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Studying confined polymers using single-molecule DNA experiments  

Hsieh, Chih-Chen (Department of Chemical Engineering, National Taiwan University)
Doyle, Patrick S. (Department of Chemical Engineering, Massachusetts Institute of Technology)
Publication Information
Korea-Australia Rheology Journal / v.20, no.3, 2008 , pp. 127-142 More about this Journal
Abstract
The development of fluorescence microscopy of single-molecule DNA in the last decade has fostered a bold jump in the understanding of polymer physics. With the recent advance of nanotechnology, devices with well-defined dimensions that are smaller than typical DNA molecules can be readily manufactured. The combination of these techniques has provided an unprecedented opportunity for researchers to examine confined polymer behavior, a topic far less understood than its counterpart. Here, we review the progress reported in recent studies that investigate confined polymer dynamics by means of single-molecule DNA experiments.
Keywords
confined polymer; single-molecule DNA; tube-like confinement; silt-like confinement; surface confinement; blob theory;
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1 Baumann, C. G., S. B. Smith, V. A. Bloomfield and C. Bustamante, 1997, Ionic effects on the elasticity of single DNA molecules, Proc. Natl. Acad. Sci. USA 94, 6185-6190
2 Brochard, F., 1977, Dynamics of polymer chains trapped in a slit, J. Phys. (Paris) 38, 1285-1291   DOI
3 Burkhardt, T. W., 1995, Free energy of a semiflexible polymer confined along an axis, J. Phys. A 28, L629-L635
4 Craighead, H., 2006, Future lab-on-a-chip technologies for interrogating individual molecules, Nature 442, 387-393   DOI   ScienceOn
5 Dechadilok, P. and W. M. Deen, 2006, Hindrance factors for diffusion and convection in pores, Ind. Engin. Chem. Res. 45, 6953-6959   DOI   ScienceOn
6 Fixman, M. and J. Skolnick, 1978, Polyelectrolyte excluded volume paradox, Macromolecules 11, 863-867   DOI
7 Guo, L. J., X. Cheng and C. F. Chou, 2004, Fabrication of sizecontrollable nanofluidic channels by nanoimprinting and its application for DNA stretching, Nano Lett. 4, 69-73   DOI   ScienceOn
8 Han, J. Y. and H. G. Craighead, 2002, Characterization and optimization of an entropic trap for DNA separation, Anal. Chem. 74, 394-401   DOI   ScienceOn
9 Israelachvili, J. N., 1991, Intermolecular and surface forces, Academic Press, London ; San Diego, 2nd edition
10 Jendrejack, R. M., E. T. Dimalanta, D. C. Schwartz, M. D. Graham and J. J. de Pablo, 2003a, DNA dynamics in a microchannel, Phys. Rev. Lett. 91, 038102   DOI   ScienceOn
11 Jendrejack, R. M., D. C. Schwartz, M. D. Graham and J. J. de Pablo, 2003b, Effect of confinement on DNA dynamics in microfluidic devices, J. Chem. Phys. 119, 1165-1173   DOI   ScienceOn
12 Juang, Y. J., S. Wang, X. Hu and L. J. Lee, 2004, Dynamics of single polymers in a stagnation flow induced by electrokinetics, Phys. Rev. Lett. 93, 268105   DOI   ScienceOn
13 Nykypanchuk, D., H. H. Strey and D. A. Hoagland, 2005, Single molecule visualizations of polymer partitioning within model pore geometries, Macromolecules 38, 145-150   DOI   ScienceOn
14 Odijk, T., 2006, DNA confined in nanochannels: Hairpin tightening by entropic depletion, J. Chem. Phys. 125, 204904   DOI
15 Olson, D. J., J. M. Johnson, P. D. Patel, E. S. G. Shaqfeh, S. G. Boxer and G. G. Fuller, 2001, Electrophoresis of DNA adsorbed to a cationic supported bilayer, Langmuir 17, 7396-7401   DOI   ScienceOn
16 Randall, G. C. and P. S. Doyle, 2005a, DNA deformation in electric fields: DNA driven past a cylindrical obstruction, Macromolecules 38, 2410-2418   DOI   ScienceOn
17 Randall, G. C. and P. S. Doyle, 2006, Collision of a DNA polymer with a small obstacle, Macromolecules 39, 7734-7745   DOI   ScienceOn
18 Shaqfeh, E. S. G., 2005, The dynamics of single-molecule DNA in flow, J. Non-Newtonian Fluid Mech. 130, 1-28   DOI   ScienceOn
19 Rubinstein, M. and R. H. Colby, 2003, Polymer physics, Oxford University Press, Oxford ; New York
20 Savin, T. and P. S. Doyle, 2005, Static and dynamic errors in particle tracking microrheology, Biophys. J. 88, 623-638   DOI   ScienceOn
21 Stigter, D., 1977, Interactions of highly charged colloidal cylinders with applications to double-stranded DNA, Biopolymers 16, 1435-1448   DOI   ScienceOn
22 Wang, Y. M., J. O. Tegenfeldt, W. Reisner, R. Riehn, X. J. Guan, L. Guo, I. Golding, E. C. Cox, J. Sturm and R. H. Austin, 2005, Single-molecule studies of repressor-DNA interactions show long-range interactions, Proc. Natl. Acad. Sci. USA 102, 9796-9801
23 Yamakawa, H., 1967, Modern Theory of Polymer Solutions, Harper and Row, New York
24 Teclemariam, N. P., V. A. Beck, E. S. G. Shaqfeh and S. J. Muller, 2007, Dynamics of DNA polymers in post arrays: Comparison of single molecule experiments and simulations, Macromolecules 40, 3848-3859   DOI   ScienceOn
25 Cabodi, M., S. W. P. Turner and H. G. Craighead, 2002, Entropic recoil separation of long DNA molecules, Anal. Chem. 74, 5169-5174   DOI   ScienceOn
26 Chen, Y. L., M. D. Graham, J. J. de Pablo, G. C. Randall, M. Gupta and P. S. Doyle, 2004, Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels, Phys. Rev. E 70, 060901
27 Cross, J. D., E. A. Strychalski and H. G. Craighead, 2007, Sizedependent DNA mobility in nanochannels, J. Appl. Phys. 102, 024701   DOI   ScienceOn
28 Maier, B., U. Seifert and J. O. Radler, 2002, Elastic response of DNA to external electric fields in two dimensions, Europhys. Letters 60, 622-628   DOI   ScienceOn
29 Reisner, W., J. P. Beech, N. B. Larsen, H. Flyvbjerg, A. Kristensen and J. O. Tegenfeldt, 2007, Nanoconfinementenhanced conformational response of single DNA molecules to changes in ionic environment, Phys. Rev. Lett. 99, 058302   DOI   ScienceOn
30 Odijk, T., 1983, On the statistics and dynamics of confined or entangled stiff polymers, Macromolecules 16, 1340-1344   DOI
31 Teraoka, I., 1996, Polymer solutions in confining geometries, Prog. Polym. Sci. 21, 89-149   DOI   ScienceOn
32 Vologodskii, A. and N. Cozzarelli, 1995, Modeling of long-range electrostatic interactions in DNA, Biopolymers 35, 289-296   DOI   ScienceOn
33 Dobrynin, A. V. and M. Rubinstein, 2005, Theory of polyelectrolytes in solutions and at surfaces, Prog. Polym. Sci. 30, 1049-1118   DOI   ScienceOn
34 Harden, J. L. and M. Doi, 1992, Diffusion of macromolecules in narrow capillaries, J. Phys. Chem. 96, 4046-4052   DOI
35 Hsieh, C. C., A. Balducci and P. S. Doyle, 2008, Ionic effects on the equilibrium dynamics of dna confined in nanoslits, Nano Lett. 8, 1683-1688   DOI   ScienceOn
36 Mannion, J. T., C. H. Reccius, J. D. Cross and H. G. Craighead, 2006, Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels, Biophys. J. 90, 4538-4545   DOI   ScienceOn
37 Nykypanchuk, D., H. H. Strey and D. A. Hoagland, 2002, Brownian motion of DNA confined within a two dimensional array, Science 297, 987-990   DOI   ScienceOn
38 Perkins, T. T., S. R. Quake, D. E. Smith and S. Chu, 1994, Relaxation of a single DNA molecule observed by optical microscopy, Science 264, 822-826   DOI
39 Randall, G. C. and P. S. Doyle, 2004, Electrophoretic collision of a DNA molecule with an insulating post, Phys. Rev. Lett. 93, 058104
40 Salieb-Beugelaar, G. B., J. Teapal, J. Van Nieuwkasteele, D. Wijnperle, J. O. Tegenfeldt, F. Lisdat, A. van den Berg and J. C. T. Eijkel, 2008, Field-dependent DNA mobility in 20 nm high nanoslits, Nano Lett. 8, 1785-1790   DOI   ScienceOn
41 Stein, D., F. H. J. van der Heyden, W. J. A. Koopmans and C. Dekker, 2006, Pressure-driven transport of confined DNA polymers in fluidic channels, Proc. Natl. Acad. Sci. USA 103, 15853-15858
42 Odijk, T., 1977, Polyelectrolyte near rod limit, J. Polym. Sci. BPolym. Phys. 15, 477-483   DOI   ScienceOn
43 Campbell, L. C., M. J. Wilkinson, A. Manz, P. Camilleri and C. J. Humphreys, 2004, Electrophoretic manipulation of single molecules in nanofabricated capillaries, Lab Chip 4, 225-229   DOI   ScienceOn
44 Gorbunov, A. A. and A. M. Skvortsov, 1995, Statistical properties of confined macromolecules, Adv. Colloid Interface Sci. 62, 31-108   DOI   ScienceOn
45 Balducci, A., P. Mao, J. Y. Han and P. S. Doyle, 2006, Doublestranded DNA diffusion in slitlike nanochannels, Macromolecules 39, 6273-6281   DOI   ScienceOn
46 Batchelor, G. K., 1967, An introduction to fluid dynamics, Cambridge University Press, Cambridge
47 Kasianowicz, J. J., E. Brandin, D. Branton and D. W. Deamer, 1996, Characterization of individual polynucleotide molecules using a membrane channel, Proc. Natl. Acad. Sci. USA 93, 13770-13773
48 Maier, B. and J. O. Rädler, 2000, DNA on fluid membranes: A model polymer in two dimensions, Macromolecules 33, 7185-7194   DOI   ScienceOn
49 Odijk, T. and A. C. Houwaart, 1978, Theory of excluded-volume effect of a polyelectrolyte in a 1-1 electrolyte solution, J. Polym. Sci. B-Polym. Phys. 16, 627-639   DOI   ScienceOn
50 Randall, G. C., K. M. Schultz and P. S. Doyle, 2006, Methods to electrophoretically stretch DNA: microcontractions, gels, and hybrid gel-microcontraction devices, Lab Chip 6, 516-525   DOI   ScienceOn
51 Eijkel, J. C. T. and A. van den Berg, 2005, Nanofluidics: what is it and what can we expect from it?, Microfluidics and Nanofluidics 1, 249-267   DOI
52 Chen, Y. L., M. D. Graham, J. J. de Pablo, K. Jo and D. C. Schwartz, 2005, DNA molecules in microfluidic oscillatory flow, Macromolecules 38, 6680-6687   DOI   ScienceOn
53 Maier, B. and J. O. Rädler, 1999, Conformation and self-diffusion of single DNA molecules confined to two dimensions, Phys. Rev. Lett. 82, 1911-1914   DOI   ScienceOn
54 Reisner, W., K. J. Morton, R. Riehn, Y. M. Wang, Z. N. Yu, M. Rosen, J. C. Sturm, S. Y. Chou, E. Frey and R. H. Austin, 2005, Statics and dynamics of single DNA molecules confined in nanochannels, Phys. Rev. Lett. 94, 196101   DOI   ScienceOn
55 Riehn, R., M. C. Lu, Y. M. Wang, S. F. Lim, E. C. Cox and R. H. Austin, 2005, Restriction mapping in nanofluidic devices, Proc. Natl. Acad. Sci. USA 102, 10012-10016
56 Rivetti, C., M. Guthold and C. Bustamante, 1996, Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis, J. Mol. Biol. 264, 919-932   DOI   ScienceOn
57 Brochard, F. and P. G. de Gennes, 1977, Dynamics of confined polymer chains, J. Chem. Phys. 67, 52-56   DOI
58 Huh, D., K. L. Mills, X. Y. Zhu, M. A. Burns, M. D. Thouless and S. Takayama, 2007, Tuneable elastomeric nanochannels for nanofluidic manipulation, Nat. Mater. 6, 424-428   DOI   ScienceOn
59 Lin, P. K., C. C. Fu, Y. L. Chen, Y. R. Chen, P. K. Wei, C. H. Kuan and W. S. Fann, 2007, Static conformation and dynamics of single DNA molecules confined in nanoslits, Phys. Rev. E 76, 011806   DOI
60 Balducci, A. and C. C. Hsieh, P. S. Doyle, 2007, Relaxation of stretched DNA in slitlike confinement, Phys. Rev. Lett. 99, 4
61 Bakajin, O. B., T. A. J. Duke, C. F. Chou, S. S. Chan, R. H. Austin and E. C. Cox, 1998, Electrohydrodynamic stretching of DNA in confined environments, Phys. Rev. Lett. 80, 2737-2740   DOI   ScienceOn
62 Rybenkov, V. V., N. R. Cozzarelli and A. V. Vologodskii, 1993, Probability of DNA knotting and the effective diameter of the DNA double helix, Proc. Natl. Acad. Sci. USA 90, 5307-5311
63 Shaw, S. Y. and J. C. Wang, 1993, Knotting of a DNA chain during ring-closure, Science 260, 533-536   DOI
64 Usta, O. B., A. J. C. Ladd and J. E. Butler, 2005, Lattice-boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries, J. Chem. Phys. 122, 094902   DOI   ScienceOn
65 Leal, L. G., 1992, Laminar flow and convective transport processes : scaling principles and asymptotic analysis, Butterworth-Heinemann, Boston
66 Han, J. and H. G. Craighead, 2000, Separation of long DNA molecules in a microfabricated entropic trap array, Science 288, 1026-1029   DOI   ScienceOn
67 Tegenfeldt, J. O., C. Prinz, H. Cao, S. Chou, W. W. Reisner, R. Riehn, Y. M. Wang, E. C. Cox, J. C. Sturm, P. Silberzan and R. H. Austin, 2004a, The dynamics of genomic-length DNA molecules in 100-nm channels, Proc. Natl. Acad. Sci. USA 101, 10979-10983
68 Daoud, M. and P. G. de Gennes, 1977, Statistics of macromolecular solutions trapped in small pores, J. Phys. (Paris) 38, 85-93
69 Maier, B. and J. O. Radler, 2001, Shape of self-avoiding walks in two dimensions, Macromolecules 34, 5723-5724   DOI   ScienceOn
70 Wall, F. T., W. A. Seitz, J. C. Chin and P. G. de Gennes, 1978, Statistics of self-avoiding walks confined to strips and capillaries, Proc. Natl. Acad. Sci. USA 75, 2069-2070
71 Perkins, T. T., D. E. Smith, R. G. Larson and S. Chu, 1995, Stretching of a single tethered polymer in a uniform-flow, Science 268, 83-87   DOI
72 Tang, J. and P. S. Doyle, 2007, Electrophoretic stretching of DNA molecules using microscale t junctions, App. Phys. Lett. 90, 224103   DOI   ScienceOn
73 Volkmuth, W. D. and R. H. Austin, 1992, DNA electrophoresis in microlithographic arrays, Nature 358, 600-602   DOI   ScienceOn
74 Dobrynin, A. V., 2005, Electrostatic persistence length of semiflexible and flexible polyelectrolytes, Macromolecules 38, 9304-9314   DOI   ScienceOn
75 Larson, J. W., G. R. Yantz, Q. Zhong, R. Charnas, C. M. D'Antoni, M. V. Gallo, K. A. Gillis, L. A. Neely, K. M. Phillips, G. G. Wong, S. R. Gullans and R. Gilmanshin, 2006, Single DNA molecule stretching in sudden mixed shear and elongational microflows, Lab Chip 6, 1187-1199   DOI   ScienceOn
76 Burkhardt, T. W., 1997, Free energy of a semiflexible polymer in a tube and statistics of a randomlyaccelerated particle, J. Phys. A 30, L167-L172
77 de Gennes, P. G., 1976, Dynamics of entangled polymer-solutions 1. rouse model, Macromolecules 9, 587-593   DOI
78 Fang, L., C. C. Hsieh and R. G. Larson, 2007, Molecular imaging of shear-induced polymer migration in dilute solutions near a surface, Macromolecules 40, 8490-8499   DOI   ScienceOn
79 Han, J., S. W. Turner and H. G. Craighead, 1999, Entropic trapping and escape of long DNA molecules at submicron size constriction, Phys. Rev. Lett. 83, 1688-1691   DOI
80 Long, D., J. L. Viovy and A. Ajdari, 1996, Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: Motion and deformation, Phys. Rev. Lett. 76, 3858-3861   DOI   ScienceOn
81 Randall, G. C., 2006, Single molecule analysis of DNA electrophoresis in microdevices, Ph.D. thesis
82 Hsieh, C. C., A. Balducci and P. S. Doyle, 2007, An experimental study of DNA rotational relaxation time in nanoslits, Macromolecules 40, 5196-5205   DOI   ScienceOn
83 Chan, E. Y., N. M. Goncalves, R. A. Haeusler, A. J. Hatch, J. W. Larson, A. M. Maletta, G. R. Yantz, E. D. Carstea, M. Fuchs, G. G. Wong, S. R. Gullans and R. Gilmanshin, 2004, DNA mapping using microfluidic stretching and single-molecule detection of fluorescent site-specific tags, Genome Res. 14, 1137-1146   DOI   ScienceOn
84 Krishnan, M., I. Monch and P. Schwille, 2007, Spontaneous stretching of DNA in a two-dimensional nanoslit, Nano Lett. 7, 1270-1275   DOI   ScienceOn
85 Des Cloizeaux, J. and G. Jannink, 1990, Polymers in solution : their modelling and structure, Oxford science publications, Oxford University Press, New York
86 Volkmuth, W. D., T. Duke, M. C. Wu, R. H. Austin and A. Szabo, 1994, DNA electrodiffusion in a 2d array of posts, Phys. Rev. Lett. 72, 2117-2120   DOI   ScienceOn
87 Milchev, A. and K. Binder, 1996, Dynamics of polymer chains confined in slit-like pores, J. Phys. (Paris) 6, 21-31
88 Ubbink, J. and T. Odijk, 1999, Electrostatic-undulatory theory of plectonemically superooiled DNA, Biophys. J. 76, 2502-2519   DOI   ScienceOn
89 Zhang, C., F. Zhang, J. A. van Kan and J. R. C. van der Maarel, 2008, Effects of electrostatic screening on the conformation of single dna molecules confined in a nanochannel, Journal of Chemical Physics 128, 225109   DOI   ScienceOn
90 Douville, N., D. Huh and S. Takayama, 2008, DNA linearization through confinement in nanofluidic channels, Anal. Bioanal. Chem. 391(7), 2395-2409   DOI
91 Ferree, S. and W. H. Blanch, 2003, Electrokinetic stretching of tethered DNA, Biophys. J. 85, 2539-2546   DOI   ScienceOn
92 Randall, G. C. and P. S. Doyle, 2005b, Permeation-driven flow in poly(dimethylsiloxane) microfluidic devices, Proc. Natl. Acad. Sci. USA 102, 10813-10818
93 Sakaue, T. and E. Raphael, 2006, Polymer chains in confined spaces and flow-injection problems: Some remarks, Macromolecules 39, 2621-2628   DOI   ScienceOn
94 Skolnick, J. and M. Fixman, 1977, Electrostatic persistence length of a wormlike polyelectrolyte, Macromolecules 10, 944-948   DOI
95 Yang, Y. Z., T. W. Burkhardt and G. Gompper, 2007, Free energy and extension of a semiflexible polymer in cylindrical confining geometries, Phys. Rev. E 76, 011804   DOI
96 Lubensky, D. K. and D. R. Nelson, 1999, Driven polymer translocation through a narrow pore, Biophys. J. 77, 1824-1838   DOI   ScienceOn
97 Dobrynin, A. V., 2006, Effect of counterion condensation on rigidity of semiflexible polyelectrolytes, Macromolecules 39, 9519-9527   DOI   ScienceOn
98 Jo, K., D. M. Dhingra, T. Odijk, J. J. de Pablo, M. D. Graham, R. Runnheim, D. Forrest and D. C. Schwartz, 2007, A singlemolecule barcoding system using nanoslits for DNA analysis, Proc. Natl. Acad. Sci. USA 104, 2673-2678
99 Turner, S. W. P., M. Cabodi and H. G. Craighead, 2002, Confinement-induced entropic recoil of single DNA molecules in a nanofluidic structure, Phys. Rev. Lett. 88, 128103   DOI   ScienceOn
100 Deen, W. M., 1987, Hindered transport of large molecules in liquid-filled pores, AICHE J. 33, 1409-1425   DOI   ScienceOn
101 Han, J. Y., J. P. Fu and R. B. Schoch, 2008, Molecular sieving using nanofilters: Past, present and future, Lab Chip 8, 23-33   DOI   ScienceOn
102 Tegenfeldt, J. O., C. Prinz, H. Cao, R. L. Huang, R. H. Austin, S. Y. Chou, E. C. Cox and J. C. Sturm, 2004b, Micro- and nanofluidics for DNA analysis, Analytical and Bioanalytical Chemistry 378, 1678-1692   DOI
103 Mannion, J. T. and H. G. Craighead, 2007, Nanofluidic structures for single biomolecule fluorescent detection, Biopolymers 85, 131-143   DOI   ScienceOn