Diffusion of macromolecules in agarose gels: Comparison of linear and globular configurations

Biophysical Journal

Volumn 77, Issue 1, 1999, Pages 542-552

  Pluen, Alain ^a   Netti, Paolo A ^a,b   Jain, Rakesh K ^a   Berk, David A ^a,c  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AGAR GEL ELECTROPHORESIS; ARTICLE; BLEACHING; DIFFUSION; MACROMOLECULE; MOLECULAR DYNAMICS; PARTICLE SIZE;

EID: 0032978690     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)76911-0     Document Type: Article

References (69)

1. Anderson, J. L., F. Rauh, and A. Morales. 1978. Particle diffusion as a function of concentration and ionic strength. J. Chem. Phys. 82: 608-616.
2. Bansil, R., S. Pajevic, and C. Karak. 1990. Diffusion of polystyrenes in gels. Macromolecules. 23:3380-3382.
3. Berk, D. A., F. Yuan, M. Leunig, and R. K. Jain. 1993. Fluorescence photobleaching with spatial Fourier analysis: measurement of diffusion in light-scattering media. Biophys. J. 65:2428-2436.
4. Berk, D. A., F. Yuan, M. Leunig, and R. K. Jain. 1997. Direct in vivo measurement of targeted binding in a human tumor xenograft. Proc. Natl. Acad. Sci. USA. 94:1785-1790.
5. Bor Fuh, C., S. Levin, and J. C. Giddings. 1993. Rapid diffusion coefficient measurements using analytical SPLITT fractionation: application to proteins. Anal. Biochem. 208:80-87.
6. Brady, J. 1994. Hindered diffusion. American Institute of Chemical Engineers, Annual Meeting, November 13-18, San Francisco, CA.
7. Brinkman, H. C. 1947. A calculation of the viscous force exerted by a flowing fluid in a dense swarm of particles. Appl. Sci. Res. A. 1:27-34.
8. Carlsson, C., A. Larrson, and M. Jonsson. 1996. Influence of optical probing with YOYO on the electrophoretic behavior of the DNA molecule. Electrophoresis. 17:642-651.
9. Carman, P. C. 1937. Fluid flow through granular beds. Trans. Inst. Chem. Eng. 15:150-166.
10. Chary, S. R. and R. K. Jain. 1989. Direct measurement of interstitial convection and diffusion of albumin in normal and neoplastic tissues by fluorescence photobleaching. Proc. Natl. Acad. Sci. USA. 86: 5385-5389.
11. Chui, M. M., R. J. Phillips, and M. J. McCarthy. 1995. Measurement of the porous microstructure of hydrogels by nuclear magnetic resonance. J. Colloid Interface Sci. 174:336-344.
12. de Gennes, P. G. 1979. Scaling Concepts in Polymer Physics. Cornell University Press, Ithac, NY.
13. Djabourov, M. A., A. H. Clark, D. W. Rowlands, and S. B. Ross-Murphy. 1989. Small angle x-ray scattering characterization of agarose sols and gels. Macromolecules. 22:180-188.
14. Doi, M., and S. F. Edwards. 1986. The Theory of Polymer Dynamics. Clarendon Press, Oxford University Press, Oxford, New York.
15. Dwyer, J. D., and V. A. Bloomfield. 1993. Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions. Biophys. J. 65:1810-1816.
16. Gaigalas, A. K., J. B. Hubbard, M. McCurley, and S. Woo. 1992. Diffusion of bovine serum albumin in aqueous solutions. J. Chem. Phys. 96: 2355-2359.
17. Gibbs, S. J., A. S. Chu, E. N. Lightfoot, and T. W. Root. 1991. Ovalbumin diffusion at different ionic strength. J. Chem. Phys. 95:467-471.
18. Giddings, J. C., E. Kucera, C. P. Russel, and M. N. Myers. 1968. Statistical theory for the equilibrium distribution of rigid molecules in inert porous network. Exclusion chromatography. J. Phys. Chem. 72:4397-4408.
19. Giddings, S. J., F. J. F. Yang, and N. N. Myers. 1976. Flow field-flow fractionation: a versatile new separation method. Science. 193: 1244-1245.
20. Granath, K. A., and B. E. Kvist. 1967. Molecular weight distribution analysis by gel chromatography on Sephadex. J. Chromatogr. 28: 69-81.
21. Griess, G. A., K. B. Guiseley, and P. Serwer. 1993. The relationship of agarose gel structure to the sieving of spheres during agarose gel electrophoresis. Biophys. J. 65:138-148.
22. Griess, G. A., E. T. Moreno, R. A. Easom, and P. Serwer. 1989. Sieving of spheres during agarose gel electrophoresis: quantification and modeling. Biopolymers. 28:1475-1484.
23. Gurrieri, S., K. S. Wells, I. D. Johnson, and C. Bustamante. 1997. Direct visualization of individual DNA molecules by fluorescence microscopy: characterization of the factors affecting signal/background and optimization of imaging conditions using YOYO. Anal. Biochem. 249:44-53.
24. Happel, J., and H. Brenner. 1965. Low Reynolds Number Hydrodynamics with Special Applications to Particulate Media. Prentice-Hall Ed., Englewood Cliffs, NJ. 392-404.
25. Jackson, G. W., and D. G. James. 1986. The permeability of fibrous porous media. Can. J. Chem. Eng. 64:362-374.
26. Jain, R. K. 1994. Barriers to drug delivery in solid tumors. Sci. Am. 271:58-65.
27. Jain, R. K. 1998. The next frontier of molecular medicine: delivery of therapeutics. Nat. Med. 4:655-657.
28. Johnson, E. M., D. A. Berk, R. K. Jain, and W. M. Deen. 1995. Diffusion and partitioning of proteins in charged agarose gels. Biophys. J. 68: 1561-1568.
29. Johnson, E. M., D. A. Berk, R. K. Jain, and W. M. Deen. 1996. Hindered diffusion in agarose gels: test of effective medium model. Biophys. J. 70:1017-1026.
30. Johnson, E. M., and W. M. Deen. 1996. Hydraulic permeability of agarose gels. AIChE J. 42:1220-1224.
31. Kosar, F. F., and R. J. Phillips. 1995. Measurement of protein diffusion in dextran solutions by holographic interferometry. AIChE J. 41:701-711.
32. Kuhn, W. 1934. Über die Gestalt für den förminger Moleküle in Lösungen. Kolloid Z. 68:2-15.
33. Laurent, T. C. 1967. Determination of the structure of agarose gels by gel chromatography. J. Chromatogr. 14:317-330.
34. Lebrun, L., and G.-A. Junter. 1993. Diffusion of sucrose and dextran through agar gel membrane. Enzyme Microb. Technol. 15:1057-1062.
35. Levick, J. R. 1987. Flow through interstitium and other fibrous matrices. Q. J. Exp. Physiol. 72:409-438.
36. Maaloum, M., N. Pemodet, and B. Tinland. 1998. Agarose gel structure using atomic force microscopy: gel concentration and ionic strengths effects. Electrophoresis. 19:1606-1610.
37. Manno, M., A. Emanuele, V. Martorana, D. Burtone, P. L. San Biagio, M. B. Palma-Vitorelli, and M. U. Palma. 1999. Multiple interactions between molecular and supramolecular ordering. Phys. Rev. E. 59: 2222-2230.
38. Maret, G., and G. Weill. 1983. Magnetic birefringence study of the electrostatic and intrinsic persistence length of DNA. Biopolymers. 22: 2727-2744.
39. Moussaoui, M., M. Benlyas, and P. Wahl. 1991. Diffusion of proteins in the chromatographic gel AcA-34. J. Chromatogr. 558:71-80.
40. Moussaoui, M. M. Benlyas, and P. Wahl. 1992. Diffusion of proteins in Sepharose Cl-B gels. J. Chromatogr. 591:115-120.
41. Muramatsu, N., and A. P. Minton. 1988. Tracer diffusion of globular proteins in concentrated protein solutions. Proc. Natl. Acad. Sci. USA. 85:2984-2988.
42. Ogston, A. G. 1958. The spaces in a uniform random suspension of fibers. Faraday Soc. Trans. 54:1754-1757.
43. Ogston, A. G., B. N. Preston, and J. D. Wells. 1973. On the transport of compact particles through solution of chain polymers. Proc. R. Soc. Lond. A. 333:297-316.
44. Olivera, B. M., P. Baine, and N. Davidson. 1964. Electrophoresis of nucleic acids. Biopolymers. 18:3111-3113.
45. Olmsted, M. C., C. F. Anderson, and M. T. Record. 1991. Importance of oligoelectrolyte effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers. 31:1593-1604.
46. Pernodet, N., M. Maaloum, and B. Tinland. 1997. Pore size of agarose gels by atomic force microscopy. Electrophoresis. 18:55-58.
47. Pernodet, N., and B. Tinland. 1997. Influence of lambda-DNA concentration on mobilities and dispersion coefficients during agarose gel electrophoresis. Biopolymers. 42:471-478.
48. Phillips, R. J., W. M. Deen, and J. F. Brady. 1989. Hindered transport of spherical macromolecules in fibrous membranes and gels. AIChE J. 35:1761-1769.
49. Phillips, R. J., W. M. Deen, and J. F. Brady. 1990. Hindered transport in fibrous membranes and gels: effect of solute size and fiber configuration. J. Colloid. Interface Sci. 139:363-373.
50. Pluen, A., B. Tinland, J. Sturm, and G. Weill. 1998. Migration of single-stranded DNA in polyacrylamide gels during electrophoresis. Electrophoresis. 19:1548-1559.
51. Renkin, E. M. 1954. Filtration, diffusion, and molecular sieving through porous cellulose membrane. J. Gen. Physiol. 38:225-243.
52. Ross, P. D., and R. L. Scruggs. 1964. Electrophoresis of DNA. III. The effect of several univalent electrolytes on the mobility of DNA. Biopolymers. 2:231-236.
53. Rouse, P. E. 1953. A theory of linear viscoelastic properties of dilute solutions of coiling polymers. J. Chem. Phys. 21:1272.
54. Saltzman, W. M., M. L. Radomsky, K. J. Whaley, and R. C. Cone. 1994. Antibody diffusion in human cervical mucus. Biophys. J. 66:508-515.
55. Slater, G. W., and H. L. Guo. 1996. An exactly solvable Ogston model of gel electrophoresis. II. Sieving through periodic gels. Electrophoresis. 17:1407-1415.
56. Slater, G. W., and J. Noolandi. 1986. On the reptation theory of gel electrophoresis. Biopolymers. 25:431-454.
57. Smith, S. B., and A. J. Bendich. 1990. Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy. Biopolymers. 29:1167-1173.
58. Smith, S. B., Y. J. Cui, and C. Bustamante. 1996b. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
59. Smith, D. E., T. T. Perkins, and S. Chu. 1996a. Dynamical scaling of DNA diffusion coefficients. Macromolecules. 29:1372-1373.
60. Stellwagen, N. C., C. Gelfi, and P. G. Righetti. 1997. The free solution mobility of DNA. Biopolymers. 42:687-703.
61. Tanford, C. 1961. Transport processes. In Physical Chemistry of Macromolecules. John Wiley & Sons, Inc., New York - London. 317-364.
62. Tinland, B., N. Pernodet, and A. Pluen. 1998. Biopolymers. Band broadening in gel electrophoresis: scaling laws for the dispersion coefficient measured by FRAP. Biopolymers. 46:201-214.
63. Tinland, B., N. Pernodet, and G. Weill. 1996. Field and pore size dependence of the electrophoretic mobility of DNA: a combination of fluorescence recovery after photobleaching and electric birefringence measurements. Electrophoresis. 17:1046-1051.
64. Tong, J., and J. L. Anderson. 1996. Partitioning and diffusion of proteins and linear polymers in polyacrylamide gels. Biophys. J. 70:1505-1513.
65. Verma, I. M., and N. Somia. 1997. Gene therapy: promises, problems and prospects. Nature. 389:239-242.
66. Waki, S., J. D. Harvey, and A. R. Bellamy. 1982. Study of agarose gels by electron microscopy of freeze fractured surfaces. Biopolymers. 21: 1909-1926.
67. Williams, J. C., L. A. Mark, and S. Eichholtz. 1998. Partition and permeation of dextran in polyacrylamide gel. Biophys. J. 75:493-502.
68. Yamakov, V., and A. Milchev. 1997. Diffusion of a polymer chain in porous media. Phys. Rev. E. 55:1704-1712.
69. Zimm, B. H. 1991. Lakes and Straits model of field inversion gel electrophoresis of DNA. J. Chem. Phys. 94:2187-2206.