D. Lilley. 1986. Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate. Nucleic Acids Res. 14:3995-4007.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 3995-4007
    • Furlong, J.1    Lilley, D.2
  • 15
    • 0001229341 scopus 로고    scopus 로고
    • Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
    • García de la Torre, J., M. Huertas, and B. Carrasco. 2000. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J. 78:719-730.
    • (2000) Biophys. J. , vol.78 , pp. 719-730
    • García De La Torre, J.1    Huertas, M.2    Carrasco, B.3
  • 18
    • 0021997474 scopus 로고
    • DNA bending induced by cruciform formation
    • Gough, G., and D. Lilley. 1985. DNA bending induced by cruciform formation. Nature. 313:154-156.
    • (1985) Nature , vol.313 , pp. 154-156
    • Gough, G.1    Lilley, D.2
  • 19
    • 0022567761 scopus 로고
    • The structure of cruciforms in supercoiled DNA: Probing the single-stranded character of nucleotide bases with bisulphite
    • Gough, G., K. Sullivan, and D. Lilley. 1986. The structure of cruciforms in supercoiled DNA: probing the single-stranded character of nucleotide bases with bisulphite. EMBO J. 5:191-196.
    • (1986) EMBO J. , vol.5 , pp. 191-196
    • Gough, G.1    Sullivan, K.2    Lilley, D.3
  • 20
    • 0034195218 scopus 로고    scopus 로고
    • Partners and pathways-repairing a double-strand break
    • Haber, J. E. 2000. Partners and pathways-repairing a double-strand break. Trends Genet. 16:259-264.
    • (2000) Trends Genet. , vol.16 , pp. 259-264
    • Haber, J.E.1
  • 21
    • 84959678845 scopus 로고
    • A mechanism for gene conversion in fungi
    • Holliday, R. 1964. A mechanism for gene conversion in fungi. Genet. Res. 5:282-304.
    • (1964) Genet. Res. , vol.5 , pp. 282-304
    • Holliday, R.1
  • 23
    • 0023179984 scopus 로고
    • Homology-dependent interactions in phage-A site-specific recombination
    • Kitts, P., and H. Nash. 1987. Homology-dependent interactions in phage-A site-specific recombination. Nature. 329:346-348.
    • (1987) Nature , vol.329 , pp. 346-348
    • Kitts, P.1    Nash, H.2
  • 24
    • 0020114103 scopus 로고
    • X-ray diffraction and scattering on disordered systems using synchrotron radiation
    • Koch, M., and J. Bordas. 1983. X-ray diffraction and scattering on disordered systems using synchrotron radiation. Nucl. Instrum. Meth. Phys. Res. 208:461-469.
    • (1983) Nucl. Instrum. Meth. Phys. Res. , vol.208 , pp. 461-469
    • Koch, M.1    Bordas, J.2
  • 25
    • 0141484613 scopus 로고    scopus 로고
    • PRIMUS: A Windows PC-based system for small-angle scattering data analysis
    • Konarev, P., V. Volkov, A. Sokolova, M. Koch, and D. Svergun. 2003. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36:1277-1282.
    • (2003) J. Appl. Crystallogr. , vol.36 , pp. 1277-1282
    • Konarev, P.1    Volkov, V.2    Sokolova, A.3    Koch, M.4    Svergun, D.5
  • 26
    • 0025606724 scopus 로고
    • Large-scale preparation of T4 endonuclease VII from over-expressing bacteria
    • Kosak, H., and B. Kemper. 1990. Large-scale preparation of T4 endonuclease VII from over-expressing bacteria. Eur. J. Biochem. 194:779-784.
    • (1990) Eur. J. Biochem. , vol.194 , pp. 779-784
    • Kosak, H.1    Kemper, B.2
  • 27
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.2
  • 28
    • 0019087696 scopus 로고
    • The inverted repeat as a recognizable structural feature in supercoiled DNA molecules
    • Lilley, D. 1980. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA. 77:6468-6472.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 6468-6472
    • Lilley, D.1
  • 29
    • 0027486238 scopus 로고
    • The structure of branched DNA species
    • Lilley, D., and R. Clegg. 1993. The structure of branched DNA species. Q. Rev. Biophys. 26:131-175.
    • (1993) Q. Rev. Biophys. , vol.26 , pp. 131-175
    • Lilley, D.1    Clegg, R.2
  • 30
    • 0028349558 scopus 로고
    • Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo
    • McCulloch, R., L. Coggins, S. Colloms, and D. Sherratt. 1994. Xer-mediated site-specific recombination at cer generates Holliday junctions in vivo. EMBO J. 13:1344-1355.
    • (1994) EMBO J. , vol.13 , pp. 1344-1355
    • McCulloch, R.1    Coggins, L.2    Colloms, S.3    Sherratt, D.4
  • 31
    • 0019350114 scopus 로고
    • Cruciform structures in supercoiled DNA
    • Panayotatos, N., and R. Wells. 1981. Cruciform structures in supercoiled DNA. Nature. 289:466-470.
    • (1981) Nature , vol.289 , pp. 466-470
    • Panayotatos, N.1    Wells, R.2
  • 32
    • 84990419571 scopus 로고
    • Improved technique for calculating x-ray scattering intensity of biopolymers in solution-evaluation of the form, volume and surface of a particle
    • Pavlov, M., and B. Fedorov. 1983. Improved technique for calculating x-ray scattering intensity of biopolymers in solution-evaluation of the form, volume and surface of a particle. Biopolymers. 22:1507-1522.
    • (1983) Biopolymers , vol.22 , pp. 1507-1522
    • Pavlov, M.1    Fedorov, B.2
  • 33
    • 0036930752 scopus 로고    scopus 로고
    • Addition of missing loops and domains to protein models using x-ray solution scattering
    • Petoukhov, N., M. V. Eady, K. Brown, and D. Svergun. 2002. Addition of missing loops and domains to protein models using x-ray solution scattering. Biophys. J. 83:3113-3125.
    • (2002) Biophys. J. , vol.83 , pp. 3113-3125
    • Petoukhov, N.1    Eady, M.V.2    Brown, K.3    Svergun, D.4
  • 35
    • 0034009520 scopus 로고    scopus 로고
    • Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling
    • Schuck, P. 2000. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78:1606-1619.
    • (2000) Biophys. J. , vol.78 , pp. 1606-1619
    • Schuck, P.1
  • 36
    • 0028972024 scopus 로고
    • Identification of double Holliday junctions as intermediates in meiotic recombination
    • Schwacha, A., and N. Kleckner. 1995. Identification of double Holliday junctions as intermediates in meiotic recombination. Cell. 83:783-791.
    • (1995) Cell , vol.83 , pp. 783-791
    • Schwacha, A.1    Kleckner, N.2
  • 38
    • 0015527750 scopus 로고
    • Genetic recombination: The nature of a crossed strand-exchange between two homologous DNA molecules
    • Sigal, N., and B. Alberts. 1972. Genetic recombination: the nature of a crossed strand-exchange between two homologous DNA molecules. J. Mol. Biol. 71:789-793.
    • (1972) J. Mol. Biol. , vol.71 , pp. 789-793
    • Sigal, N.1    Alberts, B.2
  • 39
    • 0015402078 scopus 로고
    • Molecular mechanism for genetic recombination
    • Sobell, H. 1972. Molecular mechanism for genetic recombination. Proc. Natl. Acad. Sci. USA. 59:2483-2487.
    • (1972) Proc. Natl. Acad. Sci. USA , vol.59 , pp. 2483-2487
    • Sobell, H.1
  • 40
    • 65449121560 scopus 로고
    • Ein neues Verfahren zur Bestimmung der Oberflaechenform und der inneren Struktur von geloesten globularen Proteinen aus Roentggenkleinwinkelmessungen
    • Stuhrmann, H. B. 1970. Ein neues Verfahren zur Bestimmung der Oberflaechenform und der inneren Struktur von geloesten globularen Proteinen aus Roentggenkleinwinkelmessungen. Zeitschr. Physik. Chem. Neue Folge. 72:177-198.
    • (1970) Zeitschr. Physik. Chem. Neue Folge , vol.72 , pp. 177-198
    • Stuhrmann, H.B.1
  • 41
    • 0026910457 scopus 로고
    • Determination of the regularisation parameter in indirect transform using perceptual criteria
    • Svergun, D. 1992. Determination of the regularisation parameter in indirect transform using perceptual criteria. J. Appl. Crystallogr. 25:495-503.
    • (1992) J. Appl. Crystallogr. , vol.25 , pp. 495-503
    • Svergun, D.1
  • 42
    • 0033001996 scopus 로고    scopus 로고
    • Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
    • Svergun, D. 1999. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76:2879-2886.
    • (1999) Biophys. J. , vol.76 , pp. 2879-2886
    • Svergun, D.1
  • 43
    • 0029185933 scopus 로고
    • CRYSOL-a program to evaluate x-ray solution scattering of biological macromolecules from atomic structures
    • Svergun, D., C. Barberato, and M. Koch. 1995. CRYSOL-a program to evaluate x-ray solution scattering of biological macromolecules from atomic structures. J. Appl. Crystallogr. 28:768-773.
    • (1995) J. Appl. Crystallogr. , vol.28 , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.3
  • 44
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from x-ray solution scattering
    • Svergun, D., M. Petoukhov, and M. Koch. 2001. Determination of domain structure of proteins from x-ray solution scattering. Biophys. J. 80:2946-2953.
    • (2001) Biophys. J. , vol.80 , pp. 2946-2953
    • Svergun, D.1    Petoukhov, M.2    Koch, M.3
  • 45
    • 0028023784 scopus 로고
    • Nucleic acid modeling tool (NAMOT): An interactive graphic tool for modeling nucleic acid structures
    • Tung, C., and E. Carter. 1994. Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. Comput. Appl. Biosci. 10:427-433.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 427-433
    • Tung, C.1    Carter, E.2
  • 46
    • 0022407077 scopus 로고
    • NMR analysis of DNA junctions: Amino proton NMR studies of individual arms and intact junction
    • Wemmer, D., A. Wand, N. Seeman, and N. Kallenbach. 1985. NMR analysis of DNA junctions: amino proton NMR studies of individual arms and intact junction. Biochemistry. 24:5745-5749.
    • (1985) Biochemistry , vol.24 , pp. 5745-5749
    • Wemmer, D.1    Wand, A.2    Seeman, N.3    Kallenbach, N.4
  • 47
    • 0031588022 scopus 로고    scopus 로고
    • Recognition and manipulation of branched DNA structure by junction-resolving enzymes
    • White, M., M. Giraud-Panis, J. Pohler, and D. Lilley. 1997. Recognition and manipulation of branched DNA structure by junction-resolving enzymes. J. Mol. Biol. 269:647-664.
    • (1997) J. Mol. Biol. , vol.269 , pp. 647-664
    • White, M.1    Giraud-Panis, M.2    Pohler, J.3    Lilley, D.4
  • 48
    • 0032545184 scopus 로고    scopus 로고
    • Self-organizing neural networks bridge the biomolecular resolution gap
    • Wriggers, W., R. Milligan, K. Schulten, and J. McCammon. 1998. Self-organizing neural networks bridge the biomolecular resolution gap. J. Mol. Biol. 284:1247-1254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1247-1254
    • Wriggers, W.1    Milligan, R.2    Schulten, K.3    McCammon, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.