Single-molecule studies using magnetic traps

Cold Spring Harbor Protocols

Volumn 7, Issue 1, 2012, Pages 34-49

  Lionnet, Timothée ^a   Allemand, Jean François ^a   Revyakin, Andrey ^a   Strick, Terence R ^a   Saleh, Omar A ^a   Bensimon, David ^a   Croquette, Vincent ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; DOUBLE STRANDED DNA; RNA; RNA POLYMERASE; SINGLE STRANDED DNA; DNA; MICROSPHERE;

ANISOTROPY; ARTICLE; BASE PAIRING; CELL MANIPULATION; DNA BINDING; DNA DENATURATION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; DNA TEMPLATE; ELASTICITY; ENZYME ACTIVITY; ENZYME LINKED IMMUNOSORBENT ASSAY; EXCISION REPAIR; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE CONTROL; GENETIC DRIFT; GEOMETRY; ILLUMINATION; MAGNETIC FIELD; OPTICAL TWEEZERS; PROMOTER REGION; PROTEIN DNA INTERACTION; CHEMISTRY; MAGNETISM; METABOLISM; PROTEIN BINDING; REVIEW;

DNA; ELASTICITY; MAGNETICS; MICROSPHERES; PROTEIN BINDING;

EID: 84255189974     PISSN: 19403402     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top067488     Document Type: Article

References (59)

1. Ali BM, Amit R, Braslavsky I, Oppenheim AB, Gileadi O, Stavans J. 2001. Compaction of single DNA molecules induced by binding of integration host factor (IHF). Proc Natl Acad Sci 98: 10658-10663.
2. Allemand J-F, Bensimon D, Jullien L, Bensimon A, Croquette V. 1997. pH-dependent specific binding and combing of DNA. Biophys J 73: 2064-2070.
3. Allemand J-F, Bensimon D, Lavery R, Croquette V. 1998. Stretched and overwound DNA form a Pauling-like structure with exposed bases. Proc Natl Acad Sci 95: 14152-14157.
4. Amit R, Gileadi O, Stavans J. 2004. Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions. Proc Natl Acad Sci 101: 11605-11610.
5. Avery OT, MacLeod CM, McCarthy M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. I. Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus type III. J Exp Med 79: 137-158.
6. Berg-Sorensen K, Flyvbjerg H. 2004. Power spectrum analysis for optical tweezers. Rev Sci Instrum 75: 594-612.
7. Bouchiat C, Wang M, Block SM, Allemand J-F, Strick T, Croquette V. 1999. Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys J 76: 409-413.
8. Bracewell R. 1999. The Fourier transform and its applications, 3rd ed. McGraw-Hill, New York.
9. Bryant Z, Stone MD, Gore J, Smith SB, Cozzarelli NR, Bustamante C. 2003. Structural transitions and elasticity from torque measurements on DNA. Nature 424: 338-341.
10. Bustamante C, Marko J, Siggia E, Smith S. 1994. Entropic elasticity of λ-phage DNA. Science 265: 1599-1600.
11. Charvin G, Bensimon D, Croquette V. 2003. Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases. PNAS 100: 9820-9825.
12. Charvin G, Allemand J-F, Strick TR, Bensimon D, Croquette V. 2004. Twisting DNA: Single molecule studies. Contemp Phys 45: 383-403.
13. Charvin G, Strick TR, Bensimon D, Croquette V. 2005. Topoisomerase IV bends and overtwists DNA upon binding. Biophys J 89: 384-392.
14. Charvin G, Vologodskii A, Bensimon D, Croquette V. 2005. Braiding DNA: Experiments, simulations, and models. Biophys J 88: 4124-4136.
15. Chee M, Yang R, Hubbell E, Berno A, Huang X, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA. 1996. Accessing genetic information with high-density DNA arrays. Science 274: 610-614.
16. Danilowicz C, Coljee VW, Bouzigues C, Lubensky DK, Nelson DR, Prentiss M. 2003. DNA unzipped under a constant force exhibits multiple metastable intermediates. Proc Natl Acad Sci 100: 1694-1699.
17. Dawid A, Croquette V, Grigoriev M, Heslot F. 2004. Single-molecule study of RuvAB-mediated Holliday-junction migration. Proc Natl Acad Sci 101: 11611-11616.
18. Dessinges M-N, Lionnet T, Xi X, Bensimon D, Croquette V. 2004. Single molecule assay reveals strand switching and enhanced processivity of UvrD. Proc Natl Acad Sci 101: 6439-6444.
19. Einstein A. 1956. Investigation of the Brownian theory of movement, Dover Publications, New York.
20. Friese ME, Enger J, Rubinsztein-Dunlop H, Heckenberg NR. 1996. Optical angular-momentum transfer to trapped absorbing particles. Phys Rev A 54: 1593-1596.
21. Friese MEJ, Nieminen TA, Heckenberg NR, Rubinsztein-Dunlop H. 1998. Optical alignment and spinning of laser-trapped microscopic particles. Nature 394: 348-350.
22. Fulconis R, Bancaud A, Allemand JF, Croquette V, Dutreix M, Viovy JL. 2004. Twisting and untwisting a single DNA molecule covered by RecA protein. Biophys J 87: 2552-2563.
23. Gore J, Bryant Z, Stone MD, Nollmann M, Cozzarelli NR, Bustamante C. 2006. Mechanochemical analysis of DNA gyrase using rotor bead tracking. Nature 439: 100-104.
24. Gosse C, Croquette V. 2002. Magnetic tweezers: Micro-manipulation and force measurement at the molecular level. Biophys J 82: 3314-3329.
25. Hershey A, Chase M. 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 1: 39-56.
26. Koster DA, Croquette V, Dekker C, Shuman S, Dekker NH. 2005. Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase Ib. Nature 434: 671-674.
27. La Porta A, Wang MD. 2004. Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles. Phys Rev Lett 92: 190801.
28. Lee GU, Chrisey LA, Colton RJ. 1994. Direct measurement of the forces between complementary strands of DNA. Science 266: 771-773.
29. Leger JF, Romano G, Sarkar A, Robert J, Bourdieu L, Chatenay D, Marko JF. 1999. Structural transitions of a twisted and stretched DNA molecule. Phys Rev Lett 83: 1066-1069.
30. Leuba SH, Karymov MA, Tomschik M, Ramjit R, Smith P, Zlatanova J. 2003. Assembly of single chromatin fibers depends on the tension in the DNA molecule: Magnetic tweezers study. Proc Natl Acad Sci 100: 495-500.
31. Lia G, Bensimon D, Croquette V, Allemand JF, Dunlap D, Lewis DE, Adhya S, Finzi L. 2003. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci 100: 11373-11377.
32. Lia G, Praly E, Ferreira H, Stockdale C, Tse-Dinh YC, Dunlap D, Croquette V, Bensimon D, Owen-Hughes T. 2006. Direct observation of DNA distortion by the RSC complex. Mol Cell 21: 417-425.
33. Lionnet T, Joubaud S, Lavery R, Bensimon D, Croquette V. 2006. Wringing out DNA. Phys Rev Lett 96: 178102.
34. Lionnet T, Allemand J-F, Revyakin A, Strick TR, Saleh OA, Bensimon D, Croquette V. 2012. Magnetic trap construction. Cold Spring Harb Protoc doi: 10.1101/pdb.prot067496.
35. Maier B, Bensimon D, Croquette V. 2000. Replication by a single DNA polymerase of a stretched single stranded DNA. Proc Natl Acad Sci 97: 12002-12007.
36. Marko J, Siggia E. 1995. Stretching DNA. Macromolecules 28: 8759-8770.
37. Nieminen TA, Heckenberg NR, Rubinsztein-Dunlop H. 2001. Optical measurement of microscopic torques. J Mod Optics 48: 405-413.
38. Ovryn B. 2000. Three-dimensional forward scattering particle image velocimetry applied to a microscopic field-of-view. Exp Fluids 29: S175-S184.
39. Ovryn B, Izen SH. 2000. Imaging of transparent spheres through a planar interface using a high-numerical-aperture optical microscope. J Opt Soc Am A 17: 1202-1213.
40. Press WH, Teukolsky SA, Vetterling WT, Flannery PB. 1992. Numerical recipes in C: The art of scientific computing, 2nd ed. Cambridge University Press, London.
41. Reif F. 1965. Fundamentals of statistical and thermal physics, McGraw-Hill, New York.
42. Revyakin A, Allemand JF, Croquette V, Ebright RH, Strick TR. 2003. Single molecule DNA nanomanipulation: Detection of promoter-unwinding events by RNA polymerase. Methods Enzymol 370: 577-598.
43. Revyakin A, Ebright RH, Strick TR. 2005. Single-molecule DNA nanomanipulation: Improved resolution through use of shorter DNA fragments. Nat Methods 2: 127-138.
44. Revyakin A, Liu C, Ebright RH, Strick TR. 2006. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314: 1139-1143.
45. Saleh OA, Perals C, Barre FX, Allemand JF. 2004. Fast, DNA-sequence independent translocation by FtsK in a single-molecule experiment. EMBO J 23: 2430-2439.
46. Saleh OA, Bigot S, Barre FX, Allemand JF. 2005. Analysis of DNA supercoil induction by FtsK indicates translocation without groove-tracking. Nat Struct Mol Biol 12: 436-440.
47. Sano T, Smith CL, Cantor CR. 1992. Immuno-PCR: Very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 258: 120-122.
48. Seidel R, van Noort J, van der Scheer C, Bloom JG, Dekker NH, Dutta CF, Blundell A, Robinson T, Firman K, Dekker C. 2004. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I. Nat Struct Mol Biol 11: 838-843.
49. Shivashankar GV, Feingold M, Krichevsky O, Libchaber A. 1999. RecA polymerization on double-stranded DNA by using single-molecule manipulation: The role of ATP hydrolysis. Proc Natl Acad Sci 96: 7916-7921.
50. Smith DE, Tans SJ, Smith SB, Grimes S, Anderson DL, Bustamante C. 2001. The bacteriophage straight 29 portal motor can package DNA against a large internal force. Nature 413: 748-752.
51. Smith S, Finzi L, Bustamante C. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258: 1122-1126.
52. Strick T, Allemand J, Bensimon D, Bensimon A, Croquette V. 1996. The elasticity of a single supercoiled DNA molecule. Science 271: 1835-1837.
53. Strick T, Allemand J-F, Bensimon D, Croquette V. 1998. The behavior of supercoiled DNA. Biophys J 74: 2016-2028.
54. Strick T, Bensimon D, Croquette V. 1999. Micro-mechanical measurement of the torsional modulus of DNA. Genetica 106: 57-62.
55. Strick T, Croquette V, Bensimon D. 2000. Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature 404: 901-904.
56. Watson J, Crick F. 1953. Genetic implications of the structure of deoxyribonucleic acid. Nature 171: 964-967.
57. Watson J, Crick F. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171: 737-738.
58. Yan J, Skoko D, Marko JF. 2004. Near-field-magnetic-tweezermanipulation of single DNA molecules. Phys Rev E Stat Nonlin Soft Matter Phys 70: 011905.
59. Yang MS, Yau HCM, Chan HL. 1998. Adsorption kinetics and ligandbinding properties of thiol-modified double-stranded DNA on a gold surface. Langmuir 14: 6121-6129.