Advances in DNA electrophoresis in polymer solutions

Abstract

DNA electrophoresis in gels and solutions of agarose and polyacrylamide was objectively evaluated with regard to separation efficiency at optimal polymer concentrations. In application to DNA fragments, polyacrylamide gels were superior for separating fragments of less than 7800 bp, and agarose gels are the best choice for larger fragments. Agarose solutions are nearly as good as polyacrylamide gels for small DNA (< 300 bp). Agarose solutions have a higher efficiency than polyacrylamide solutions for DNA of less than 1200 bp. Separation efficiency sharply decreases with increasing length of DNA. Retardation in polyacrylamide solutions was found to depend on polymer length in a biphasic fashion. The choice of resolving polymer concentrations depends on the progressive stretching of DNA in proportion to polymer concentration. The rate of that stretching appears higher in polyacrylmide solution than in gels or in liquid or gelled agarose. Application of polymer solutions to capillary electrophoresis raises further problems concerning agarose plugs, DNA interactions with the polymers, operation at low field strength and long durations as well as detection sensitivity.

Electrophoresis in lyotropic polymer liquid crystals

“…CE separations of oligonucleotides on Pluronic gels were investigated by using several standards including dT 4-16 even , dT [12][13][14][15][16][17][18] , dT [19][20][21][22][23][24] , dN 20-60, even , and a ''poly(U)'' sample (Sigma). Optimal separations were achieved in 25% gels.…”

“…The presence of these contaminants degraded the apparent resolution of larger oligomers. The resolution between oligomers differing by 1 nt up to 24 nt long in the dT [12][13][14][15][16][17][18] and dT [19][20][21][22][23][24] standards ranged from 2.8 to 3.5, about twice that calculated from several published electropherograms of separations that used capillaries filled with linear polymer solutions or polyacrylamide gels (11,17,31).…”

“…CE is often performed in concentrated solutions of uncrosslinked, hydrophilic linear polymers such as polyacrylamide, agarose, and poly(ethylene oxide) (e.g., see refs. [16][17][18][19][20] and references therein). Replacement of polymer solutions between runs enhances reproducibility and avoids problems associated with the physical and chemical instabilities of crosslinked gels under the conditions of CE.…”

When can the Ogston-Morris-Rodbard-Chrambach model be applied to gel electrophoresis?

“…Empirical modifications of Eq. (3) have been suggested by Morris [2] and Rodbard and Chrambach [3], and there is experimental evidence for deviations from this equation for cases with very large molecular size [8]. Recent results from analytical models and computer simulations have claimed that extension of the OMRC model to ordered media (i.e., media consisting of nonrandomly oriented obstacles) is invalid and that indeed, even for random media, the basic relationship given by Eq.…”

Cross-linked poly(N-acetylethylenimine) as an isoelectric focusing matrix

“…The most successful oxidant was H 2 O 2 (added in molar equivalent to thiols) with FeSO 4 (0.01 mM) as catalyst; with these reagents, a viscous liquid was obtained. Perhaps, this polymer system could have applications for electrophoresis where mechanical strength is not as essential, such as in capillary electrophoresis [21].…”