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Single-Molecule Mechanics of DNA

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DNA Nanotechnology
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Abstract

Mechanics is crucial for life. The single molecular mechanics of biomacromolecules lays the base of mechanical movements of organism. Here in this chapter, we will introduce the progress in single chain mechanics of DNA. The related studies are very important not only to the understanding of phenomena of life but also to the design and preparation of artificial nanomachines.

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References

  1. Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491–505

    Article  CAS  Google Scholar 

  2. Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258:1122–1126

    Article  CAS  Google Scholar 

  3. Gosse C, Croquette V (2002) Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys J 82:3314–3329

    Article  CAS  Google Scholar 

  4. Ashkin A (1970) Acceleration and trapping of particles by radiation pressure. Phys Rev Lett 24:156–159

    Article  CAS  Google Scholar 

  5. Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S (1986) Observation of a single-beam gradient force optical trap for dielectric particles. Opt Lett 11:288–290

    Article  CAS  Google Scholar 

  6. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933

    Article  Google Scholar 

  7. Florin E-L, Moy VT, Gaub HE (1994) Adhesion force between individual ligand-receptor pairs. Science 264:415–417

    Article  CAS  Google Scholar 

  8. Florin E, Rief M, Lehmann H, Ludwig M, Dornmair C, Moy V, Gaub HE (1995) Sensing specific molecular-interactions with the atomic-force microscope. Biosens Bioelectron 10(9–10):895–901

    Article  CAS  Google Scholar 

  9. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE (1997) Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276(5315):1109–1112

    Article  CAS  Google Scholar 

  10. Oesterhelt F, Rief M, Gaub HE (1999) Single molecule force spectroscopy by AFM indicates helical structure of poly(ethylene-glycol) in water. New J Phys 1:6.1

    Article  Google Scholar 

  11. Viani MB, Schaeffer TE, Chand A, Rief M, Gaub HE, Hansma PK (1999) Small cantilevers for force spectroscopy of single molecules. J Appl Phys 86:2258–2262

    Article  CAS  Google Scholar 

  12. Kuehner F, Gaub HE (2006) Modelling cantilever-based force spectroscopy with polymers. Polymer 47:2555–2563

    Article  CAS  Google Scholar 

  13. Janshoff A, Neitzert M, Oberdorfer Y, Fuchs H (2000) Force spectroscopy of molecular systems-single molecule spectroscopy of polymers and biomolecules. Angew Chem Int Ed 39:3212–3237

    Article  CAS  Google Scholar 

  14. Hugel T, Seitz M (2001) The study of molecular interactions by AFM force spectroscopy. Macromol Rapid Commun 22:989–1016

    Article  CAS  Google Scholar 

  15. Zhang WK, Zhang X (2003) Single molecule mechanochemistry of macromolecules. Prog Polym Sci 28:1271–1295

    Article  CAS  Google Scholar 

  16. Liu C, Shi W, Cui S, Wang Z, Zhang X (2005) Force spectroscopy of polymers: beyond single chain mechanics. Curr Opin Solid State Mater Sci 9:140–148

    Article  Google Scholar 

  17. Noy A (2011) Force spectroscopy 101: how to design, perform, and analyze an AFM-based single molecule force spectroscopy experiment. Curr Opin Chem Biol 15:710–718

    Article  CAS  Google Scholar 

  18. Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of lambda-phage DNA. Science 265(5178):1599–1600

    Article  CAS  Google Scholar 

  19. Smith S, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double stranded and single stranded DNA molecules. Science 271:795–799

    Article  CAS  Google Scholar 

  20. Wang MD, Yin H, Landick R, Gelles J, Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72:1335–1346

    Article  CAS  Google Scholar 

  21. Strick TR, Allemand J-F, Bensimon D, Croquette V (1998) Behavior of supercoiled DNA. Biophys J 74:2016–2028

    Article  CAS  Google Scholar 

  22. Baumann CG, Smith SB, Bloomfield VA, Bustamante C (1997) Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci U S A 94:6185–6190

    Article  CAS  Google Scholar 

  23. Flory P (1989) Statistical mechanics of chain molecules. Hanser, Munich

    Google Scholar 

  24. Cui S, Liu C, Wang Z, Zhang X, Strandman S, Tenhu H (2004) Single molecule force spectroscopy on polyelectrolytes: effect of spacer on adhesion force and linear charge density on rigidity. Macromolecules 37:946–953

    Article  CAS  Google Scholar 

  25. Mirkin SM (2001) DNA topology: fundamentals. In: Encyclopedia of life sciences. Nature Publishing Group, London

    Google Scholar 

  26. DNA supercoil. http://en.wikipedia.org/wiki/DNA_supercoil

  27. Strick TR, Allemand J-F, Bensimon D, Bensimon A, Croquette V (1996) The elasticity of a single supercoiled DNA molecule. Science 271:1835–1837

    Article  CAS  Google Scholar 

  28. Strick T, Allemand J-F, Bensimon D, Lavery R, Croquette V (1999) Phase coexistence in a single DNA molecule. Physica A 263(1–4):392–404

    Article  CAS  Google Scholar 

  29. 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

    Article  CAS  Google Scholar 

  30. Allemand JF, Bensimon D, Lavery R, Croquette V (1998) Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc Natl Acad Sci U S A 95:14152–14157

    Article  CAS  Google Scholar 

  31. Rief M, Clausen-Schaumann H, Gaub H (1999) Sequence-dependent mechanics of single DNA molecules. Nat Struct Biol 6(4):346–349

    Article  CAS  Google Scholar 

  32. Hugel T, Rief M, Seitz M, Gaub HE, Netz RR (2005) Highly stretched single polymers: atomic-force-microscope experiments versus Ab-initio theory. Phys Rev Lett 94:048301

    Article  Google Scholar 

  33. Cui S, Albrecht C, Kühner F, Gaub HE (2006) Weakly bound water molecules shorten single-stranded DNA. J Am Chem Soc 128(20):6636–6639

    Article  CAS  Google Scholar 

  34. Grandbois M, Beyer M, Rief M, Clausen-Schaumann H, Gaub HE (1999) How strong is a covalent bond? Science 283:1727–1730

    Article  CAS  Google Scholar 

  35. Cui S, Yu Y, Lin Z (2009) Modeling single chain elasticity of single-stranded DNA: a comparison of three models. Polymer 50:930–935

    Article  CAS  Google Scholar 

  36. Dessinges M-N, Maier B, Zhang Y, Peliti M, Bensimon D, Croquette V (2002) Stretching single stranded DNA, a model polyelectrolyte. Phys Rev Lett 89:248102

    Article  Google Scholar 

  37. Breslauer KJ, Frank R, Bloecker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A 83:3746–3750

    Article  CAS  Google Scholar 

  38. Liu C, Cui S, Wang Z, Zhang X (2005) Single-chain mechanical property of poly(N-vinyl-2-pyrrolidone) and interaction with small molecules. J Phys Chem B 109:14807–14812

    Article  CAS  Google Scholar 

  39. Cui S (2010) The possible roles of water in the prebiotic chemical evolution of DNA. Phys Chem Chem Phys 12:10147–10153

    Article  CAS  Google Scholar 

  40. Williams MC, Rouzina I, Bloomfield VA (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc Chem Res 35:159–166

    Article  CAS  Google Scholar 

  41. Cui S, Yu J, Kühner F, Schulten K, Gaub HE (2007) Double stranded DNA dissociates into single strands when dragged into a poor solvent. J Am Chem Soc 129:14710–14716

    Article  CAS  Google Scholar 

  42. Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub HE (2000) Mechanical stability of single DNA molecules. Biophys J 78(4):1997–2007

    Article  CAS  Google Scholar 

  43. Rouzina I, Bloomfield VA (2001) Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys J 80:882–893

    Article  CAS  Google Scholar 

  44. Rouzina I, Bloomfield VA (2001) Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophys J 80:894–900

    Article  CAS  Google Scholar 

  45. Tanaka K, Okahata Y (1996) A DNA -lipid complex in organic media and formation of an aligned cast film. J Am Chem Soc 118(44):10679–10683

    Article  CAS  Google Scholar 

  46. Bonner G, Klibanov AM (2000) Structural stability of DNA in nonaqueous solvents. Biotechnol Bioeng 68(3):339–344

    Article  CAS  Google Scholar 

  47. Fang Y, Spisz TS, Hoh JH (1999) Ethanol-induced structural transitions of DNA on mica. Nucleic Acids Res 27:1943–1949

    Article  CAS  Google Scholar 

  48. Pereira GG, Williams DRM (2001) Toroidal condensates of semiflexible polymers in poor solvents: adsorption, stretching, and compression. Biophys J 80:161–168

    Article  CAS  Google Scholar 

  49. Montesi A, Pasquali M, MacKintosh FC (2004) Collapse of a semiflexible polymer in poor solvent. Phys Rev E 69:021916

    Article  Google Scholar 

  50. Bloomfield VA, Crothers DM, Tinoco I (2000) Nucleic acids: structures, properties, and functions. University Science, Sausalito, CA

    Google Scholar 

  51. Essevaz-Roulet B, Bockelmann U, Heslot F (1997) Mechanical separation of the complementary strands of DNA. Proc Natl Acad Sci U S A 94:11935–11940

    Article  CAS  Google Scholar 

  52. Krautbauer R, Rief M, Gaub HE (2003) Unzipping DNA oligomers. Nano Lett 3:493–496

    Article  CAS  Google Scholar 

  53. Strunz T, Oroszlan K, Schäfer R, Güntherodt H-J (1999) Dynamic force spectroscopy of single DNA molecules. Proc Natl Acad Sci U S A 96:11277–11282

    Article  CAS  Google Scholar 

  54. Albrecht CH, Neuert G, Lugmaier RA, Gaub HE (2008) Molecular force balance measurements reveal that double-stranded DNA unbinds under force in rate-dependent pathways. Biophys J 94:4766–4774

    Article  CAS  Google Scholar 

  55. Liu C, Jiang Z, Zhang Y, Wang Z, Zhang X, Feng F, Wang S (2007) Intercalation interactions between dsDNA and acridine studied by single molecule force spectroscopy. Langmuir 23:9140–9142

    Article  CAS  Google Scholar 

  56. Kuehner F, Erdmann M, Sonnenberg L, Serr A, Morfill J, Gaub HE (2006) Friction of single polymers at surfaces. Langmuir 22:11180–11186

    Article  CAS  Google Scholar 

  57. Manohar S, Mantz AR, Bancroft KE, Hui C-Y, Jagota A, Vezenov DV (2008) Peeling single stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy. Nano Lett 8:4365–4372

    Article  CAS  Google Scholar 

  58. Sowerby SJ, Cohn CA, Heckl WM, Holm NG (2001) Differential adsorption of nucleic acid bases: relevance to the origin of life. Proc Natl Acad Sci U S A 98:820–822

    Article  CAS  Google Scholar 

  59. Lulevich V, Kim S, Grigoropoulos CP, Noy A (2011) Frictionless sliding of single-stranded DNA in a carbon nanotube pore observed by single molecule force spectroscopy. Nano Lett 11:1171–1176

    Article  CAS  Google Scholar 

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Correspondence to Shuxun Cui .

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Cui, S. (2013). Single-Molecule Mechanics of DNA. In: Fan, C. (eds) DNA Nanotechnology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36077-0_6

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