DNA gel electrophoresis: effect of field intensity and agarose concentration on band inversion

Separation of topological forms of plasmid DNA by anion-exchange HPLC: Shifts in elution order of linear DNA

We sought to establish a single anion-exchange HPLC method for the separation of linear, open circular and supercoiled plasmid topoisomers using purified topoisomeric forms of three plasmids (3.0, 5.5 and 7.6 kb). However, finding one condition proved elusive as the topoisomer elution order was determined to depend on salt gradient slope. The observed change in selectivity increased with plasmid size and was most pronounced for the linear form. Indeed, the elution order of the linear 7.6 kb plasmid was reversed relative to the supercoiled form. This observation may have implications for methods used in quality control of plasmid DNA.

Field-inversion electrophoresis on a microchip device

We have proposed a field-inversion electrophoresis on a microchip for a shorter effective length, and investigated the external frequency for the DNA analysis based on the field-inversion electrophoresis device. By using the optimized frequency, we demonstrated that the field-inversion electrophoresis has great potentials for the separation of DNA fragments with shorter effective length.

Gel electrophoretic mobility of single-stranded DNA: the two reptation field-dependent factors

The reptation model is the dominant theory in understanding the electrophoretic separation of single-stranded DNA molecules in gels or entangled polymer solutions. Recently, we showed that the Ogston and reptation regimes are separated by an entropic trapping regime at low field intensities. Here, we report the first comparison of the field-dependent part of the DNA mobility for both small and long reptating molecules. We show that both mobilities increase linearly with field intensity, with the mobility of the longer (comigrating) fragments increasing faster than that of the smaller ones. We compare our results to the predictions of the biased reptation model.

Unlimited increase in the resolution of DNA ladders

Fractionation of DNA ladders by gel electrophoresis is limited by the progressive compressing of the long DNA end of a ladder. Improvement in the resolution of this DNA is achieved by use of the following two-step electrophoresis. Initially, the DNA ladder is fractionated by conventional constant field agarose gel electrophoresis. Subsequently, gel electrophoresis is performed in the reverse direction by pulsing the electrical field (PFGE). A newly developed type of pulsing is used, which causes inversion of a double-stranded DNA ladder: the distance migrated increases as the length of the DNA molecule increases. Thus, the resolution of DNA bands continues to increase during the PFGE. These two stages of electrophoresis are serially repeated. Eventually, both the short and the long DNA ends of the ladder migrate out of the gel while a selected region of the ladder undergoes progressive increase in resolution during back-and-forth migration. Improved resolution of DNA bands is achieved, without a known limit.

Replaceable polymers in DNA sequencing by capillary electrophoresis

Much progress has been made in the development of replaceable sieving polymers and capillary coatings for high-performance DNA sequencing by capillary electrophoresis. Several studies of parameters that affect resolution, read length and reproducibility have begun to reveal the physical mechanisms acting on single-stranded DNA during electrophoresis through semidilute polymer solutions. Recently developed electro-osmosis-inhibiting matrix polymers have simplified the process of coating capillaries, facilitating the automation of high-throughput parallel systems for large-scale sequencing.

Dispersion coefficients of lambda DNA in agarose gels during electrophoresis by fringe recovery after photobleaching

By combining an electrophoretic cell with a fringe recovery after photobleaching setup, we have measured both the electrophoretic mobility mu and the dispersion coefficient D of double-stranded lambda-DNA in agarose gel as a function of the applied electric field E. Besides the determination of the mobilities, the analysis of the exponential decay of the signal gives, for the first time, experimental values of the longitudinal Dx and transverse Dy dispersion coefficients (field E perpendicular and parallel to the light fringes, respectively). Time dispersion measurements are complicated by the existence of a bleached area drift time. We present an analysis of their different contributions. Both dispersion coefficients increase linearly with increasing field E and, in the range of field we used, Dx is larger than Dy. Our results are consistent with the recent theoretical predictions of Slater (Electrophoresis 1993, 14, 1-7) and Duke et al. (Biopolymers 1994, 94, 239-247).

Capillary electrophoresis with polymeric separation media: considerations for theory

The theory of capillary electrophoresis with polymeric separation media is reviewed. Some of the major theories of gel electrophoresis are examined in terms of the experimental observations that they support. The considerations and difficulties in applying these theories to capillary electrophoresis with polymeric separation media are investigated, particularly the use of high electric field strengths and low concentration polymer solutions. Recent advances in this area, including some empirically-derived relationships and models currently found in the literature, and future directions for theory development are discussed.

Diffusion, Joule heating, and band broadening in capillary gel electrophoresis of DNA

We calculated the longitudinal and transverse diffusion coefficients for a DNA molecule undergoing gel electrophoresis in the limit where it is reptating through a dense polymer matrix. Our results indicate that both diffusion coefficients increase with the electric field intensity. The transverse and longitudinal diffusion coefficients are roughly equal for regular field intensities, but the former dominates for the high field intensities normally used for capillary gel electrophoresis (CE). This has important implications for the optimization of CE. Our results clearly show that the naive use of the zero-field diffusion constant, the Einstein relation or the longitudinal diffusion constant when calculating the contribution of the parabolic temperature profile to band broadening may lead to large overestimates under typical CE conditions. Finally, we show that the field-dependent diffusion coefficients may be responsible for the existence of an optimal field intensity for CE, even if Joule heating is neglected.

Influence of the agarose matrix in pulsed-field electrophoresis

Properties of agarose potentially relevant to PFGE (pulsed-field gel electrophoresis) are reviewed, and some new information is presented. Agarose polymers appear to have molecular weights in the range of 100,000 to 200,000 Da, but this is not tightly related to the effective gel strength. Agarose has some residual charge, and hence exhibits electroendosmosis (EEO). It is possible to markedly increase the speed of separation of DNA molecules by using agarose of low EEO, especially in low ionic strength, non-borate buffers. This increase is especially noticeable in the relatively long experiments required for separation of large DNAs. It is also possible to increase the range of separation in a single run by use of step gradients of agarose concentration, which allows visualization of yeast chromosomes and lambda-phage restriction fragments in the same lane. Because of the strong influence of concentration on separation, it may be useful for investigators to control water content and related variables. Our lack of knowledge of the detailed microstructure of gels may be barrier to complete understanding of PFGE.

Biased sinusoidal field gel electrophoresis for the separation of large DNA

In agarose gel electrophoresis, in a steady, continuous field, it is well known that the mobility mu, versus size M relation for linear DNAs (L-DNAs) can be divided into three regimes: Ogston regime I for small DNAs, where M dependence of mu, is weak; entangled but unstretched regime II for intermediate-size L-DNAs (of M < 20 kbp), where mu, sigma M-1 so that efficient fractionation is possible; and entangled and stretched regime III for large L-DNAs, where M dependence of mu s is again weak. Although mu s and the regimen boundaries can be altered by adjusting the gel concentration Cgel and/or the field strength E, the features of the M dependence of mu s are essentially unchanged. As to the effect of DNA topology on mu s, we found that in dilute gels (Cgel < 1.0 wt%) coiled, circular DNAs (C-DNAs) of 2-7 kbp size migrate faster than L-DNAs of comparable size, while in concentrated gels (Cgel > 1.5 wt%) C-DNAs migrate much slower than L-DNAs. To facilitate separation of large DNAs in the regime III range, we proposed biased sinusoidal field gel electrophoresis (BSFGE), which utilizes a sinusoidal field of strength Es and frequency f superposed on a steady bias field of strength Eb.(ABSTRACT TRUNCATED AT 250 WORDS)

Theory of band broadening for DNA gel electrophoresis and sequencing

The problem of (thermal) band broadening during DNA gel electrophoresis is studied analytically and numerically using the reptation model. It is shown that the orientation of the end-to-end vector of the molecules leads to increased diffusion and even to molecular size-independent band broadening. Thus, the Einstein relation between mobility and diffusion holds for only very small molecules. Also, "self-trapped" molecules are predicted to give fuzzy bands, as observed experimentally. Finally, megabase molecules are discussed and the consequences of our predictions for the improvement of sequencing are considered.

Problems and prospects in the theory of gel electrophoresis of DNA

Electrophoresis of DNA through gels of agarose or polyacrylamide (PA) has been one of the most widely used techniques of molecular biology during the past decade, serving both analytical and preparative purposes. The molecular theory of this process has been developing slowly over the same period of time as the result of the efforts of a small but expanding group of people. Initially simple, the theory has grown in ways that no one anticipated at the beginning, partly in response to unexpected experimental discoveries. In this review we describe its current state, including both solved and unsolved problems.

Microscopic behaviour of DNA during electrophoresis: electrophoretic orientation

The study of the behaviour of DNA when subjected to electric fields poses several intriguing problems of fundamental physico-chemical importance. Electric field (Kerr effect) orientation of DNA in free solution as well as migration of DNA in gel electrophoresis are two well-established, but so far rather separate, research fields. Whereas the first one has been generally concerned with basic structural and dynamical properties of DNA (Charney, 1988), the second is closely related to techniques of molecular biology (for a review on DNA electrophoresis, see stellwagen 1987).

An improved pulsed-field polyacrylamide gel electrophoresis system for physical selection of linking clones: isolation of SfiI linking clones from a chromosome 21-specific library

We had previously developed an efficient procedure for selective cloning of rare-cutter linking fragments that is based on physical separation of linking clone DNAs by pulsed-field polyacrylamide gel electrophoresis (PF-PAGE). An advantage of the physical selection procedure over the conventional cloning-based ones utilizing the insertion of selection marker or vector sequences into the rare-cutter sites is that it can be readily applied to the selection of linking fragments for rare-cutters, generating ambiguous cohesive end sequences such as SfiI (GGCCNNNN/NGGCC). In the present work, the physical separation procedure was improved by introducing a discontinuous buffer system into PF-PAGE, and its feasibility was exemplified by the selective isolation of SfiI linking clones from a human chromosome 21-specific library. This simple and efficient procedure will provide a useful tool for genome analysis.

The biased reptation model of DNA gel electrophoresis: mobility vs molecular size and gel concentration

The biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility-molecular size and mobility-gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still needed.