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G W Slater

Publications and source records attributed to G W Slater.

44 records · Page 3Linked to original sources
PubMed1989

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

We study the effect of electric field intensity and agarose gel concentration on the anomalous electrophoretic mobility recently predicted by the biased reptation model and experimentally observed for linear DNA fragments electrophoresed in continuous electric fields. We show that high fields and low agarose concentrations eliminate the physical mechanism responsible for anomalous DNA mobility and band inversion, in good agreement with theory, thus restoring the monotonic mobility-size relationship necessary for unambiguous interpretation of the results of DNA gel electrophoresis.

DNA↗
PubMed1988

Scrambling of bands in gel electrophoresis of DNA.

Under certain conditions of agarose gel electrophoresis, larger DNA molecules migrate faster than smaller ones. This anomalous mobility of DNA, which can lead to serious errors in the measurement of DNA fragment lengths, is related to near-zero velocity conformations which can trap DNA chains during electrophoresis. Intermittent electric fields can be used to alter the chain conformations so as to restore the monotonic mobility-size relationship which is necessary for a correct interpretation of the gel. These data are in agreement with the results of a computer simulation based on a theoretical model of electrophoresis.

Bacteriophage lambda↗
PubMed1988

Electric field gradients and band sharpening in DNA gel electrophoresis.

A mathematical study of the effect of non-uniform electric fields on the width of DNA electrophoretic bands is presented. Using a simple model, we show that field gradients sharpen these bands during an experiment if the corresponding gradient of electrophoretic velocity is large enough. This is in agreement with experimental results indicating that narrower bands form when pulsed field electrophoresis is carried out in the presence of field gradients. Moreover, it is shown that there is in fact an optimal experimental duration that maximizes separation. Finally, gradients are also predicted to reduce the relative mobilities of the DNA fragments, which is a serious drawback of this technique.

DNA↗
PubMed1987

Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules.

The biased reptation theory has been applied to the pulsed-field electrophoresis of DNA in agarose gels. A computer simulation of the theoretical model that calculates the mobility of large DNA molecules as a function of agarose pore size, DNA chain properties, and electric field conditions has been used to generate mobility curves for DNA molecules in the size range of the larger yeast chromosomes. Pulsed-field electrophoresis experiments resulting in the establishment of an electrophoretic karyotype for yeast, where the mobility of the DNA fragments is a monotonic function of molecular size for the entire size range that is resolved (200-2200 kilobase pairs), has been compared to the theoretical mobility curves generated by the computer model. The various physical mechanisms and experimental conditions responsible for band inversion and improved electrophoretic separation are identified and discussed in the framework of the model.

Chromosomes↗
PubMedDate not supplied

Effect of nonparallel alternating fields on the mobility of DNA in the biased reptation model of gel electrophoresis.

Chromosome-size DNA molecules can now be separated using a variety of pulsed field gel electrophoresis techniques. In this article, we study the predictions of the biased reptation model concerning the effect of two pulsed fields, making an arbitrary angle, on the power of separation of gel electrophoresis. Separation is predicted to be largely enhanced for obtuse angles, in agreement with experiments. Interestingly, very large molecules, which are not separated by pulsed fields, are predicted not to migrate along the gel diagonal for fairly long periods of time. Finally, we discuss the optimization of these techniques using the results of the theory, and the limitations of the latter when fluctuations and intramolecular modes probably dominate the system.

Computer Simulation↗
PubMedDate not supplied

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.

Chemical Phenomena↗