Progress in developing improved programs for pulsed field agarose gel electrophoresis of DNA

Abstract

Details are described here for using a rotating gel to perform pulsed field agarose gel electrophoresis (PFGE) with programmable control of the following variables: magnitude of the electrical field, polarity of the electrical field, temperature of the gel and position of the rotating disk upon which the agarose gel rests. By use of this procedure for programmable control, modes of PFGE have been explored that have the following characteristics: (i) resolution by DNA length is completely lost for DNA shorter than a critical length that increases as the pulse times increase, and (ii) resolution by DNA length is enhanced for longer DNAs that are shorter than a second critical length. This window of resolution can be moved to the position of the 2-6 Mb chromosomes of Schizosaccharomyces pombe.

Micropump based on electroosmosis of the second kind

“…The two last decades have witnessed a large volume of publications within the field of microfluidics, including capillary electrochromatography [1,2], capillary electrophoresis [3,4], gel electrophoresis [5][6][7], drug delivery systems [8][9][10][11][12]; biochemical analysis, genomics and proteomics [13][14][15], separation of colloids and cells [16][17][18], medical investigations [19,20], and microelectronics cooling [21].…”

Computer‐assisted 2‐D agarose electrophoresis of Haemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

“…In fact, bidirectional agarose electrophoresis has been used to separate linear, branched, and circular DNA fragments [12,13], multienzyme complexes [31], and, more recently, the analysis of bacteriophage DNA packaging motors [32]. Although bidirectional agarose electrophoresis is the method of choice for sieving large particles, large linear dsDNA fragments would require PFGE to achieve separation [33]. Technology developed for PFGE, e.g., the concept of a small footprint apparatus equipped with thermoelectric Peltier cells for temperature control [33,34], could likely benefit horizontal bidirectional electrophoresis in submerged agarose gels.…”

“…Although bidirectional agarose electrophoresis is the method of choice for sieving large particles, large linear dsDNA fragments would require PFGE to achieve separation [33]. Technology developed for PFGE, e.g., the concept of a small footprint apparatus equipped with thermoelectric Peltier cells for temperature control [33,34], could likely benefit horizontal bidirectional electrophoresis in submerged agarose gels.…”

Unlimited increase in the resolution of DNA ladders

“…The power supply was computer-controlled by addition of a digital-to-analog converter. The control signals were generated by software and hardware previously described for controlling both E and the orientation of a gel on a circular disk [11]. The control of orientation of the gel was bypassed for the experiments performed here.…”