Abstract
In polyacrylamide gel electrophoresis, the retardation of DNA molecules containing regions of intrinsic curvature can be explained by a novel reptation model that includes the elastic free energy of the DNA chain. Computer simulations based on this model give results that reproduce the dependence of anomalous mobility on gel concentration, which is quantified by new experimental data on the mobilities of circularly permuted isomers of kinetoplast DNA fragments. Fitting of the data required allowing for the elasticity of the gel.
References
39
Referenced
57
-
ATTWOOD, T.K., ELECTRON-MICROSCOPY OF BEADED AGAROSE GELS, BIOPOLYMERS 27: 201 (1988).
(
10.1002/bip.360270204
) / BIOPOLYMERS (1988) -
BAUMGARTNER, A, SIMULATION OF POLYMER MOTION, ANNUAL REVIEW OF PHYSICAL CHEMISTRY 35: 419 (1984).
(
10.1146/annurev.pc.35.100184.002223
) / ANNUAL REVIEW OF PHYSICAL CHEMISTRY (1984) -
CEPERLEY, D, COMPUTER-SIMULATION OF THE STATIC AND DYNAMIC PROPERTIES OF A POLYMER-CHAIN, MACROMOLECULES 14: 1472 (1981).
(
10.1021/ma50006a065
) / MACROMOLECULES (1981) 10.1126/science.172.3982.440
-
DEGENNES, P.G., REPTATION OF A POLYMER CHAIN IN PRESENCE OF FIXED OBSTACLES, JOURNAL OF CHEMICAL PHYSICS 55: 572 (1971).
(
10.1063/1.1675789
) / JOURNAL OF CHEMICAL PHYSICS (1971) - deGennes, P. G., Scaling Concepts in Polymer Physics: 223 (1982). / Scaling Concepts in Polymer Physics (1982)
-
DOI, M, DYNAMICS OF CONCENTRATED POLYMER SYSTEMS .1. BROWNIAN-MOTION IN EQUILIBRIUM STATE, JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS II 74: 1789 (1978).
(
10.1039/F29787401789
) / JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS II (1978) -
FAWCETT, J.S., SEPARATION SCIENCE 1: 9 (1966).
(
10.1080/01496396608049432
) / SEPARATION SCIENCE (1966) 10.1038/333824a0
-
GRIFFITH, J, VISUALIZATION OF THE BENT HELIX IN KINETOPLAST DNA BY ELECTRON-MICROSCOPY, CELL 46: 717 (1986).
(
10.1016/0092-8674(86)90347-8
) / CELL (1986) -
HAGERMAN, P.J., SEQUENCE DEPENDENCE OF THE CURVATURE OF DNA - A TEST OF THE PHASING HYPOTHESIS, BIOCHEMISTRY 24: 7033 (1985).
(
10.1021/bi00346a001
) / BIOCHEMISTRY (1985) -
HAGERMAN, P.J., INVESTIGATION OF THE FLEXIBILITY OF DNA USING TRANSIENT ELECTRIC BIREFRINGENCE, BIOPOLYMERS 20: 1503 (1981).
(
10.1002/bip.1981.360200710
) / BIOPOLYMERS (1981) -
HAGERMAN, P.J., SEQUENCE-DIRECTED CURVATURE OF DNA, NATURE 321: 449 (1986).
(
10.1038/321449a0
) / NATURE (1986) - Hagerman, P. J., Proceedings of the National Academy of Sciences of the United States of America 81: 4632 (1984). / Proceedings of the National Academy of Sciences of the United States of America (1984)
-
KOO, H.S., CHEMICAL DETERMINANTS OF DNA BENDING AT ADENINE-THYMINE TRACTS, BIOCHEMISTRY 26: 3745 (1987).
(
10.1021/bi00386a070
) / BIOCHEMISTRY (1987) -
KOO, H.S., DNA BENDING AT ADENINE . THYMINE TRACTS, NATURE 320: 501 (1986).
(
10.1038/320501a0
) / NATURE (1986) -
LERMAN, L.S., WHY DOES THE ELECTROPHORETIC MOBILITY OF DNA IN GELS VARY WITH THE LENGTH OF THE MOLECULE, BIOPOLYMERS 21: 995 (1982).
(
10.1002/bip.360210511
) / BIOPOLYMERS (1982) -
LEVENE, S.D., BIOCHEMISTRY-US 25: 3988 (1986).
(
10.1021/bi00362a003
) / BIOCHEMISTRY-US (1986) -
LEVENE, S.D., A COMPUTER-GRAPHICS STUDY OF SEQUENCE-DIRECTED BENDING IN DNA, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 1: 429 (1983).
(
10.1080/07391102.1983.10507452
) / JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (1983) -
LEVENE, S.D., RING-CLOSURE PROBABILITIES FOR DNA FRAGMENTS BY MONTE-CARLO SIMULATION, JOURNAL OF MOLECULAR BIOLOGY 189: 61 (1986).
(
10.1016/0022-2836(86)90381-5
) / JOURNAL OF MOLECULAR BIOLOGY (1986) - Lifshitz, E. M., Statistical Physics: 396 (1980). / Statistical Physics (1980)
10.1016/0092-8674(86)90814-7
-
LUMPKIN, O.J., MOBILITY OF DNA IN GEL-ELECTROPHORESIS, BIOPOLYMERS 21: 2315 (1982).
(
10.1002/bip.360211116
) / BIOPOLYMERS (1982) -
LUMPKIN, O.J., THEORY OF GEL-ELECTROPHORESIS OF DNA, BIOPOLYMERS 24: 1573 (1985).
(
10.1002/bip.360240812
) / BIOPOLYMERS (1985) -
Lumpkin, O. J., Physical Review A 39: 6557 (1989).
(
10.1103/PhysRevA.39.6557
) / Physical Review A (1989) - Marini, J. C., Proceedings of the National Academy of Sciences of the United States of America 79: 7664 (1982). / Proceedings of the National Academy of Sciences of the United States of America (1982)
- Proceedings of the National Academy of Sciences of the United States of America 80: 7678 (1983). / Proceedings of the National Academy of Sciences of the United States of America (1983)
-
NOOLANDI, J, SELF-TRAPPING AND ANOMALOUS DISPERSION OF DNA IN ELECTROPHORESIS, PHYSICAL REVIEW LETTERS 58: 2428 (1987).
(
10.1103/PhysRevLett.58.2428
) / PHYSICAL REVIEW LETTERS (1987) -
SCHELLMAN, J.A., FLEXIBILITY OF DNA, BIOPOLYMERS 13: 217 (1974).
(
10.1002/bip.1974.360130115
) / BIOPOLYMERS (1974) -
SERWER, P, EXCLUSION OF SPHERES BY AGAROSE GELS DURING AGAROSE-GEL ELECTROPHORESIS - DEPENDENCE ON THE SPHERES RADIUS AND THE GELS CONCENTRATION, ANALYTICAL BIOCHEMISTRY 158: 72 (1986).
(
10.1016/0003-2697(86)90591-9
) / ANALYTICAL BIOCHEMISTRY (1986) -
SERWER, P, AGAROSE-GEL ELECTROPHORESIS OF BACTERIOPHAGES AND RELATED PARTICLES, JOURNAL OF CHROMATOGRAPHY-BIOMEDICAL APPLICATIONS 418: 345 (1987).
(
10.1016/0378-4347(87)80014-2
) / JOURNAL OF CHROMATOGRAPHY-BIOMEDICAL APPLICATIONS (1987) -
SLATER, G.W., PREDICTION OF CHAIN ELONGATION IN THE REPTATION THEORY OF DNA GEL-ELECTROPHORESIS, BIOPOLYMERS 24: 2181 (1985).
(
10.1002/bip.360241202
) / BIOPOLYMERS (1985) -
SLATER, G.W., ON THE REPTATION THEORY OF GEL-ELECTROPHORESIS, BIOPOLYMERS 25: 431 (1986).
(
10.1002/bip.360250305
) / BIOPOLYMERS (1986) - ULANOVSKY, L, CURVED DNA - DESIGN, SYNTHESIS, AND CIRCULARIZATION, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 83: 862 (1986). / PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (1986)
- Valleau, J. P., Statistical Mechanics: CH4 (1977). / Statistical Mechanics (1977)
-
WAKI, S, STUDY OF AGAROSE GELS BY ELECTRON-MICROSCOPY OF FREEZE-FRACTURED SURFACES, BIOPOLYMERS 21: 1909 (1982).
(
10.1002/bip.360210917
) / BIOPOLYMERS (1982) 10.1038/308509a0
10.1126/science.2951850
-
ZIMM, B.H., SIZE FLUCTUATIONS CAN EXPLAIN ANOMALOUS MOBILITY IN FIELD-INVERSION ELECTROPHORESIS OF DNA, PHYSICAL REVIEW LETTERS 61: 2965 (1988).
(
10.1103/PhysRevLett.61.2965
) / PHYSICAL REVIEW LETTERS (1988)
Dates
Type | When |
---|---|
Created | 18 years, 10 months ago (Oct. 5, 2006, 5:21 p.m.) |
Deposited | 1 year, 7 months ago (Jan. 12, 2024, 11:59 p.m.) |
Indexed | 1 year ago (Aug. 12, 2024, 7:16 a.m.) |
Issued | 36 years, 1 month ago (July 28, 1989) |
Published | 36 years, 1 month ago (July 28, 1989) |
Published Print | 36 years, 1 month ago (July 28, 1989) |
@article{Levene_1989, title={Understanding the Anomalous Electrophoresis of Bent DNA Molecules: a Reptation Model}, volume={245}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.2756426}, DOI={10.1126/science.2756426}, number={4916}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Levene, Stephen D. and Zimm, Bruno H.}, year={1989}, month=jul, pages={396–399} }