Generalized Tube Model of Biased Reptation for Gel Electrophoresis of DNA

Noolandi, Jaan; Slater, Gary W.; Lim, Hwa A.; Viovy, Jean‐Louis

doi:10.1126/science.2928779

Cited by 86 publications

(54 citation statements)

References 18 publications

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“…Large DNA was pictured as a deformable bag (Fig. 1A) (21). In the chain model, the chain responds to the reoriented field by developing a new set of configurations, retaining a memory that diminishes as it gradually deforms toward the new orientation.…”

Section: Formulation Of the Modelmentioning

confidence: 99%

Bag model for DNA migration during pulsed-field electrophoresis.

Chu

1991

Proc. Natl. Acad. Sci. U.S.A.

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A model for pulsed-field electrophoresis was developed by picturing large DNA as a deformable "bag" that (i) moves with limiting mobility in a continuous electric field,(ii) adopts an orientation aligned with the field direction, and (ii) reorients after a change in field direction in a sizedependent manner. The model correctly predicted the resolution of large DNA in a pulsed field inoudin the surprising phenomena of mobility inversion, lateral band spreading, and improved resolution for obtuse angles. A simple parametrization agreed with observations of two completely different aspects ofDNA behavior: bulk mobility as measured during gel electrophoresis and molecular reorientation as measured by linear dichroism. The model also provides quantitative guidelines for setting experimental parameters in pulsed-field electrophoresis experiments.Gel electrophoresis in a continuous electric field does not resolve DNA molecules larger than =50 kilobase pairs (kbp) (1). Large DNA moves through the gel matrix but with a velocity that is independent of size. However, if the electric field is reoriented periodically, DNA up to several megabase pairs (Mbp) may be resolved (2-4). Because of widespread interest in separating large DNA molecules, there has been a growing effort to understand the physical basis ofpulsed-field electrophoresis (5). An early model assumes that DNA moves through the gel in a fully extended conformation: when the field is reoriented by an angle >90°, the DNA begins moving in the new direction led by what was formerly its back end (6). This simple model successfully predicts the separation of large DNA in a pulsed electric field. However, contrary to what is observed, it also predicts that the upper size limit of resolution is accompanied by zero DNA mobility. This model will not be considered further, since the goal here is to build a model that is quantitatively correct.A second model pictures the motion of the DNA as a "reptating" chain that crawls snakelike through a tube in the gel in response to the electric field. As the DNA moves forward, its leading end creates additional segments in the tube. Each step forward is in a random direction but with a bias in favor of the electric field direction. This relaxation from the rigid assumption of a fully extended conformation allows more complex DNA behavior. The reptation model successfully predicts that continuous fields will fail and pulsed fields will succeed in separating large DNA (7-9) and that in a pulsed field the size limit of separation increases proportionally to pulse time and is associated with a nonzero mobility (10). It also predicts two unexpected phenomena. First, under some conditions, transversely pulsed fields should cause larger DNA molecules to migrate faster than smaller species ("mobility inversion"). This has been experimentally observed in electrophoresis with periodic inversion of the electric field (3), but the reptation model predicts that it should also occur in transversely pulsed fields (10). Second, similar co...

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Section: Formulation Of the Modelmentioning

confidence: 99%

Bag model for DNA migration during pulsed-field electrophoresis.

Chu

1991

Proc. Natl. Acad. Sci. U.S.A.

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“…Despite the success of the original ͑Doi-Edwards͒ reptation model to elucidate a great deal of puzzling phenomena unique to entangled polymers [1][2][3][4] and biopolymers, 5,6 its quantitative predictions were not convincing in all aspects. 7,8 For example, for the particular case where the function ͑s , t͒ is analytically given by the simple formula ͑s , t͒ = ͚ p:odd ͑4 / p ͒sin͑p s / L͒exp͑−p 2 t / d ͒ as in the original Doi-Edwards theory, 1 the resulting expressions for the zero shear rate viscosity 0 and the chain center-of-mass selfdiffusion coefficient D G suggest that 0 ϳ N 3 and D G ϳ N −2 , which do not agree completely well with experimental data.…”

Section: Introductionmentioning

confidence: 99%

Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

Stephanou

Baig

Tsolou

et al. 2010

The Journal of Chemical Physics

106

153

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Articles you may be interested inTemperature dependent micro-rheology of a glass-forming polymer melt studied by molecular dynamics simulation J. Chem. Phys. 141, 124907 (2014) The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static ͑statistical͒ properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics ͑MD͒ trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability ͑s , t͒ that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed ͑s , t͒ curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic properties such as the zero shear rate viscosity and the spectra of storage and loss moduli obtained on the basis of the obtained ͑s , t͒ curves for three different polymer melts ͑polyethylene, cis-1,4-polybutadiene, and trans-1,4-polybutadiene͒ are consistent with experimental rheological data and in qualitative agreement with the double reptation and dual constraint models. The new methodology is general and can be routinely applied to analyze primitive path dynamics and chain reptation in atomistic trajectories ͑accumulated through long MD simulations͒ of other model polymers or polymeric systems ͑e.g., bidisperse, branched, grafted, etc.͒; it is thus believed to be particularly useful in the future in evaluating proposed tube models and developing more accurate theories for entangled systems.

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“…1 and 3; Table 1). Since previous studies have shown that D13S21 and D13S22 map to proximal 13q14 (30,31) and since D13S22 is present in two copies in the GM07312 cell line ( Fig. 3; Table 1), the order of the three loci is cen-D13S22-D13S21-D13S10-tel.…”

Section: Discussionmentioning

confidence: 99%

Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

Higgins

Turmel²,

Noolandi³

et al. 1990

Proc. Natl. Acad. Sci. U.S.A.

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Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage ofthe two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a dell3(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D1310-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis.

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Generalized Tube Model of Biased Reptation for Gel Electrophoresis of DNA

Cited by 86 publications

References 18 publications

Bag model for DNA migration during pulsed-field electrophoresis.

Bag model for DNA migration during pulsed-field electrophoresis.

Quantifying chain reptation in entangled polymer melts: Topological and dynamical mapping of atomistic simulation results onto the tube model

Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

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