Agarose electrophoresis of DNA in discontinuous buffers, using a horizontal slab apparatus and a buffer system with improved properties

Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions

Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre sample volumes, and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.

Accelerated separation of random complex DNA patterns in gels: comparing the performance of discontinuous and continuous buffers

Complex DNA fragment patterns produced by random amplified polymorphic DNA (RAPD) assays were separated in agarose as well as polyacrylamide gels using a continuous buffer and two discontinuous buffer systems, with and without urea, respectively. The effect of very high field strength/current levels on the duration of separation, the relative mobilities of the selected bands, and the appearance of the pattern was tested. The use of discontinuous buffer systems resulted in sharper bands and better resolution at 30 min duration of separation for DNA fragments in the size range of 200-2000 base pairs. These observations could help researchers in the rapid separation of band patterns produced by polymerase chain reaction (PCR)-based methods utilized in small- to mid-scale genome searches.

Horizontal gel electrophoresis with sample volumes up to 1.5 mL, using a discontinuous buffer system and automated apparatus

Horizontal gel electrophoresis has previously suffered from lack of an instrumental design that would allow for application of large sample volumes. A recently introduced commercial apparatus (HPGE-1000, LabIntelligence) remedies that problem in application to gel electrophoresis with intermittent scanning of fluorescence by using the concentrator module of that apparatus as a stacking gel reservoir. By using this technique and a 3 mL stacking gel, protein samples of up to 1.5 mL yield bands in the horizontal resolving gel that are independent of sample volume in their width, area and migration rate. A remaining procedural problem relates to the apparent nonsimultaneity of dye and protein entrance into the resolving gel, which necessitates peak characterization by absolute rather than relative mobilities.

Commercial automated gel electrophoresis apparatus: application to DNA, band dispersion, nonlinear Ferguson curves, and isolation

Recently available commercial automated gel electrophoresis apparatus with intermittent scanning of fluorescently labeled gel patterns (the HPGE-1000 apparatus of LabIntelligence, Menlo Park CA) was tested with regard to (i) its applicability to DNA in its native conformation, (ii) its ability to recognize the correct number of components, (iii) its capability to evaluate the width and shape of bands detected during electrophoresis, (iv) its ability to yield nonlinear Ferguson plots in a labor-saving fashion, and (v) its preparative potential. Ethidium homodimer (EtD) DNA (bp) ratios were systematically varied and the mobility of DNA fragments labeled at each ratio was measured in order to find a ratio which provided an unaltered mobility and presumably therefore an unaltered conformation of the fragment. That ratio was found to be 1/40 EtD/DNA (bp) or less. With such weak labeling of DNA, a representative fragment of 527 bp length requires a minimum load of 200 ng and a 2 micrograms load for a full-scale peak height. Using the baseline automatically selected by the software of the apparatus, the band areas of the 17 components of a DNA digest were consistently evaluated by the software, as evidenced by the proportionality between DNA length and area. The areas of the separated bands of DNA fragments of 1857 and 121 bp length were found to be constant with time of electrophoresis. The dispersion coefficient was found to decrease with agarose concentration in electrophoresis at 1 V/cm; however, at higher field strength, the band width of the 1857 bp fragment was surprisingly found to increase with gel concentration, presumably due to stretching.(ABSTRACT TRUNCATED AT 250 WORDS)

Band width measurement in automated gel electrophoresis apparatus: DNA dispersion in a discontinuous system and in a single buffer

Recent commercial introduction of automated gel electrophoresis apparatus allows for band width measurements during electrophoresis and therefore promises to open up the exploitation of band width and shape for the physical characterization of charged macromolecules in the same manner in which to date quantitative gel electrophoresis had exploited electrophoretic mobility at multiple gel concentrations. The measurements demonstrate decreased band width and therefore increased resolving power for a discontinuous buffer system compared to Tris-borate EDTA buffer. The dispersion coefficients (D' = (sigma 2-sigma 2o)/t) of homogeneous DNA components appear to decrease with gel concentration when either the field strength or the DNA length is small, and increase with gel concentration when these are large. This contrasting response of D' to increasing gel concentration is presumably due to DNA stretching, which increases in proportion to DNA length and field strength, and to the progressive orientation of agarose with increasing field strength.

Transverse pore gradient gel electrophoresis, using the PhastSystem

The application of pore gradient gels prefabricated for the PhastSystem (Pharmacia) to transverse pore gradient gel electrophoresis is demonstrated. It has the twofold advantage of (i) horizontal positioning, avoiding gel stretching during the preparation of these gels and resulting pore size irreproducibility experienced with vertically applied pore gradient gels, which necessitate an orthogonal transfer of spacers, and (ii) miniaturized gel dimensions, which allow a small sample load and a short duration of electrophoresis and staining.