Molecular dynamics simulation of peeling a DNA molecule on substrate
Tóm tắt
Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.
Tài liệu tham khảo
Bruchez, M, Moronne, M, Gin, P, Weiss, S, Alivisatos, AP: Semiconductor nanocrystals as fluorescent biological labels. Science, 281: 2013–2016 (1998)
Chan, W, Nie, S: Quantum dot bioconjugates for ultrasensitive nonisotopic detection. Science, 281: 2016–2018 (1998)
Wong, SS, Joselevich, E, Woolley, AT, Cheung, CL, Lieber, CM: Covalently functionalised nanotubes as nanometre-sized probes in chemistry and biology. Nature, 394: 52–55 (1998)
Taton, T, Mirkin, C, Letsinger, R: Scanometric DNA array detection with nanoparticle probes. Science, 289: 1757–1760 (2000)
Cui, Y, Wei, Q, Park, H, Lieber, CM: Nanowire nanosensors for highly sensitive and selective detection of biological and chemical species. Science, 293: 1289–1292 (2001)
Qi, P, Vermesh, O, Grecu, M, Javey, A, Wang, Q, Dai, H: Toward large arrays of multiplex functionalized carbon nanotube sensors for highly sensitive and selective molecular detection. Nano Lett, 3: 347–351 (2003)
Miemeyer, CM: Nanoparticles, proteins, and nucleic acids: biotechnology meets materials science. Angew Chem Int Ed, 40: 4128–4158 (2001)
Martin, CR, Kohli, P: The emerging field of nanotube biotechnology. Nature Reviews Drug Discovery, 2: 29–37 (2003)
Bashir, R: DNA-mediated artificial nanobiostructures: state of the art and future directions. Superlattice and Microstructures, 29: 1–16 (2001)
Xin, H, Woolley, AT: DNA-templated nanotube localization. J Am Chem Soc, 125: 8710–8711 (2003)
Reches, M, Gazit, E: Casting metal nanowires within discrete self-assembled peptide nanotubes. Science, 300: 625–627 (2003)
Kendall, K: Thin-film peeling the elastic term. J Phys D: Appl Phys, 8: 1449–1452 (1975)
Kendall, K: The adhesion and surface energy of elastic solids. J Phys D: Appl Phys, 4: 1186–1195 (1971)
Kendall, K: Transition between cohesive and interfacial failure in a laminate. Proc R Soc A, 344: 287–302 (1975)
Lindley, PB: Ozone attack at a rubber-metal bond. J Instn Rubb Ind, 5(6): 243–248 (1971)
MacKerell, Jr AD, Wi-rkiewicz-Kuczera, J, Karplus, M: An all-atom empirical energy function for the simulation of nucleic acids. J Am Chem Soc, 117: 11946–11975 (1995)
Brooks, BR, Bruccoleri, RE, Olafson, BD, States, DJ, Swaminathan, S, Karplus, M: CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J Comp Chem, 4: 187–217 (1983)
Rappé, AK, Casewit, CJ, Colwell, KS, Goddard, III WA, Skiff, WM: UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc, 114: 10024–10035 (1992)
Walther, JH, Jaffe, R, Halicioglu, Koumoutsakos, P: Carbon nanotubes in water: structural characteristics and energetics. J Phys Chem B, 105: 9980–9987 (2001)
van der Spoel, D et al.: GROMACS user manual, version 3.1.1. Groningen, The Netherlands.
Jorgensen, WL, Chandrasekhar, J, Madura, JD, Impey, RW, Klein, ML: Comparison of simple potential functions for simulating liquid water. J Chem Phys, 79: 926–935 (1983)
Ryckaert, JP, Cicotti, G, Berensden, HJC: Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comp Phys, 23: 327–341 (1977)
Honeycutt, RW: The potential calculation and some applications. Methods in Computational Physics, 9: 136–211 (1970)
Grubmüller, H, Heymann, B, Tavan, P: Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science, 271: 997–999 (1996)
Heymann, B, Grubmüller, H: AN02/DNP-hapten unbinding forces studied by molecular dynamics atomic force microscopy simulations. Chem Phys Lett, 303: 1–9 (1999)
Izrailev, S, Stepaniants, S, Balsera, M, Ono, Y, Schulten, K: Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys J, 72: 1568–1581 (1997)
Marrink, SJ, Berger, O, Tieleman, P, Jähnig, F: Adhesion forces of lipids in a phospholipid membrand studied by molecular dynamics simulations. Biophys J, 74: 931–943 (1998)
Evans, E, Ritchrie, K: Dynamic strength of molecular adhesion bonds. Biophys J, 72: 1541–1555 (1997)
Merkel, R, Nassoy, P, Leung, A, Ritchrie, K, Evans, E: Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature, 397: 50–53 (1999)
Humphrey, W, Dalke, A, Schulten, K: VMD-visual molecular dynamics. J Molecular Graphics, 14: 33–38 (1996)
Edelwirth, M, Freund, J, Sowerby, SJ, Heckl, WM: Molecular mechanics study of hydrogen bonded self-assembled adenine monolayers on graphite. Surf. Sci, 417: 201–209 (1998)
Smith, S, Cui, Y, Bustamante, C: Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271: 795–799 (1996)
Wuite, G, Smith, S, Young, M, Keller, D, Bustamante, C: Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature, 404: 103–106 (2000)
Maier, B, Bensimon, D, Croquette, V: Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc Natl Acad Sci USA, 97: 12002–12007 (2000)
Dessinges, MN, Maier, B, Peliti, M, Bensimon, D, Croquette, V: Stretching single stranded DNA, a model polyelectrolyte. Phys Rev Lett, 89: 248102 (2002)
Bell, G: Models for the specific adhesion of cells to cells. Science, 200: 618–627 (1978)