Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 11, 2010, Pages 4985-4990

  Lee, Mina ^a   Kim, Sook Ho ^a   Hong, Seok Cheol ^a  

^a Korea University   (South Korea)

Author keywords

Magnetic tweezers; Single molecule FRET; Z DNA

Indexed keywords

CYTOSINE; DNA B; DNA Z; GUANINE;

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA STRUCTURE; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MAGNETISM; PRIORITY JOURNAL; TEMPERATURE; THERMODYNAMICS;

BASE COMPOSITION; BIOMECHANICS; DNA, Z-FORM; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; NUCLEIC ACID CONFORMATION; TEMPERATURE; TIME FACTORS; TORSION, MECHANICAL;

EID: 77950444848     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0911528107     Document Type: Article

References (40)

1. Rich A (1993) DNA comes in many forms. Gene 135:99-109.
2. Wells RD (2007) Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci 32:271-278.
3. Wang AH-J (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282:680-686.
4. Pohl FM, Jovin TM (1972) Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetics studies with poly(dG-dC). J Mol Biol 67:375-396.
5. Fuertes MA, Cepeda V, Alonso C, Pérez JM (2006) Molecular mechanisms for the B-Z transition in the example of poly[d(G-C) • d(G-C)] polymers. A critical review. Chem Rev 106:2045-2064.
6. Rich A, Nordheim A, Wang AH-J (1984) The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem 53:791-846.
7. Jovin TM, Soumpasis DM, McIntosh L (1987) The transition between B-DNA and Z-DNA. Annu Rev Phys Chem 38:521-560.
8. Nordheim A, et al. (1982) Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell 31:309-318.
9. Rahmouni AR,Wells RD (1989) Stabilization of Z-DNA in vivo by localized supercoiling. Science 246:358-363.
10. Wittig B, Dorbic T, Rich A (1989) The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain. J Cell Biol 108:755-764.
11. Rich A, Zhang S (2003) Z-DNA: The long road to biological function. Nat Rev Genet 4:566-572.
12. Lafer EM, Möller A, Nordheim A, Stollar BD, Rich A (1981) Antibodies specific for left-handed Z-DNA. Proc Natl Acad Sci USA 78:3546-3550.
13. Herbert A, Lowenhaupt K, Spitzner J, Rich A (1995) Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proc Natl Acad Sci USA 92:7550-7554.
14. Wittig B, Wölfl S, Dorbic T, Vahrson W, Rich A (1992) Transcription of human c-myc in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene. EMBO J 11:4653-4663.
15. Liu R, et al. (2001) Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 106:309-318.
16. Wang G, Vasquez KM (2007) Z-DNA, an active element in the genome. Front Biosci 12:4424-4438.
17. Anitha S, Rao KSJ, Latha KS, Viswamitra MA (2002) First evidence to show the topological change of DNA from B-DNA and Z-DNA conformation in the hippocampus of Alzheimer's brain. Neuromol Med 2:289-297.
18. Ha SC, Lowenhaupt K, Rich A, Kim Y-G, Kim KK (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437:1183-1186.
19. Peck LJ, Wang JC (1983) Energetics of B-to-Z transition in DNA. Proc Natl Acad Sci USA 80:6206-6210.
20. Lipps HJ, et al. (1983) Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate Stylonychia mytilus. Cell 32:435-441.
21. Shroff H, et al. (2005) Biocompatible force sensor with optical readout and dimensions of 6 nm3. Nano Lett 5:1509-1514.
22. Hohng S, et al. (2007) Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science 318:279-283.
23. Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5:507-516.
24. Selvin PR, Ha T (2008) Single-Molecule Techniques: A Laboratory Manual (Cold Spring Harbor, New York).
25. Nöllmann M, et al. (2007) Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol 14:264-271.
26. 5dC). Proc Natl Acad Sci USA 78:1619-1623.
27. Kypr J, Kejnovská I, Renčiuk D, Vorličková M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37:1713-1725.
28. Pohl FM (1986) Dynamics of the B-to-Z transition in supercoiled DNA. Proc Natl Acad Sci USA 83:4983-4987.
29. Peck LJ, Wang JC, Nordheim A, Rich A (1986) Rate of B to Z structural transition of supercoiled DNA. J Mol Biol 190:125-127.
30. Mosconi F, Allemand J-F, Bensimon D, Croquette V (2009) Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers. Phys Rev Lett 102:078301.
31. Charvin G, Allemand J-F, Strick TR, Bensimon D, Croquette V (2004) Twisting DNA: Single molecule studies. Contemp Phys 45:383-403.
32. McKinney SA, Joo C, Ha T (2006) Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys J 91:1941-1951.
33. Depew RE, Wang JC (1975) Conformational fluctuations of DNA helix. Proc Natl Acad Sci USA 72:4275-4279.
34. Marko JF (2007) Torque and dynamics of linking number relaxation in stretched supercoiled DNA. Phys Rev E 76:021926.
35. Strick TR, Allemand J-F, Croquette V, Bensimon D (2000) Twisting and stretching single DNA molecules. Prog Biophys Mol Biol 74:115-140.
36. Pulleyblank DE, Shure M, Tang D, Vinograd J, Vosberg H-P (1975) Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: Formation of a Boltzmann distribution of topological isomers. Proc Natl Acad Sci USA 72:4280-4284.
37. Harvey SC (1983) DNA structural dynamics: Longitudinal breathing as a possible mechanism for the B ↔ Z transition. Nucleic Acids Res 11:4867-4878.
38. Rasnik I, et al. (2008) Branch migration enzymes as a Brownian ratchet. EMBO J 27:1727-1735.
39. Schroth GP, Chou P-J, Ho PS (1992) Mapping Z-DNA in the human genome. J Biol Chem 267:11846-11855.
40. Park J-S, Hyon J-Y, Lee KJ, Hong S-C (2008) Temperature dependence of DNA elasticity and cisplatin activity studied with a temperature-controlled magnetic tweezers system. J Korean Phys Soc 52:1927-1931.