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
Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491–505
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
Gosse C, Croquette V (2002) Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophys J 82:3314–3329
Ashkin A (1970) Acceleration and trapping of particles by radiation pressure. Phys Rev Lett 24:156–159
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
Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56:930–933
Florin E-L, Moy VT, Gaub HE (1994) Adhesion force between individual ligand-receptor pairs. Science 264:415–417
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
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
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
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
Kuehner F, Gaub HE (2006) Modelling cantilever-based force spectroscopy with polymers. Polymer 47:2555–2563
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
Hugel T, Seitz M (2001) The study of molecular interactions by AFM force spectroscopy. Macromol Rapid Commun 22:989–1016
Zhang WK, Zhang X (2003) Single molecule mechanochemistry of macromolecules. Prog Polym Sci 28:1271–1295
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
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
Bustamante C, Marko JF, Siggia ED, Smith S (1994) Entropic elasticity of lambda-phage DNA. Science 265(5178):1599–1600
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
Wang MD, Yin H, Landick R, Gelles J, Block SM (1997) Stretching DNA with optical tweezers. Biophys J 72:1335–1346
Strick TR, Allemand J-F, Bensimon D, Croquette V (1998) Behavior of supercoiled DNA. Biophys J 74:2016–2028
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
Flory P (1989) Statistical mechanics of chain molecules. Hanser, Munich
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
Mirkin SM (2001) DNA topology: fundamentals. In: Encyclopedia of life sciences. Nature Publishing Group, London
DNA supercoil. http://en.wikipedia.org/wiki/DNA_supercoil
Strick TR, Allemand J-F, Bensimon D, Bensimon A, Croquette V (1996) The elasticity of a single supercoiled DNA molecule. Science 271:1835–1837
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
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
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
Rief M, Clausen-Schaumann H, Gaub H (1999) Sequence-dependent mechanics of single DNA molecules. Nat Struct Biol 6(4):346–349
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
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
Grandbois M, Beyer M, Rief M, Clausen-Schaumann H, Gaub HE (1999) How strong is a covalent bond? Science 283:1727–1730
Cui S, Yu Y, Lin Z (2009) Modeling single chain elasticity of single-stranded DNA: a comparison of three models. Polymer 50:930–935
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
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
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
Cui S (2010) The possible roles of water in the prebiotic chemical evolution of DNA. Phys Chem Chem Phys 12:10147–10153
Williams MC, Rouzina I, Bloomfield VA (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc Chem Res 35:159–166
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
Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub HE (2000) Mechanical stability of single DNA molecules. Biophys J 78(4):1997–2007
Rouzina I, Bloomfield VA (2001) Force-induced melting of the DNA double helix 1. Thermodynamic analysis. Biophys J 80:882–893
Rouzina I, Bloomfield VA (2001) Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophys J 80:894–900
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
Bonner G, Klibanov AM (2000) Structural stability of DNA in nonaqueous solvents. Biotechnol Bioeng 68(3):339–344
Fang Y, Spisz TS, Hoh JH (1999) Ethanol-induced structural transitions of DNA on mica. Nucleic Acids Res 27:1943–1949
Pereira GG, Williams DRM (2001) Toroidal condensates of semiflexible polymers in poor solvents: adsorption, stretching, and compression. Biophys J 80:161–168
Montesi A, Pasquali M, MacKintosh FC (2004) Collapse of a semiflexible polymer in poor solvent. Phys Rev E 69:021916
Bloomfield VA, Crothers DM, Tinoco I (2000) Nucleic acids: structures, properties, and functions. University Science, Sausalito, CA
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
Krautbauer R, Rief M, Gaub HE (2003) Unzipping DNA oligomers. Nano Lett 3:493–496
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
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
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
Kuehner F, Erdmann M, Sonnenberg L, Serr A, Morfill J, Gaub HE (2006) Friction of single polymers at surfaces. Langmuir 22:11180–11186
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
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
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
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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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DOI: https://doi.org/10.1007/978-3-642-36077-0_6
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