Pulsed field gel electrophoresis techniques for separating 1- to 50-kilobase DNA fragments

Conventional agarose gel electrophoresis separates DNA using a static electric field. The maximum size limit for separation of DNA by this method is about 20 kilobase pairs (kb). A number of new electrophoretic techniques which employ periodic reorientation of electric fields permit separation of DNA well beyond this size limit. We sought to determine whether the use of very fast (millisecond) field switching could improve separation of DNA in the size range of 1 to 50 kb. Additionally, we have compared the resolution obtained with each of the different field switching regimens for DNA in this size range. Switching intervals of from 0.2 to 900 ms were used with unidirectional pulsing of a single electric field, with pulsed field gels, and with field inversion gel electrophoresis. Plotting the mobility of DNA as a function of size demonstrates that under the conditions used, each of these techniques offers comparable resolution. We also have examined the separation obtained when field inversion gels are run with forward and reverse fields of equal voltage and different durations, versus using fields of equal duration and different voltages. Field inversion which uses forward and reverse fields of different voltages yields resolution which is superior to the other methods examined.     

Cost‐effective media for the rapid and high resolution of small DNA fragments using polyacrylamide‐based electrophoresis

Current Tris‐based solutions for DNA electrophoresis produce a positive feedback loop between current and temperature at high voltage, resulting in long running times for the separation of even small DNA fragments. We optimized the separation of small DNA fragments (90–300 bp) in polyacrylamide‐based electrophoresis at high voltages (200volts/cm) by substituting Tris with low concentration alkali salts (e.g. 1 mm LiCl and CsCl). These media reduced the heat produced during electrophoresis, enhanced the DNA fragment resolution, and allowed gels to be run at higher voltages, reducing gel running times by 25%. In addition, the elimination of Tris and EDTA from the buffer reduced material costs approximately 10‐fold.     

Microfluidic separation of DNA

DNA separation is important for numerous applications in biotechnology and medicine. Efforts to improve DNA separation in microdevices have led to advances in capillary electrophoresis and the development of novel separation strategies. Current research on microcapillary electrophoresis materials is focused on the development of separation matrices with low injection viscosities and wall-coating capabilities. Microcapillary injector geometries are being designed to allow increased control of sample plug volumes. Novel separation strategies using entropic traps, arrays of pillars and Brownian ratchets are also being developed.     

The influence of agarose--DNA affinity on the electrophoretic separation of DNA fragments in agarose gels

The effects of DNA concentration, buffer composition, added "carrier" DNA, and chemical modification of agarose on the electrophoretic separation of DNA restriction fragments in agarose gels were tested. Electrophoretic zones of migrating DNA were found to broaden by trailing as sample load was decreased, and this effect was found to be more pronounced for species of higher molecular weight. As DNA sample load was increased, DNA fragments were found to move faster in the direction of electrophoresis (front forward). Sharp, well-resolved electrophoretic zones were obtained at very low DNA loads only when a high-salt, high-pH, high-EDTA buffer was employed or when "carrier DNA" having a broad and uniform molecular weight distribution was included in the sample. Moreover, DNA in high concentration was found to displace DNA in low concentration from a given gel region. Unmodified agaroses were found to differ only slightly in their effectiveness in retarding DNA fragments at a given agarose concentration. However, hydroxyethylated agarose was much more effective in retarding DNA, at a given gel concentration, than the unmodified agaroses tested. These results show that it is useful to consider the agarose gel matrix as possessing the properties of both a molecular sieve and a chromatographic adsorbent when designing electrophoretic separation techniques for DNA. A model for these separations which includes the effects of DNA-agarose interaction and molecular sieving is discussed.     

Separation of branched from linear DNA by two-dimensional gel electrophoresis

A general method for separating branched DNA molecules, such as replication forks and recombination intermediates, from linear forms has been developed. Using as a model a stable X-shaped molecule constructed in vitro, it was found that this branched form migrated more slowly during agarose gel electrophoresis than did a linear form of the same mass. Higher agarose concentrations and higher electrophoretic voltages enhanced the extent of retardation. These properties provided the basis for an electrophoretic method of separating branched from linear molecules by variation of agarose concentration and voltage over two dimensions. In the first dimension, concentration and voltage were low; in the second, both parameters were increased, thereby forcing X-shaped molecules to migrate to positions distinct from a diagonal arc of linear molecules. In addition, two-dimensional electrophoresis was capable of separating X-shaped forms of different mass from each other, as well as from linear molecules.     

A new approach for on-line enrichment in electrophoresis of dilute protein solutions

A method is described for on-line enrichment/zone sharpening of a sample of negatively charged proteins (an analogous method for cationic proteins can be designed). The sample is applied on the top of a 5-mm thick layer of a neutral polyacrylamide gel which rests on another 5-mm thick, large-pore polyacrylamide gel which contains positively charged groups. The latter gel layer is attached to the neutral gel column, used for the electrophoretic separation of the proteins. When a voltage is applied the proteins start migrating and become electrostatically adsorbed at the top of the charged, large-pore gel layer (pH 5.4). With the upper electrode vessel filled with a buffer of a pH higher (pH 7.7) than that employed in the enrichment step and with a voltage between the electrodes, these enriched proteins are released (because the enrichment gel is non-charged at pH 7.7) with zone sharpening and migrate into the 5-cm long column (i.d. 5 mm) of a neutral, large-pore polyacrylamide gel for electrophoretic analysis. Upon the electrophoretic migration from the enrichment gel into the separation gel a second zone sharpening may occur, if the increase in pH from 5.4 to 7.7 in the separation gel is not close to momentary. By employing colored test proteins the efficiency of the enrichment step is visually illustrated by a picture. The principle of the concentration method described has been employed also in chromatographic experiments and can with appropriate modifications also be used in other electrophoretic methods, such as capillary electrophoresis.     

Rapid isoelectric focusing in a vertical polyacrylamide minigel system

A rapid method is described for the resolution of proteins employing isoelectric focusing in a vertical polyacrylamide minigel system. Isoelectric focusing can be performed in only 3 h, utilizing low voltage, under either native conditions or denaturing conditions in the presence of 8 M urea. The procedure permits the application of larger sample volumes containing more protein than other isoelectric focusing procedures, and provides the additional advantages of slab gels over tube gels for analytical purposes. The procedure is also well adapted for use in two-dimensional electrophoretic techniques, making it possible to complete a two-dimensional gel in 1 day.     

Thermal microdevices for biological and biomedical applications

Temperature strongly influences the form and function of biologically important macromolecules and cells. Advances in microfabrication technology have enabled highly localized and accurate temperature control and manipulation, allowing the investigation of thermal effects on biological microsystems. This paper reviews progress in this field, with emphasis on techniques and microdevices with biomedical applications. Recent advances in the study of thermal effects on cellular behavior, enabled by MEMS-based structures are reported. These studies focus on investigating thermal interactions between the cell and its microenvironment. Thermal-based tools for concentration and purification of biologically important macromolecules like DNA and proteins are summarized. These tools address common issues in protein/DNA research, like concentration, separation and purification of samples. With the increasing research focus on the integration of biomedicine with engineering technologies and the several incentives of miniaturization, MEMS-based devices are likely to become increasingly prevalent in biology and medicine. Thermal engineering is expected to continue to play an important role in the improvement of current microdevices and the development of new ones.     

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.     

An angle-variable three-dimensional pulsed field gel electrophoresis system

A three-dimensional pulsed field electrophoretic method based on the simultaneous application of fixed and cyclically alternating polarity fields at a right angle is described. Requiring only minimal electronic hardware it provides highly homogeneous field conditions over a large gel area and the versatility to vary the pulse vector angle. The electrophoretic parameters critical to achieve fast high resolution separation over a wide range of molecular sizes have been optimized and applied to megabase-size chromosomal DNA molecules. The empirical relationships between pulse time, field strength conditions, and resolution limits derived allow selection of coordinated experimental conditions for the separation of specific DNA size ranges.     

Electrophoresis of DNA restriction fragments in poly-N-acryloyl-tris gels

Poly-N-acryloyl-tris(hydroxymethyl)aminomethane (NAT) gels were evaluated as a matrix for DNA electrophoresis. The resolution of DNA restriction fragments in three poly(NAT)-N,N'-methylenebisacrylamide (Bis) gels (4, 5, and 6%) was compared with the resolution in polyacrylamide (AA)-Bis gels of the same percentage. Poly(NAT) gels were found to give a substantially improved separation of DNA fragments larger than 200 bp. In contrast to poly(AA) gels, DNA fragments of up to 4 kbp were well resolved in the new matrix. By pulse-field electrophoresis the useful separation range of poly(NAT) gels was expanded to at least 23 kbp. For DNA fragments below 10 kbp, the resolution was better than that in a 0.7% agarose gel. Thus poly(NAT) gels are most suitable for the electrophoretic separation of DNA molecules whose size is out of the optimal fractionation range of poly(AA) or agarose gels.     

Ultra-fast high-resolution agarose electrophoresis of DNA and RNA using low-molarity conductive media

Current DNA electrophoretic solutions employ high ionic concentrations and require long electrophoretic run times. Here we demonstrate that high and low molecular weight double-stranded DNA, single-stranded DNA (ssDNA), and RNA can be separated rapidly in agarose-based low-molarity conductive media. Separation of small DNA fragments was optimized by substituting 1-mM solutions of alkali metals or a nonbiological amine that distributed voltage with a minute current. These ultra-dilute solutions can separate DNA at least 15-fold faster Low-molarity media at 5-10 mM adequately separated RNA and larger DNA fragments as well. These novel media reduce the Joule heating of the electrophoretic system and allow for easy-to-use, ultra-fast separation of DNA fragments.     

Capillary gel electrophoresis for rapid, high resolution DNA sequencing.

Capillary gel electrophoresis has been demonstrated for the separation and detection of DNA sequencing samples. Enzymatic dideoxy nucleotide chain termination was employed, using fluorescently tagged oligonucleotide primers and laser based on-column detection (limit of detection is 6,000 molecules per peak). Capillary gel separations were shown to be three times faster, with better resolution (2.4 x), and higher separation efficiency (5.4 x) than a conventional automated slab gel DNA sequencing instrument. Agreement of measured values for velocity, resolution and separation efficiency with theory, predicts further improvements will result from increased electric field strengths (higher voltages and shorter capillaries). Advantages of capillary gel electrophoresis for automatic DNA sequencing instruments and for genomic sequencing are discussed.     

Control of pulsed field gel electrophoresis at short switching intervals by a microcomputer

Pulsed field gel electrophoresis allows not only the separation of very large DNA molecules (up to 10 megabase pairs) but also gives an enhanced resolution in separations of DNA in the size range of 10-100 kilobase pairs (kbp). For this application, rapid alternation of the electrical field polarity is required. Here we describe equipment for the delivery of short switching pulses that is easy and inexpensive to build and is controlled by a standard microcomputer. It has proved to be useful in the separation of lambda DNA and its fragments. Parameters for enhanced separation of 23- and 48-kbp DNA molecules at high voltage gradients (15 V/cm) are presented and shown to provide superior resolution when compared to those for conventional electrophoresis at both high and low voltage gradients.     

Multiplexed fluorescence detection in microfabricated devices with both time-resolved and spectral-discrimination capabilities using near-infrared fluorescence

We examined the feasibility of using a two-color time-resolved detection scheme with microdevices for DNA sequencing applications. A home-built dual-color optical-fiber-based time-resolved near-infrared (IR) fluorescence microscope successfully coupled lifetime discrimination with color discrimination, increasing fluorescence multiplexing capabilities. The instrument was constructed by using two pulsed-diode lasers (680/780-nm excitation) and two avalanche photodiodes as the basic building blocks. The data were processed using electronics configured in a time-correlated single-photon counting format. The use of near-IR fluorescence detection greatly simplified the hardware and allowed low detection limits (< 0.1nM). We examined the separation of a single-base tract on a microchip and compared the performance with that of conventional capillary gel electrophoresis. The microchip was fabricated in glass and contained an effective separation length of 7.0 cm. It was found that, without incorporating a solid-phase reversible immobilization cleanup procedure, the calculated lifetime of the dye label on the microchip was longer and the standard deviation was larger than those of the same sample analyzed using capillary electrophoresis. Using cleanup steps, the accuracy and precision of the measurements improved. Lifetimes of four near-IR dyes (AlexaFluor680, IRD700, IRD800, and IRD40) used in this study were determined to be 986 ps (RSD=2.1%), 1551 ps (RSD=1.8%), 520 ps (RSD=3.3%), and 788 ps (RSD=4.9%), respectively, in a microchannel filled with poly(dimethylacrylamide) (POP-6) gel. The lifetimes calculated using maximum likelihood estimators provided favorable precision on the microchip, where small numbers of photocounts were collected. An M13mp18 template was sequenced on the microchip using a two-color two-lifetime format with POP-6 as the sieving polymer. Read lengths of 294 bp with calling accuracies of 90.8 and 83.7% were achieved in each color channel. The relatively low calling accuracy and the short read length resulted primarily from the short separation channel, which yielded low electrophoretic resolution.     

Application of continuous zone electrophoresis to preparative separation of proteins

A comprehensive study of the application of continuous zone electrophoresis to preparative separation of proteins in free solution is presented. First, the influence of electric field strength, buffer residence time in the chamber, sample flow rate, and sample concentration on separation resolution and throughput were studied. Using multiple injections of sample into the electrophoresis chamber, a throughput of 500 mg protein/h was achieved for partially purified model proteins. Experiments on Escherichia coli crude extracts yielded a fivefold purification of beta-galactosidase along with a simultaneous separation of proteins from cell debris in a single step. Experiments correlating the electrophoretic mobility in continuous electrophoresis with the elution behavior in ion-exchange chromatography were performed on more than a dozen proteins which conclusively showed that separation of proteins in continuous zone electrophoresis is governed by net surface charge. Based on these results, the fraction numbers in which the proteins eluted could be correctly predicted. Proteins and enzymes with differences >0.5 M elution molarities in ion-exchange chromatography were separated by continuous zone electrophoresis on a preparative scale (mg/h or g/h) with >90% recovery. This corresponds to a preparative scale separation of proteins and enzymes which differ in apparent electrophoretic mobility by only 0.70 x 10(-5) cm(2)/V . s. (c) 1993 John Wiley & Sons, Inc.     

Improved resolution of DNA fragments in polysaccharide-supplemented agarose gels

The electrophoretic separation of nucleic acids, including small DNA fragments in the range 50-1000 bp, is presently carried out in polyacrylamide gels or in gels containing high concentrations of agarose. We have developed an alternative gel matrix composition which is inexpensive, nontoxic, easy to prepare, and highly transparent to visible and uv light. The composition combines a soluble nonionic polysaccharide such as hydroxyethylcellulose, methylcellulose, or galactomannan with a minimum but sufficient concentration of agarose to form a gel which immobilizes the "liquid phase sieve." These mixtures do not replace polyacrylamide for resolving fragments smaller than approximately 75 nucleotides. However, the new gels show DNA fragment resolution (band separation versus distance traveled) and optical clarity superior to those of conventional agarose.     

Two-dimensional DNA typing

DNA typing based on gel electrophoretic separation of DNA fragments, followed by hybridization analysis, has become an important analytical tool in areas ranging from forensic science to population biology. This approach can be extended by combining size separation with sequence-specific separation in denaturing gradient gels; this creates a high resolution two-dimensional pattern. The high information content of this system means that very closely related individuals (even monozygotic twins) can be distinguished and that the genetic events associated with development or cancer, for instance, can be followed. Ultimately, 2-D DNA typing could lead to computerized matching of a single individual's genome to a database of genetic markers.     

Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis

A simple agarose-gel apparatus has been developed that allows the separation of DNA molecules in the size range from 50 kb to well over 750 kb, the largest size for which size standards were available. The apparatus is based on the recent discovery that large DNA molecules are readily fractionated on agarose gels if they are alternately subjected to two approximately orthogonal electric fields. The switching time, which was on the order of 20-50 sec in our experiments, can be adjusted to optimize fractionation in a given size range. The resolution of the technique is sufficient to allow the fractionation of a sample of self-ligated lambda DNA into a ladder of approximately 15 bands, spaced at 50 kb intervals. We have applied the technique to the fractionation of yeast DNA into 11 distinct bands, several of which have been shown by DNA-DNA hybridization to hybridize uniquely to different chromosome-specific hybridization probes. In this paper, we describe the design of the apparatus, the electrophoretic protocol, and the sample-handling procedures that we have employed.     

High-speed microchip electrophoresis method for the separation of (R,S)-naproxen

In this research, a capillary electrophoretic method for the fast enantiomeric resolution of (R,S)-naproxen was investigated. Method development involved variation of applied potential, buffer concentration, buffer pH, and cyclodextrin concentration. The optimum electrophoretic separation conditions were 110 mM sodium acetate run buffer (pH 6.0), 30 mM methyl-beta-cyclodextrin, 20% (v/v) acetonitrile, 25 degrees C. The total length of capillary was 48 cm, (50 microm I.D.) with ultra violet (UV) detection at 232 nm. Using these conditions, the number of theoretical plates was close to one million (896,000/m). The possibility of achieving a fast chiral separation of (R,S)-naproxen on a microchip of 2.5 cm in length was investigated. Complete enantiomeric resolution of naproxen was achieved in less than 1 min, on this microchip platform, with linear imaging UV detection. This system had the advantage of real-time separation monitoring, so that enantiomeric resolution could be visually observed, and high-speed chiral analysis was realized. The microchip electrophoresis (MCE) separation was compared with the capillary electrophoresis (CE) separation with regards to speed, efficiency, separation platform, and precision. This work highlights the potential of CE and MCE in future chiral separations.