Field inversion gel electrophoresis in denaturing polyacrylamide gels

Separation of double-stranded and single-stranded DNA in polymer solutions: I. Mobility and separation mechanism

We have studied the separation of single-stranded and double-stranded DNA in a matrix of entangled, linear poly-N,N-dimethylacrylamide. Our results give better insight into the mechanisms involved during separations in polymer solutions. The dependence of different parameters on DNA size, electric field, pore size and the polymer chain length are evaluated and compared to theoretical predictions. Striking differences between experimental data and predicted scaling laws are found. Our data should help to optimize DNA separation in capillary electrophoresis and to improve existing models for DNA separation in porous matrices.

Finding a universal low viscosity polymer for DNA separation (II)

When investigating the use of different polymers for capillary electrophoresis we found that poly-N,N-dimethylacrylamide (pDMA) has a very low viscosity compared to other polymers of comparable molecular mass and resolving power. This makes it a potentially useful matrix for DNA separation in multi-capillary electrophoresis, where short cycle times or low pressure for matrix replacement are preferred. We have characterized this matrix by systematic studies on concentration, chain length and field strength dependence. It is shown that pDMA performs well for the separation of oligonucleotides and double-stranded DNA fragments. Together with the application of DNA sequencing, pDMA is a universal polymer for the separation of biological macromolecules.

DNA separation with field inversion capillary electrophoresis

We have built an automated pulsed field capillary electrophoresis system on the basis of a commercially available device. Using entangled polymer solutions as separating matrix, we demonstrate a considerable improvement of separation of double-stranded DNA in the range of 1-50 kbp under pulsed field conditions. The influence of the main parameters, i.e. pulse frequency and electric field, is studied and the results are compared to existing electrophoresis theories.

Trapping gel electrophoresis of end-labeled DNA: an analytical model for mobility and diffusion

As shown by Ulanovsky, Drouin and Gilbert (Nature 1990, 343, 190-192), the gel electrophoretic migration of DNA is severely reduced by steric trapping when streptavidin is attached to one end of the polyelectrolyte. We present a model that allows us to calculate both the mobility and the diffusion coefficient, hence the resolution factor of the resulting separation. We compare our results to those of Défontaines and Viovy (Electrophoresis 1993, 14, 8-17) and we show that the averages over the molecular conformations must be done carefully. We also show that trapping increases diffusion substantially and that this makes constant-field trapping electrophoresis incapable of increasing the number of bases read per sequencing run. Finally, we conclude that severe trapping may lead to highly anomalous transport behavior where one cannot define a velocity or a diffusion constant.

Separating field strength, temperature, and pulsing effects in pulsed field electrophoresis

The utility of pulsed field electrophoresis for DNA sequencing is investigated. Previous studies have indicated a beneficial retardation of sequencing fragments when pulsed fields are employed. The interpretation of these results is complicated, however, by concomitant variations in electric field strength and/or temperature. Methods are presented here permitting discrimination of such mobility effects due to pulsing, field strength, and temperature. It is demonstrated that under the conditions employed here, observed mobility effects are due to electric field variations rather than pulsing. These conditions thus correspond to the low frequency/small molecule limit. The effect of temperature is estimated from the steady state solution to the heat conduction equation under appropriate boundary conditions. No temperature effect upon mobility is operative in the thin gel system employed, due to the high efficiency of heat transfer. However, it is shown that in conventional gel systems large temperature-related mobility effects can occur. These methods for dissecting and understanding mobility effects in pulsed field electrophoresis are expected to be of general utility.

Simulation of reduced band broadening during single-stranded DNA pulsed field electrophoresis in polyacrylamide gels

Using a computer simulation algorithm based on the reptation model, we investigated the effects of pulsed field gel electrophoresis on the separation of single-stranded DNA molecules in denaturing polyacrylamide gels. Pulsed fields that combine two different field intensities were found to affect the orientation of the reptation tube as well as the electrophoretic velocity, the rate of band broadening, the plate height and the molecular length for which the minimum of mobility was found, in agreement with available experimental results. Due to "memory" effects, pulses alternating between the forward and backward directions can reduce the diffusion constant by many orders of magnitude. Pulses of identical polarity but different intensities reduce the diffusion because stretches of less-oriented DNA segments are conserved during the migration. We suggest that, for DNA sequencing, pulsed fields of fixed polarity should be used to reduce band broadening and not to overcome band inversion or suppress molecular orientation. We conclude that, using a low intensity, constant electric field will lead to smaller band widths than any pulsed field regime, in a similar length of experimental time, but with less complications.