Restricted access
Articles
ArticlesConfined dynamics of a single DNA molecule
Published:13 June 2011https://doi.org/10.1098/rsta.2011.0096
Abstract
The effect of a slit-like confinement on the relaxation dynamics of DNA is studied via a mesoscale model in which a bead and spring model for the polymer is coupled to a particle-based Navier–Stokes solver (multi-particle collision dynamics). The confinement is found to affect the equilibrium stretch of the chain when the bulk gyration radius is comparable to or smaller than the channel height and our data are in agreement with the (Rg,bulk/h)1/4 scaling of the polymer extension in the wall tangential direction. Relaxation simulation at different confinements indicates that, while the overall behaviour of the relaxation dynamics is similar for low and strong confinements, a small, but significant, slowing of the far-equilibrium relaxation is found as the confinement increases.
References
- 1
Balducci A., Mao P., Han J.& Doyle P. S. . 2006Double-stranded DNA diffusion in slitlike nanochannels. Macromolecules 39, 6273-6281doi:10.1021/ma061047t (doi:10.1021/ma061047t). Crossref, ISI, Google Scholar - 2
Chen Y.-L., Graham M. D., de Pablo J. J., Randall G. C., Gupta M.& Doyle P. S. . 2004Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels. Phys. Rev. E 70, 060901 doi:10.1103/PhysRevE.70.060901 (doi:10.1103/PhysRevE.70.060901). Crossref, ISI, Google Scholar - 3
Balducci A., Hsieh C. C.& Doyle P. S. . 2007Relaxation of stretched DNA in slit-like confinement. Phys. Rev. Lett. 99, 238102 doi:10.1103/PhysRevLett.99.238102 (doi:10.1103/PhysRevLett.99.238102). Crossref, PubMed, ISI, Google Scholar - 4
Bakajin O. B., Duke T. A. J., Chou C. F., Chan S. S., Austin R. H.& Cox E. C. . 1998Electrohydrodynamic stretching of DNA in confined environments. Phys. Rev. Lett. 80, 2737-2740doi:10.1103/PhysRevLett.80.2737 (doi:10.1103/PhysRevLett.80.2737). Crossref, ISI, Google Scholar - 5
Brochard F.& De Gennes P. G. . 1977Dynamical scaling for polymers in theta solvents. Macromolecules 10, 1157-1161doi:10.1021/ma60059a048 (doi:10.1021/ma60059a048). Crossref, ISI, Google Scholar - 6
Chinappi M., Melchionna S., Casciola C. M.& Succi S. . 2008Mass flux through asymmetric nanopores: microscopic versus hydrodynamic motion. J. Chem. Phys. 129, 124717 doi:10.1063/1.2987408 (doi:10.1063/1.2987408). Crossref, PubMed, ISI, Google Scholar - 7
Travis K. P., Todd B. D.& Evans D. J. . 1997Departure from Navier–Stokes hydrodynamics in confined liquids. Phys. Rev. E 55, 4288-4295doi:10.1103/PhysRevE.55.4288 (doi:10.1103/PhysRevE.55.4288). Crossref, ISI, Google Scholar - 8
Jendrejack R. M., de Pablo J. J.& Graham M. D. . 2002Stochastic simulations of DNA in flow: dynamics and the effects of hydrodynamic interactions. J. Chem. Phys. 116, 7752-7759doi:10.1063/1.1466831 (doi:10.1063/1.1466831). Crossref, ISI, Google Scholar - 9
Jendrejack R. M., Schwartz D. C., Graham M. D.& de Pablo J. J. . 2003Effect of confinement on DNA dynamics in microfluidic devices. J. Chem. Phys. 119, 1165-1173doi:10.1063/1.1575200 (doi:10.1063/1.1575200). Crossref, ISI, Google Scholar - 10
Jendrejack R. M., Schwartz D. C., de Pablo J. J.& Graham M. D. . 2004Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels. J. Chem. Phys. 120, 2513-2539doi:10.1063/1.1637331 (doi:10.1063/1.1637331). Crossref, PubMed, ISI, Google Scholar - 11
Ahlrichs P.& Dünweg B. . 1999Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics. J. Chem. Phys. 111, 8225-8239doi:10.1063/1.480156 (doi:10.1063/1.480156). Crossref, ISI, Google Scholar - 12
Jiang W., Huang J., Wang Y.& Laradji M. . 2007Hydrodynamic interaction in polymer solutions simulated with dissipative particle dynamics. J. Chem. Phys. 126, 044901 doi:10.1063/1.2428307 (doi:10.1063/1.2428307). Crossref, PubMed, ISI, Google Scholar - 13
Watari N., Makino M., Kikuchi N., Larson R. G.& Doi M. . 2007Simulation of DNA motion in a microchannel using stochastic rotation dynamics. J. Chem. Phys. 126, 094902 doi:10.1063/1.2538831 (doi:10.1063/1.2538831). Crossref, PubMed, ISI, Google Scholar - 14
Malevanets A.& Kapral R. . 1999Mesoscopic model for solvent dynamic. J. Chem. Phys. 110, 8605-8613doi:10.1063/1.478857 (doi:10.1063/1.478857). Crossref, ISI, Google Scholar - 15
Gompper G., Ihle T., Kroll D. M.& Winkler R. G. Multi-particle collision dynamics: a particle-based mesoscale simulation approach to the hydrodynamics of complex fluids. Adv. Polym. Sci. 221, 1-88doi:10.1007/12_2008_5 (doi:10.1007/12_2008_5). Crossref, ISI, Google Scholar - 16
Mussawisade K., Ripoll M., Winkler R. G.& Gompper G. . 2005Dynamics of polymers in a particle-based mesoscopic solvent. J. Chem. Phys. 123, 144905 doi:10.1063/1.2041527 (doi:10.1063/1.2041527). Crossref, PubMed, ISI, Google Scholar - 17
Ripoll M., Mussawisade K., Winkler R. G.& Gompper G. . 2004Low-Reynolds-number hydrodynamics of complex fluids by multi-particle-collision dynamics. Europhys. Lett. 68, 106-112doi:10.1209/epl/i2003-10310-1 (doi:10.1209/epl/i2003-10310-1). Crossref, Google Scholar - 18
Lamura A., Gompper G., Ihle T.& Kroll D. M. . 2001Multi-particle collision dynamics: flow around a circular and a square cylinder. Europhys. Lett. 56, 319-325doi:10.1209/sepl/i2001-00522-9 (doi:10.1209/sepl/i2001-00522-9). Crossref, Google Scholar - 19
Kikuchi N., Pooley C., Ryder J. F.& Yeomans J. . 2003Transport coefficients of a mesoscopic fluid dynamics model. J. Chem. Phys. 119, 6388-6395doi:10.1063/1.1603721 (doi:10.1063/1.1603721). Crossref, ISI, Google Scholar - 20
Ihle T., Tüzel E.& Kroll D. M. . 2005Equilibrium calculation of transport coefficients for a fluid-particle model. Phys. Rev. E 72, 046707 doi:10.1103/PhysRevE.72.046707 (doi:10.1103/PhysRevE.72.046707). Crossref, ISI, Google Scholar - 21
Ihle T.& Kroll D. M. . 2001Stochastic rotation dynamics: a Galilean-invariant mesoscopic model for fluid flow. Phys. Rev. E 63, 020201 doi:10.1103/PhysRevE.63.020201 (doi:10.1103/PhysRevE.63.020201). Crossref, ISI, Google Scholar - 22
