Electrophoresis of DNA in novel thermoreversible matrices.

We demonstrate the feasibility of temperature-sensitive polymers as novel matrices for capillary and slab electrophoresis of DNA. These matrices combine the case-of-use of agarose with resolution properties of polyacrylamide. Two classes of matrices are used: (i) aqueous suspensions of gel microspheres and (ii) solutions containing uncross-linked temperature-sensitive polymers. When heated, the viscosity of these solutions drops dramatically because of the phase transition behavior of these polymers, and therefore these formulations are easy to pour or load. Results are presented for separation of double-stranded DNA fragments (< 2000 bp) in capillary, tube, and slab electrophoresis. Preliminary results are also presented for separation of single-stranded sequencing fragments by capillary electrophoresis. In the tube format, good resolution was obtained for phi X174/HaeIII fragments. In the slab format, excellent resolution of double-stranded DNA was obtained, including simultaneous separation of a 10 bp ladder up to 150 base pairs. In the capillary format, pBR322/MspI fragments were completely resolved, and single-base resolution of sequencing fragments was obtained up to 150 bases. We believe that temperature-sensitive polymers represent a new and promising class of electrophoretic media.

A transient entanglement coupling mechanism for DNA separation by capillary electrophoresis in ultradilute polymer solutions.

Using capillary electrophoresis, large DNA molecules (2.0-23.1 kbp) may be rapidly separated in ultradilute polymer solutions (< 0.002% w/w) under a high-voltage, steady field (265 V/cm). At this polymer concentration, the separation mechanism appears to be significantly different from that postulated to occur in crosslinked gels. Based on experimental results obtained with DNA restriction fragments and with negatively charged latex microspheres, we conclude that the Ogston and reptation models typically used to describe gel electrophoresis are not appropriate for DNA separations in such dilute polymer solutions. Electrophoresis experiments employing solutions of both small and large hydroxyethyl cellulose polymers highlight the importance of polymer length and concentration for the optimum resolution of DNA fragments varying in size from 72 bp to 23.1 kbp. A transient entanglement coupling mechanism for DNA separation in dilute polymer solutions is developed, which suggests that there is no a priori upper size limit to DNA that can be separated by capillary electrophoresis in a constant field.

Capillary electrophoresis of DNA in uncross-linked polymer solutions.

We have used dilute and semi-dilute uncross-linked hydroxyethyl cellulose (HEC) solutions as separation matrices for capillary electrophoresis of DNA restriction fragments. In these experiments, we investigated the effects of HEC molecular weight and concentration on resolution, attempting to relate these parameters to the polymer entanglement threshold concentration. The entanglement thresholds of seven molecular weight fractions of hydroxyethyl cellulose were determined from viscosity-concentration data; the entanglement threshold was found to scale as N-1.2, where N = number of HEC monomers. This finding is not in agreement with classical scaling arguments. We present a relationship to predict the observed entanglement threshold of HEC in solution as a function of number average molecular weight. It was found that excellent separation of phi X174/HaeIII DNA restriction fragments (72-1353 base pairs) by capillary electrophoresis in HEC solutions can be achieved significantly below the entanglement threshold, depending on DNA size and HEC molecular weight. The mechanism of separation in these uncross-linked polymer solutions must therefore be reexamined. Our experiments show that the entanglement threshold is a useful parameter in predicting a range of HEC concentrations which will separate certain DNA fragments for a given HEC molecular weight. However, the presence of a fully entangled network is not a prerequisite for separation.

Capillary electrophoresis of DNA in entangled polymer solutions.

Electrophoretic separations of DNA restriction fragments were performed in solutions of hydroxyethylcellulose (HEC) using capillary electrophoresis. Rheological studies confirmed that the entanglement threshold (phi*) for the solution is ca. 0.003 g/ml, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels was calculated using polymer-entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.

Experimental and theoretical studies of DNA separations by capillary electrophoresis in entangled polymer solutions.

Studies of electrophoretic separations of DNA restriction fragments by capillary electrophoresis in solutions of (hydroxyethyl) cellulose (HEC) were performed. Rheological studies were used to confirm that the entanglement threshold (phi*) for the HEC solutions used is approximately 0.004 g/mL, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels (on a per weight basis) was calculated using polymer-entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.

Orientation effects on the electrophoretic mobility of rod-shaped molecules in free solution.

The effect of molecular orientation on the electrophoretic mobility of rod-shaped polylons as measured by free solution capillary electrophoresis is studied by using the tobacco mosaic virus (TMV) as a model solute. This orientational dependence of molecular mobility is measured by observing the influence of electrical field strength (up to 400 V/cm) on the electrophoretic mobility of TMV. The electrophoretic mobility of TMV increases with increasing field strength. This increase can be quantitatively correlated with the decrease in the translational frictional coefficient (f) due to the increasing alignment of TMV with the electric field. A model is developed relating the decrease in f to the alignment of TMV with the electric field through its polarizability and aspect ratio. To confirm the observed orientational affects on mobility, control experiments were performed with 0.364 micron diameter Latex spheres. Due to their spherical symmetry, no orientational effects would be expected. Indeed, no increase in mobility was observed for these spherical particles. Calculations are presented to demonstrate that the increase in mobility is unlikely to be caused by either the Wien effect or any temperature variation resulting from Joule heating of the electrophoresis buffer.

Controlled phase separation of polymer-liquid crystal mixtures for reversible optical data storage.

A system for reversible optical data storage has been studied, using mixtures of polymers with liquid crystal molecules. A thin coating of a polymer-liquid crystal mixture with a laser absorbing dye would be spin coated onto a substrate and recording would be done with two types of write laser pulses. One laser pulse would be of high intensity and focused to small diameter, giving large temperature gradients and relatively fast cooling rates. The other write pulse would have lower intensity and larger diameter, resulting in smaller temperature gradients and slower cooling. A third pulse, reserved for reading, would not have sufficient intensity at the wavelength absorbed by the system to heat significantly. It would be scattered at different intensities into a photodetector depending on the cooling history of the spot being read. The feasibility of the principle was demonstrated through an experiment in which a 4-8-microm sample coating is applied to clear resistor coated glass. Energy was put into the system by a pulse generator whose power and pulse duration can be controlled. Low intensity laser light scattering patterns were observed during and after the resistive pulse to monitor the sample morphology during the experiment. A short heating pulse resulted in more intense light scattering at small angles than longer, lower power pulses.