Biased reptation

At extremely high electric field strengths, reptation turns into biased reptation mode (Figure 1, biased reptation regime) and the resulting mobility of the analyte is described by... 

In the reptation region the electrophoretic mobility depends on the solute s molecular size NP and on the field strength E according to the biased reptation model [13] ... 

Slater, GW. and Noolandi, J., The biased reptation model of DNA gel electrophoresis mobility vs. molecular size and gel concentration, Biopolymers, 28, 1781, 1989. 

Duke, T., Viovy, J.-L., and Semenov, A.N., Electrophoretic mobUity of DNA in gels. I. New biased reptation theory including fluctuations. Biopolymers, 34, 239,1994. 

The first experiments using colloidal templates were performed without the polymerization step, using silica beads with a diameter of 1.04 0.4 jxm [20]. The beads were not well-packed over the entire 0(cm) region, with monocrystalline regimes periodically interspersed by polycrystalline regimes. Electrophoresis experiments with a range of DNA samples essentially confirmed that the DNA dynamics in this array correspond to the predictions of biased reptation [33]—the mobility scales likeA ° ° and the diffusivity scales like A reptation plot [36] of the mobility... 

The mobility of flexible chains in gels is well described by the biased reptation model [1], which is indicated schematically in Fig. 4. In the model, the fibers of the gel are coarse grained into a reptation tube that confines the chain. The chain thus slithers along the tube contour (the reptation part) under the influence of the electric field, which provides a tendency for the slithering motion to be in the direction of the electric field (the biased part). 

Figure 2 Schematic view of DNA migration regimes (A) Ogston sieving (B) biased reptation and (C) reptation with permanent stretching. Rg - radius of hydrodynamic equivaient sphere of DNA coii S - average mesh size.

As a result, the separation is lost and all chains wUl move at the same speed. These scaling results agree weU with experiments, and the so-called compression band, where all of the long chains co-migrate, is a major limitation of gel electrophoresis. As a result, a great deal of effort in microfluidics and nanofluidics research has focused on designing systems which permit the separation of long DNA and other polyelectrolyte chains by methods other than biased reptation. 

DNA gel electrophoresis is one of the most widely used tools of molecular genetics research. The biased reptation model has proven to be useful to understand most continuous field and low-frequency pulsed field effects. In this paper, we review how we have generalized the reptation model to include the electric forces acting on the DNA polymer, and we give an analysis of the main results obtained from analytical and numerical calculations. 

Finally, the biased reptation model (BRM) predicts that under some conditions of field strengths and gel concentrations, the electrophoretic mobility becomes a non-monotonic function of the... 

Fig.4 In the biased reptation model, the biased walk of the chain in its tube, which creates new tube sections, is similar to the motion of a point-like particle between two absorbing walls. A biased Jump ends when the molecule has migrated over a distance a along the tube axis, i.e., when it has reached the next point defining the end of the next pore. This process is similar to the absorbtion of the particle by one of the walls, each at distance a from the starting position. The particle and the chain both have a one-dimensional velocity and diffusion constant D.

XIQT N seconds for a 100 kbp molecule, we thus have Xg 3 seconds," consistent with experiments. We thus conclude that the initial tube stretching is due to biased reptation, but that intra-tube modes also play a role on a time scale [Pg.575]

The biased reptation model provides a good framework to discuss the experimental results of the various gel electrophoresis techniques used to separate nucleic acids. Although more experiments are needed to fully characterize these techniques, available results indicate that the simplified version of the model discussed in this paper is satisfactory when low-frequency pulsed fields are used, or when transient intra-tube effects are not dominant. This is the case in continuous fields, for small molecules in intermittent fields, and possibly also for crossed fields. However, intra-tube effects are observed to play a role in field-inversion electrophoresis, for long molecules in intermittent fields, and during the first stages of an experiment (where an orientation overshoot is observed). 

The large number of cases where the biased reptation model is reliable indicates that the intra-tube effects do not rule out reptation as the basic migration mechanism. Further theoretical advances will include the effects of both intra-tube molecular orientation and tube orientation on the electrophoretic properties of large nucleic acids. 

These ideas are the basis of biased reptation theories [120-150] and computer simulations [122-127,141-147], which have in the last years encountered considerable success in the description of gel electrophoresis of DNA. 

Numerical simulations have been very helpful in the understanding of electrophoretic transport mechanisms in gels. As a first contribution, numerical simulations of the biased reptation model have permitted progress beyond the... 

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