Structural dynamics of individual Holliday junctions

Nature Structural Biology

Volumn 10, Issue 2, 2003, Pages 93-97

  McKinney, Sean A ^a   Déclais, Anne Cécile ^b   Lilley, David M J ^b   Ha, Taekjip ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CELL JUNCTION; CELL MIGRATION; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA RECOMBINATION; DNA STRUCTURE; ENERGY; EQUILIBRIUM CONSTANT; FLUORESCENCE; GENE EXPRESSION; HOLLIDAY JUNCTION; HUMAN; MOLECULAR DYNAMICS; PHASE TRANSITION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SINGLE MOLECULE FLUORESCENCE; STRUCTURE ANALYSIS;

BASE SEQUENCE; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MODELS, GENETIC; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RECOMBINATION, GENETIC; THERMODYNAMICS;

EID: 0037315675     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb883     Document Type: Article

References (28)

1. Cox, M.M. et al. The importance of repairing stalled replication forks. Nature 404, 37-41 (2000).
2. Holliday, R. A mechanism for gene conversion in fungi. Genet. Res. 5, 282-304 (1964).
3. Potter, H. & Dressler, D. On the mechanism of genetic recombination: electron microscopic obervation of recombination intermediates. Proc. Natl. Acad. Sci. USA 73, 3000-3004 (1978).
4. Schwacha, A. & Kleckner, N. Identification of double Holliday junctions as intermediates in meiotic recombination. Cell 83, 783-791 (1995).
5. Lilley, D.M.J. & White, M.F. The junction-resolving enzymes. Nat. Rev. Mol. Cell. Biol. 2, 433-443 (2001).
6. Lilley, D.M.J. Structure of helical junctions in nucleic acids. Q. Rev. Biophys. 33, 109-159 (2000).
7. Clegg, R.M., Murchie, A.I.H. & Lilley, D.M.J. 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).
8. Duckett, D.R. et al. The structure of the Holliday junction, and its resolution. Cell 55, 79-89 (1988).
9. Murchie, A.I. et al. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763-766 (1989).
10. Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D. & Joyce, G.F. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nat. Struct. Biol. 6, 151-156 (1999).
11. Ortiz-Lombardia, M. et al. Crystal structure of a DNA Holliday junction. Nat. Struct. Biol. 6, 913-917 (1999).
12. Eichman, B.F., Vargason, J.M., Mooers, B.H.M. & Ho, P.S. The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proc. Natl. Acad. Sci. USA 97, 3971-3976 (2000).
13. Mueller, J.E., Kemper, 8., Cunningham, R.P., Kallenbach, N.R. & Seeman, N.C. T4 endonuclease VII cleaves the crossover strands of Holliday junction analogs. Proc. Natl. Acad. Sci. USA 85, 9441-9445 (1988).
14. Bennett, R.J. & West, S.C. RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands. Proc. Natl. Acad. Sci. USA 92, 5635-5639 (1995).
15. Miick, S.M., Fee, R.S., Millar, D.R & Chazin, W.J. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc. Natl. Acad. Sci. USA 94, 9080-9084 (1997).
16. Grainger, R.J., Murchie, A.I.H. & Lilley, D.M.J. Exchange between stacking conformers in a four-way DNA junction. Biochemistry 37, 23-32 (1998).
17. Chen, J.H., Churchill, M.E., Tullius, T.D., Kallenbach, N.R. & Seeman, N.C. Construction and analysis of monomobile DNA junctions. Biochemistry 27, 6032-6038 (1988).
18. Carlstrom, G. & Chazin, W.J. Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy. Biochemistry 35, 3534-3544 (1996).
19. Overmars, F.J.J. & Altona, C. NMR study of the exchange rate between two stacked conformers of a model Holliday junction. J. Mol. Biol. 273, 519-524 (1997).
20. Weiss, S. Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat. Struct. Biol. 7, 724-729 (2000).
21. Zhuang, X.W. et al. Correlating structural dynamics and function in single ribozyme molecules. Science 296, 1473-1476 (2002).
22. Ha, T. et al. Initiation and reinitiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419, 638-641 (2002).
23. Johnson, R.D. & Symington, L.S. Crossed-stranded DNA structures for investigating the molecular dynamics of the Holliday junction. J. Mol. Biol. 229, 812-820 (1993).
24. Panyutin, I.G. & Hsieh, P. The kinetics of spontaneous DNA branch migration. Proc. Natl. Acad. Sci. USA 91, 2021-2025 (1994).
25. Mulrooney, S.B., Fishel, R.A., Hejna, J.A. & Warner, R.C. Preparation of figure B and cruciform DNAs and their use in studies of the kinetics of branch migration. J. Biol. Chem. 271, 9648-9659 (1996).
26. Panyutin, I.G., Biswas, I. & Hsieh, P. A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J. 14, 1819-1826 (1995).
27. Parson, C.A., Stasiak, A., Bennett, R.J. & West, S.C. Structure of a multisubunit complex that promotes DNA branch migration. Nature 374, 375-378 (1995).
28. Ha, T.J. et al. Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proc. Natl. Acad. Sci. USA 96, 893-898 (1999).