Influence of the agarose matrix in pulsed-field electrophoresis.

Electrophoresis (1993-04-01)
F H Kirkpatrick, M M Dumais, H W White, K B Guiseley
ABSTRACT

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.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Agarose, BioReagent, for molecular biology, low EEO
Sigma-Aldrich
Agarose, Type I, low EEO
Sigma-Aldrich
Agarose, for molecular biology
Sigma-Aldrich
Sepharose® 4B, 45-165 μm bead diameter
Sigma-Aldrich
Agarose, Low EEO
Sigma-Aldrich
Agarose, Ultra-low Gelling Temperature, molecular biology grade
Sigma-Aldrich
Agarose, Ultra-low Gelling Temperature
Sigma-Aldrich
Agarose, Medium EEO, for molecular biology
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Agarose, Type I-A, low EEO
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Agarose, High Gelling Temperature
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Agarose, For pulsed field electrophoresis running gel
Sigma-Aldrich
Sepharose® 6B, 6% Beaded Agarose, 45-165 μm (wet), fractionation range 10,000-1,000,000 Da (dextrans)
Sigma-Aldrich
Agarose, Type II-A, Medium EEO
Sigma-Aldrich
Agarose, Wide range, for molecular biology
Sigma-Aldrich
Agarose, Low EEO, for Immunoelectrophoresis
Sigma-Aldrich
Agarose, High EEO, for molecular biology
Sigma-Aldrich
Agarose, High EEO
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Agarose, BioReagent, for molecular biology, Wide range/Standard 3:1
Sigma-Aldrich
Agarose, Type IV, Special High EEO
Sigma-Aldrich
Agarose, Special High EEO
Sepharose® 4B, Cytiva 17-0120-01, pack of 1 L
Sepharose® 6B, Cytiva 17-0110-01, pack of 1 L