纳米通道中 DNA 环化和松弛的电熵排斥体积效应。
Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels.
机构信息
Institute of Physics, Academia Sinica, Taipei, Taiwan ; Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan ; Department of Physics, National Taiwan University, Taipei, Taiwan.
出版信息
Biomicrofluidics. 2013 Oct 22;7(5):54119. doi: 10.1063/1.4826157. eCollection 2013.
Abstract
We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length. In nanochannels smaller than the persistence length, the chain relaxation time is found to have cubic dependence on the channel size. It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement. For thinner chains, looped chain configurations are found in channels with height comparable to the persistence length, with very slow relaxation compared to un-looped chains. Larger effective chain widths inhibit the formation of hairpin loops.
摘要
我们研究了熵限制的 DNA 分子在方纳米通道中的涨落松弛动力学，纳米通道的大小范围从 0.09 倍到 19.9 倍的 persistence length。在小于 persistence length 的纳米通道中，发现链松弛时间与通道大小呈立方关系。研究发现，有效聚合物宽度在强约束下显著改变链构象和松弛时间。对于较薄的链，在高度与 persistence length 相当的通道中发现了环状链构型，与未缠绕链相比，其松弛速度非常慢。较大的有效链宽度抑制了发夹环的形成。
相似文献
1
Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels.
Biomicrofluidics. 2013 Oct 22;7(5):54119. doi: 10.1063/1.4826157. eCollection 2013.
2
Erratum: "Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels" [Biomicrofluidics 7, 054119 (2013)].
Biomicrofluidics. 2013 Nov 12;7(6):69901. doi: 10.1063/1.4831857. eCollection 2013.
3
DNA confined in nanochannels: hairpin tightening by entropic depletion.
J Chem Phys. 2006 Nov 28;125(20):204904. doi: 10.1063/1.2400227.
4
Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size.
Soft Matter. 2015 Jan 21;11(3):472-88. doi: 10.1039/c4sm02007c.
5
Knotting and Unknotting Dynamics of DNA Strands in Nanochannels.
ACS Macro Lett. 2014 Sep 16;3(9):876-880. doi: 10.1021/mz500402s. Epub 2014 Aug 19.
6
Role of confinement, molecular connectivity and flexibility in entropic driven surface segregation of polymer-colloid mixtures.
Soft Matter. 2019 Aug 28;15(32):6495-6503. doi: 10.1039/c9sm00883g. Epub 2019 Jul 25.
7
Dynamic simulations show repeated narrowing maximizes DNA linearization in elastomeric nanochannels.
Biomicrofluidics. 2016 Nov 23;10(6):064108. doi: 10.1063/1.4967963. eCollection 2016 Nov.
8
The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels.
Polymers (Basel). 2016 Mar 14;8(3):79. doi: 10.3390/polym8030079.
9
Scaling theory of DNA confined in nanochannels and nanoslits.
Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jun;77(6 Pt 1):060901. doi: 10.1103/PhysRevE.77.060901. Epub 2008 Jun 9.
10
Modeling the relaxation of internal DNA segments during genome mapping in nanochannels.
Biomicrofluidics. 2016 Oct 13;10(5):054117. doi: 10.1063/1.4964927. eCollection 2016 Sep.
引用本文的文献
1
Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations.
Polymers (Basel). 2018 Dec 22;11(1):15. doi: 10.3390/polym11010015.
2
Distribution of label spacings for genome mapping in nanochannels.
Biomicrofluidics. 2018 Jun 25;12(3):034115. doi: 10.1063/1.5038417. eCollection 2018 May.
3
Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels.
Biophys J. 2017 Mar 14;112(5):838-849. doi: 10.1016/j.bpj.2017.01.027.
4
Kirkwood diffusivity of long semiflexible chains in nanochannel confinement.
Macromolecules. 2015 Apr 28;48(8):2829-2839. doi: 10.1021/acs.macromol.5b00377.
5
Stretching of DNA confined in nanochannels with charged walls.
Biomicrofluidics. 2014 Dec 10;8(6):064121. doi: 10.1063/1.4904008. eCollection 2014 Nov.
6
Probing transient protein-mediated DNA linkages using nanoconfinement.
Biomicrofluidics. 2014 Jun 12;8(3):034113. doi: 10.1063/1.4882775. eCollection 2014 May.
7
Simulations of DNA stretching by flow field in microchannels with complex geometry.
Biomicrofluidics. 2014 Feb 7;8(1):014106. doi: 10.1063/1.4863802. eCollection 2014 Jan.
8
Erratum: "Electro-entropic excluded volume effects on DNA looping and relaxation in nanochannels" [Biomicrofluidics 7, 054119 (2013)].
Biomicrofluidics. 2013 Nov 12;7(6):69901. doi: 10.1063/1.4831857. eCollection 2013.
本文引用的文献
1
Extension of DNA in a nanochannel as a rod-to-coil transition.
Phys Rev Lett. 2013 May 17;110(20):208103. doi: 10.1103/PhysRevLett.110.208103. Epub 2013 May 13.
2
Modeling the relaxation time of DNA confined in a nanochannel.
Biomicrofluidics. 2013 Oct 22;7(5):54118. doi: 10.1063/1.4826156. eCollection 2013.
3
Conformation and diffusion behavior of ring polymers in solution: a comparison between molecular dynamics, multiparticle collision dynamics, and lattice Boltzmann simulations.
J Chem Phys. 2011 Nov 14;135(18):184901. doi: 10.1063/1.3656761.
4
Partial hydrodynamic screening of confined linear and circular double-stranded DNA dynamics.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 1):031917. doi: 10.1103/PhysRevE.84.031917. Epub 2011 Sep 19.
5
Simulation of DNA Extension in Nanochannels.
Macromolecules. 2011 Aug 23;44(16):6594-6604. doi: 10.1021/ma201277e.
6
Nanochannel confinement: DNA stretch approaching full contour length.
Lab Chip. 2011 May 21;11(10):1721-9. doi: 10.1039/c0lc00680g. Epub 2011 Mar 23.
7
Coil-stretch Transition of DNA Molecules in Slit-like Confinement.
Macromolecules. 2010 Mar 23;43(6):3081-3089. doi: 10.1021/ma902689c.
8
Combined simulation and experimental study of large deformation of red blood cells in microfluidic systems.
Ann Biomed Eng. 2011 Mar;39(3):1041-50. doi: 10.1007/s10439-010-0232-y. Epub 2010 Dec 14.
9
Fluctuations of a long, semiflexible polymer in a narrow channel.
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82(4 Pt 1):041801. doi: 10.1103/PhysRevE.82.041801. Epub 2010 Oct 1.
10
Shape transition of semi-flexible macromolecules confined in channel and cavity.
Eur Phys J E Soft Matter. 2010 Jul;32(3):273-9. doi: 10.1140/epje/i2010-10626-y. Epub 2010 Jul 27.
Zotero 插件