High-Performance Electrophoresis Including Separation of Nucleic Acids and their Degradation Products. Interplay Between Theory and Practical Experiments

Recent developments towards a unified theory for separation science (minireview)

Various techniques for chemical separation can be described using a generally applicable theory. There are several schools of thought on how a unified separation science should be developed. The theories described include the mass balance equation (i.e. moving boundary), virtual migration distances, and the use of individual capacity factors.

High-performance field inversion capillary electrophoresis of 0.1-23 kbp DNA fragments with low-gelling, replaceable agarose gels

Field inversion capillary gel electrophoresis (FICGE) has been used for the separation of 0.1-23 kbp DNA fragments in a low-melting, low-gelling agarose gel. The influence of the amplitude of the voltage pulses, the pulse times and gel concentrations on the separation factor has been studied and found to be similar to that of polyacrylamide gels. Very high resolution can be obtained by altering continuously the pulse times and/or voltage according to a program tailor-made for the size of the DNA molecules to be separated (programmed FICGE). The advantage of these agarose gels in comparison with polyacrylamide gels is that they are nontoxic, easy to prepare and they have high UV transmission. They give a resolution that is equivalent to or better than that of polyacrylamide gels, and the risk of bubble formation in the gel is small. In addition, they are replaceable and, therefore, very convenient for automated analyses.

Separation of long DNA fragments by capillary gel electrophoresis with laser-induced fluorescence detection

Long DNA fragments were separated by capillary gel electrophoresis with laser-induced fluorescence detection, and two approaches to obtaining high-resolution separation of DNA fragments were examined. One method achieved high resolution at the expense of detection time, while the other achieved both high resolution and fast detection. The former approach used a 300 cm long capillary with a gel concentration of 4% T and an electric field strength of 70 V/cm. The resolution limit in this electrophoresis was 800 bases with a resolution value of 0.5 for adjacent peaks. Under these conditions, the measurement time was 44 h. The latter approach used a 200 cm long capillary with a gel concentration of 3% T and an electric field strength of 170 V/cm. The resolution limit in this electrophoresis was 680 bases with a resolution value of 0.5 for adjacent peaks, and the measurement time was only 10 h. With both approaches, fragments with less than 600 bases were efficiently separated. The resolution values for adjacent peaks with less than 500 bases are greater than 1.0, and those for peaks with less than 100 bases are greater than 2.7. These approaches thus improve the accuracy of the base sequence determination.

Zone broadening in electrophoresis with special reference to high-performance electrophoresis in capillaries: an interplay between theory and practice

Approximate equations have been derived for the total (final) zone width (plate height, plate number and resolution) as a function of the width of the starting zone and of the zone broadening caused by diffusion. Joule heat, adsorption and the difference in conductivity (delta kappa) between a solute zone and the surrounding buffer. Two cases are treated: (A) the conductivity differences eliminate entirely or (B) partially, the diffusional broadening at one boundary of a zone. When adsorption is negligible one can derive from these equations the field strength - and for case A also the electrical conductivity - that gives the minimum zone broadening (plate height). Interestingly, at this minimum, contributions to the zone broadening from diffusion. Joule heat and conductivity differences have the ratio 4:1:1 in case A. In case B the ratio between the broadening caused by diffusion (including that caused by conductivity and pH differences) and broadening due to Joule heat is 4:1. The total zone width, plate height and optimal field strength calculated from the derived equations agree satisfactorily with experimental values. A simple method to estimate the variance of the zone broadening caused by the Joule heat led to a formula similar to that calculated mathematically. An appropriate width of the starting zone can be calculated rapidly by means of a simple formula. Following a run the true width can be estimated graphically from measurements of plate heights or zone widths at low field strengths. For high resolution the width of the starting zone usually should not exceed 0.5 mm. A new principle for the design of multi-buffer systems which generate sufficiently narrow starting zones has been developed for carrier-free zone electrophoresis. This zone sharpening method permits application of wide zones of concentrations below the detection limit of the monitor. The diffusion coefficient (D) and the universal parameter D/mu (mu = mobility) appear in many of the equations derived and are often the only variables which are not easily accessible. Simple methods have therefore been developed by which they can be determined with sufficient accuracy. Fortunately, they are raised to the power of 1/5 in many formulas and therefore only a rough estimation is required. True plate numbers (calculated in the absence of electroendosmosis) often differ considerably from apparent plate numbers (calculated in the presence of electroendosmosis). A mathematical relationship between the true and apparent plate numbers has been derived.(ABSTRACT TRUNCATED AT 400 WORDS)