HydroLink gel electrophoresis (HLGE). I. Matrix characterization

A new gelatinous matrix is reported, having intermediate properties between those of polyacrylamide and agarose gels. The matrix has the unique property of being amphiphilic, i.e. of swelling in both plain water and polar organic solvents, and seems particularly well suited for electrophoresis of DNA. The compatibility with organic solvents includes 50% dimethyl sulphoxide, 50% tetramethyl urea, 50% acetonitrile and 50% tetrahydrofuran, the latter having a dielectric constant of 20. The matrix is hypothesized to consist of brush-like pillars, having a hydrophobic core and a hydrophilic coating. The latter is formed by short chains protruding in the surrounding liquid and able to coordinate large amounts of water.     

HydroLink gel electrophoresis (HLGE). II. Applications of a new polymer matrix to dsDNA analysis

HydroLink materials represent a novel family of gels composed of unique polymer matrices. The applications of HydroLink to molecular biology and, specifically, to DNA technology have been carefully investigated. Our results indicate that the HydroLink matrix developed for double-stranded DNA (dsDNA) is an excellent tool for electrophoretic separations in fixed electric fields. Excellent linear resolution from 100 to 5000 base pairs is easily achieved with good resolution albeit non-linear from 6000 to 23000 base pairs. The broad range of separation in addition to increased mechanical strength of dsDNA HydroLink represents a distinct advantage over other matrices currently used in DNA electrophoretic analysis.     

HydroLink gel electrophoresis: rapid electroblotting of dsDNA

Blotting and probing of DNA, RNA and proteins after electrophoresis is a powerful technique for the study of the structure and function of biomolecules. Key factors in successful blotting experiments are efficiency of transfer, maintenance of the resolution obtained during gel electrophoresis, accuracy of the probes used and sensitivity of the detection method. We have recently developed a system for the high performance resolution of DNA with 10-fold greater capacity for sample loads than agarose or polyacrylamide. In the present study, we describe conditions for the rapid (less than one hour) and quantitative electrotransfer of DNA in the 100-23,000-base pair range, with subsequent conditions for probing of transfer membranes using radioactive or biotinylated probes. Our results suggest complete maintenance of the high-resolution characteristic of HydroLink gel electrophoresis and potentially increased sensitivity due to the high loading capacity in HydroLink gel electrophoresis.     

High capacity gel preparative electrophoresis for purification of fragments of genomic DNA

We have designed a high-capacity gel electrophoretic device for the purification of large amounts of restriction endonuclease fragments of genomic DNA. This device exploits the high resolution of gel electrophoresis in conjunction with an electronic system permitting discontinuous sample elution over a large gel surface area. This feature preserves resolution and greatly increases capacity and yield. The resulting DNA fractions may be used in restriction endonuclease, ligation, transfection, and transformation reactions without further extensive manipulation. Furthermore, DNA fragments of a broad size range are recovered with high efficiency from the gel.     

Pulsed-field gel electrophoresis of circular DNA.

Mobility of supercoiled (form I) and nicked circular (form II) plasmid DNAs was determined on two major forms of pulsed-field electrophoresis, CHEF and OFAGE. Plasmids with molecular lengths ranging from 2.30 to 17.8 kilobase pairs (kb) were used with Saccharomyces cerevisiae chromosomes as standards. Agarose gel concentrations were varied from 0.3 to 2.0 percent, with higher percentage gels resolving forms I and II of smaller plasmids. The pulsing range of 3.7 to 240 seconds resulted in quite variable Saccharomyces chromosomal mobilities on both 0.5 and 1.0 percent gels, while both form I and II of all plasmid DNAs showed relatively constant mobilities with some increase at the shortest pulse times. Using a 30 second pulse time and gel concentrations of at least 1.0 percent, the usual order of migration of plasmid forms for a 17.8 kb plasmid could be changed. We interpret this result as an increase in the relative mobility of form II in our pulsed-field gel conditions.     

Pulsed homogeneous orthogonal field gel electrophoresis (PHOGE).

A versatile system (PHOGE) has been developed that allows resolution of molecules of DNA megabase pair size by the use of homogeneous, orthogonal, pulsed fields. The resulting electrophoretograms have characteristics that differ from those produced by other systems for pulsed field electrophoresis. Molecules in a two-fold range of sizes can be separated with maximum resolution, or a much larger range of sizes may be separated with lower resolution but with a linear relationship of mobility to size from 50 kb, or below, to at least 1 Mb. Straight lanes and large useable gel areas, characteristic of PHOGE, are also valuable for mapping procedures or for any other circumstance in which large numbers of samples of DNA are to be directly compared. Existing models cannot explain the results obtained, because a stage of the molecular reorientation appears to result in a rate of migration greater than that occurring by reptation. We suggest a mechanism that might account for the resolution observed and also suggest that the resolution achieved by existing OFAGE-type systems may be the result of the superimposition of PHOGE and FIGE separatory mechanisms. No maximum size of molecules that may be resolved by the PHOGE system has yet been determined.     

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.     

Theory of gel electrophoresis of DNA

A theory of the electrophoresis of DNA through gels with large interfiber spacing, such as dilute agarose, is presented. We assume that the DNA molecule moves along its axis through a “tube” in a neutral gel under the influence of the electric field. The tube is random except for possible bias due to the effects of the field. When the field is small, we easily recover the inverse-length dependence of the mobility found previously by de Gennes and by Doi and Edwards. At higher fields, a new effect appears; the tube becomes oriented because the field biases the direction of the leading end of the chain as it moves to form an extension of the tube. This leads to an increase of the mobility with increasing field by adding a field-dependent but length-independent term to the mobility expression. In agreement with experiment, we find that the field effect can be important at fields as low as 1 V/cm and that the effect can seriously decrease the sensitivity of the mobility to chain length. We also examine the fluctuation of the migration distance, the degree of orientation induced by the field, and the transient effects occurring when the feld direction is rotated by a right angle.     

Transverse agarose pore gradient gel electrophoresis of DNA.

Transverse agarose pore gradient gels were prepared on GelBond in the concentration range of nominally 0.2-1.5% SeaKem GTG agarose, using density stabilization by glycerol and incorporation of a dye to define the gel concentration at each point on the pore gradient gel. The distribution of the dye was evaluated by photography, video-acquisition and digitization of the gradient mixture and by densitometry of the gel. The gel was applied to the electrophoresis of a 1-kb standard ladder of DNA fragments, using standard submarine apparatus. The method extends to agarose gel electrophoresis the benefits of semi-automated analysis of 'Ferguson curves' described in application to polyacrylamide gel by Wheeler et al. (J. Biochem. Biophys. Methods 24, 171-180).     

High resolution preparative gel electrophoresis of DNA fragments and plasmid DNA using a continuous elution apparatus

An apparatus designed for preparative gel electrophoretic separation of proteins (M. A. Hediger, (1984) Anal. Biochem. 142, 445-454) has been used successfully for separating DNA restriction fragments. The apparatus displayed yields and resolutions that are higher than those obtainable with commercially available devices. The amounts of DNA applied to the column range from a few micrograms to milligram quantities. Restriction DNA fragments very similar in size were isolated in pure form with the apparatus. After ethanol precipitation, these fragments were successfully used for restriction enzyme cleavages, ligation, or chemical sequencing. Furthermore the apparatus provides a convenient method for the large-scale isolation of plasmid DNA. The method requires only 4 h of electrophoresis and therefore greatly reduces the preparation time compared with the conventional equilibrium centrifugation method which requires centrifugation times of up to 60 h. In contrast to the centrifugation method, contaminants such as RNA, proteins, and chromosomal DNA are efficiently removed by this technique.     

Neighboring nucleotide interactions during DNA sequencing gel electrophoresis.

Electrophoretic separation of oligonucleotides in denaturing polyacrylamide gels is primarily a function of length-dependent mobility. The 3' terminal nucleotide sequence of the oligonucleotide is a significant, secondary determinant of mobility and separation. Oligomers with 3'-ddT migrate more slowly than expected on the basis of length alone, and thus are better separated from the preceding, shorter oligomers in the sequencing ladder. Oligomers with 3'-ddC are relatively faster than expected, and are therefore less separated. At the 3' penultimate position, -dC- increases and -dT- reduces separation. Purines at the 3' terminal or penultimate positions of oligonucleotides affect separation less than the pyrimidines. These results suggest specific interactions among neighboring nucleotides with important effects on the conformation of oligonucleotides during electrophoresis. These interactions are compared to compression artifacts, which represent more extreme anomalies of length-dependent separation of oligonucleotides. Knowledge of base-specific effects on electrophoretic behavior of DNA oligomers supplements the usual information available for determination of sequences; additionally it provides an avenue to thermodynamic and hydrodynamic investigations of DNA structure.     

Rapid DNA sequencing by horizontal ultrathin gel electrophoresis.

A horizontal polyacrylamide gel electrophoresis apparatus has been developed that decreases the time required to separate the DNA fragments produced in enzymatic sequencing reactions. The configuration of this apparatus and the use of circulating coolant directly under the glass plates result in heat exchange that is approximately nine times more efficient than passive thermal transfer methods commonly used. Bubble-free gels as thin as 25 microns can be routinely cast on this device. The application to these ultrathin gels of electric fields up to 250 volts/cm permits the rapid separation of multiple DNA sequencing reactions in parallel. When used in conjunction with 32P-based autoradiography, the DNA bands appear substantially sharper than those obtained in conventional electrophoresis. This increased sharpness permits shorter autoradiographic exposure times and longer sequence reads.     

Removal of DNA curving by DNA ligands: gel electrophoresis study.

The removal of inherent curving in Crithidia fasciculata kinetoplast DNA by various small DNA ligands, groove binders and mono- and bisintercalators, has been studied by gel retardation and electron microscopy. The migration of the kinetoplast DNA fragment is highly retarded during gel electrophoresis. We demonstrate that this retardation is suppressed by DNA ligands such as distamycin and ditercalinium, which have different modes of binding and sequence specificities. Observation by electron microscopy confirms that the effect of ditercalinium on gel migration of curved DNA is linked to DNA uncurving. As the drug is progressively added to DNA, a large broadening of the retarded band is observed during gel electrophoresis for distamycin and ditercalinium. In the case of distamycin, the retarded DNA band splits into two broad bands, whereas the noncurved DNA bands remain homogeneous. This indicates that the drug-DNA exchange is extremely slow in the gel and that a limited number of specific sites on DNA are critical for the removal of bending. GC-specific quinomycin, monointercalators, and bisintercalators act in a manner similar to that of AT-specific distamycin. This indicates that direct drug binding at the dAn tracts is not required for DNA uncurving. We propose that the uncurving of kinetoplast DNA by drugs is caused by a global alteration of DNA structure; subsequent increased flexibility leads to the suppression of rigid bending at the AT tract junctions.     

Analysis of heat-denatured DNA using native agarose gel electrophoresis.

The use of native or neutral gels to resolve denatured DNA affords a rapid and convenient analytical method for assessing the consequences of a number of procedures employed in molecular biology research. We demonstrate that this method can be used to analyze transition melting temperature (Tm) and strand breakage in heat-denatured duplex DNA. This shows that some commonly recommended denaturation procedures can result in significant degradation of DNA and that reannealing or aggregation can occur when samples are concentrated or ionic conditions altered.     

Unhooking dynamics of U-shaped DNA molecule undergoing gel electrophoresis.

It has been found that DNA molecules are often hooked around obstacles in a U-shaped configuration in gel electrophoresis. To understand the dynamics of the unhooking of U-shaped DNA molecules undergoing gel electrophoresis, we have examined the length changes of the longer and shorter arms of the U-shape as a function of time. Two types of unhooking have been found. In one type, the length changes of both arms are expontential in time but with different time constants. In another type, the length changes of the shorter arm is exponential and that of the longer one is linear with time. The interpretation is that the extent of stretch of the spring-like DNA chain decreases as the length difference between the two arms increases during the unhooking processes, and that the frictions at the pivot point can be relatively large depending upon the local structure of the gel. The friction coefficient at the pivot point is estimated to be nu 0 = (2.98 +/- 1.42)x10(-5) g/sec.     

Polyacrylamide gel electrophoresis: recovery of non-stained and stained proteins from gel slices

Following electrophoresis or isoelectric focusing in gels of polyacrylamide the protein band of interest is cut out and placed above a sucrose gradient column, containing carrier ampholytes (Pharmalyte). By electrophoresis, isoelectric focusing or displacement electrophoresis the proteins migrate out of the gel slice and into the isoelectric focusing column for concentration and further purification. From this column, the proteins can be withdrawn and their isoelectric points determined. Even after staining with Coomassie Brilliant Blue at least some proteins can be recovered by this technique and used for further analyses, for instance amino acid determinations. The focusing in a pH gradient by carrier ampholytes can be replaced by an electrophoresis in a conductivity gradient column. However, in comparison with isoelectric focusing, this concentration technique has the drawback of not permitting further purification of the eluted protein.