Pulsed-field gel electrophoresis (PFGE) of agarose gels enables the reproducible separation of large DNA fragments. In concept, PFGE is an extension of conventional electrophoresis, in which two alternating (or pulsed) electric fields are used instead of the traditional single static field. Separation occurs when these fields are oriented at an obtuse angle to one another. In a pulsed-field gel, the end of each molecule migrates in a new direction, with each change of the electric fields. The DNA molecules, thus, migrate through the agarose matrix in a zigzag motion. The tardiness of the larger molecules, in turning corners (e.g., in PFGE) or in running forward and backward [e.g., in field-inversin gel electrophoresis (FIGE)], separates them from the smaller size fragments. The effectiveness of PFGE, however, is not limited to the separation of very large DNA molecules. PFGE can improve the resolution of DNA molecules of only a few hundred bases and permits separation up to 12,000 kilobase pairs (kb). A number of models and theories have been proposed to explain some of the more complex behavior of DNA molecules in PFGE. However, biologists rarely need to consult these physical models or equations for practical PFGE applications. This chapter discusses the optimum PFG electrophoretic conditions for the separation of DNA fragments from 1 to 6000 kb.

It has been reported that secondary pulsed field gel (SPFG) electrophoresis can dramatically increase the speed of separation of large DNA molecules without a decrease in resolution (Zhang, T. Y., Smith, C. L., and Canter, C. R. (1991) Nucleic Acids Res. 19, 1291-1296). However, our attempts to duplicate previous SPFG conditions were unsuccessful. We therefore sought to more precisely define the effects of secondary pulsing on the separation of large DNA and to determine the value of the technique in separating molecules up to 1100 kb. Here we report on two of the key SPFG parameters, namely the frequency and duration of the secondary pulse on the migration and resolution of DNA in SPFG. We found that the size range of separation is determined by the sum of the duration of the primary and secondary pulses. Under optimal conditions, a 25-70% increase in velocity can be achieved without loss in resolution.

We have determined the structure and organization of a 630-kb extrachromosomal element (amplisome) containing the dihydrofolate reductase-encoding gene (DHFR) in a methotrexate (MTX)-resistant human cell line, HeLa-Bu25-10B3. The size and copy number of amplisomes have previously been found to remain remarkably stable with or without selection. Both linear and open circular 630-kb amplisomes are present in these cells. We have been able to isolate the linear amplisomes after pulsed-field gel electrophoresis (PFGE), and transfect the amplisomes into MTX-sensitive recipient cells by electroporation, thus demonstrating that DNA as large as 630 kb can be transfected into mammalian cells. The NotI restriction site immediately upstream from DHFR on the circular amplisome is devoid of methylation, suggesting that it is transcriptionally active. Restriction mapping by PFGE reveals that there is only one copy of DHFR per amplisome and no repetitive structure is observed. The small size of the amplisomes, their stability and our ability to transfect large DNA molecules provide the necessary ingredients for the development of mammalian cloning vectors for large DNA fragments.

The mouse T-cell receptor (TCR) α/δ locus was mapped using 17 Vα and 4 Vδ subfamily-specific probes. Four complementary methods were used: (1) an estimate of the V gene repertoire by Southern blot analysis of genomic DNA with subfamily-specific probes; (2) an analysis of V gene segments deleted by TCR gene rearrangements from a panel of T-cell tumors and hybridomas; (3) an analysis of overlapping clusters of cosmid clones; and (4) an analysis of large DNA fragments separated by field-inversion gel electrophoresis. The α/δ locus spans about 1 Mb. The distance between the 3′-most V gene segment (Vδ1) and the δ constant gene (Cδ) is no more than 150 kb. Sixty-six V gene segments have been mapped physically on cosmids. The members of individual Vα gene segment subfamilies are dispersed throughout the locus. In contrast, the Vδ gene segments Vδ1 to 5 are clustered at the 3′ end of the V gene segment cluster. At least two DNA segment duplications, 45 to 80 kb in length, are present in the locus. These data provide information on the evolution of the α/δ locus and on organizational features that might influence the expression of specific V gene segments in γδ cells.

This paper describes a number of techniques for rapid restriction mapping of cosmid clones. First, we have replaced the cloning site of cosmid vector pWE15 with a polylinker containing 15 infrequently cleaved restriction enzyme sites that are placed asymmetrically on each side of the BamHI cloning site. DNA cloned into this vector can be fully recovered by using several pairs of restriction enzymes. Second, we have designed a simple electrical circuit device that allows the performance of asymmetric voltage gradient field inversion gel electrophoresis (AFIGE) to improve the resolution of DNA molecules in the range of 20-50 kbp. AFIGE can be obtained by simply placing the device in between a commercially available switching unit and the gel box in a standard field inversion system. Finally, the restriction digestion procedure has been automated by using a Beckman Biomek 1000 robotic workstation. Using this automated system, 96 restriction reactions, including gel loading, can be performed in less than two hours. In summary, these methods represent at least a tenfold improvement in the speed and/or mapping data that can be obtained in a single gel.

We have previously shown that asymmetric-voltage field inversion electrophoresis produces more uniform separation for fragments between 1 and 50 kilobases (kb) than other modes of pulsed field gel electrophoresis. We now report on the basis of this phenomenon. As in conventional electrophoresis, the pulsed field mobility of DNAs between 1 and 50 kb varies with voltage in a size dependent manner. The complex migration pattern obtained with asymmetric-voltage field inversion electrophoresis reflects the difference between the mobilities of each sized fragment under the conditions used for the forward and reverse fields. We have applied this technique to DNA sequencing gels and find improvement in resolution for single-stranded fragments in polyacrylamide gels.

Submicroscopic extrachromosomal elements (amplisomes) containing amplified dihydrofolate reductase (DHFR) genes have been investigated in a methotrexate-resistant derivative of the human cell line HeLa BU25, 10B3, by field-inversion gel electrophoresis. The amount and kinetics of formation of these elements have been correlated with the level and time course of overall DHFR gene amplification. The amplisomes account for the great majority and possibly the totality of the amplified DHFR genes in 10B3 cells. They appear very early during the development of methotrexate resistance and increase in parallel with the amplified genes. These observations suggest that these elements are involved in an early event, possibly the first event, of gene amplification in this system. Amplisomes tend to be lost from 10B3 cells in the absence of selective pressure, although much more slowly than expected from simple dilution of nonreplicating elements. Surprisingly, under selective pressure, these elements have shown no tendency to become integrated into chromosomes or to generate minute chromosomes over a period of almost 1 year, in contrast to what has been described in other systems.

We have examined the effects of pulsed electric fields on the separation of single‐stranded DNA molecules in polyacrylamide sequencing gels. Using different electric field pulsing regimens, the mobilities of single‐stranded DNA molecules can be retarded or increased as compared to conventional electrophoresis. These results indicated that pulsed field techniques can be applied to gel electrophoresis of small single‐stranded DNA molecules.

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.

We have studied the migration of DNA in pulsed field agarose gels under a variety of electrophoresis conditions. We have made use of an instrument which can generate electric fields of any orientation, magnitude, or duration to compare different separation techniques for DNA molecules of from 1 to several thousand kilobase pairs. We discuss the capabilities of the system and present results of gel runs in which electrophoresis conditions were changed individually or in combination. The mobility of DNA in pulsed field gels is shown to reflect a number of interdependent physical parameters.

ffhe searation of large (>50 kilcibase pairs) DIN molecules has been made possible by the introducticn of pulsed field gel (Pm) electrcoresis by Schwartz and Cantor (1). Intact dcrcmosames fram a mnurber of micror isM and large imalian lt fragments have been successfully searated by this tednique. IHwever, the uper limit of resolution of this tecnique and the cmrditicris for the searation of very large DM mlecules have not been thoroughly investigated. This is in part due to the lack of suitable DE markers

This chapter summarizes the methods that are currently available for generating physical maps and discuss the advantages and disadvantages of each method. The immune system is highly complex and consists of many different cell types; each carrying out their unique function. The primary task of the immune response is to distinguish between self and foreign antigens. This function is mediated by cell-surface receptors located on two major types of lymphocytes, T cells and B cells. B cells constitute the humoral pathway of the immune system, which defends primarily against acute bacterial and viral infections. The cell-surface antigen receptor of B cells is a membrane-bound immunoglobulin (Ig) of the IgM class. Immunoglobulins are composed of two chains, heavy (H) and light (L). Like immunoglobulins, the α and β or У and δ chains associate following protein synthesis to form a heterodimeric receptor molecule. The molecules encoded by the genes of the major histocompatibility complex (MHC) also play an important role in the vertebrate immune response. These proteins present foreign peptide antigens to the α/β T cell receptors, thus facilitating the ability of T cells to identify and respond to foreign antigens. The chapter groups these gene families as immunoglobulin-like loci, because they are molecular families that are constructed based on the immunoglobulin homology unit. Each immunoglobulin homology unit is approximately 110 amino acids in size, and has several conserved amino acids and a centrally placed cysteine disulfide bridge usually spanning 60–75 amino acids. The tertiary structure of the homology unit is highly conserved and composed of two sheets of three to four antiparallel, 0- pleated strands. In addition to their structural similarities, discontinuous gene segments that are organized on the chromosomes as discrete loci encode these molecules all. During the course of cellular differentiation and development, gene segments in these loci are rearranged and joined to produce the final coding sequence. Because most of the discontinuous gene segments exist as multiple-member pools, the combination of different sequences gives rise to a high degree of diversity in the final protein product.

Journal Article Rapid colony screening of YAC libraries by using alginate as matrix support Get access Eric Lai, Eric Lai * Department of Pharmacology, University of North CarolinaChapel Hill, NC 27599-7365, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Celeste Cantrell Celeste Cantrell Department of Pharmacology, University of North CarolinaChapel Hill, NC 27599-7365, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 19, 11 October 1989, Page 8008, https://doi.org/10.1093/nar/17.19.8008 Published: 11 October 1989 Article history Received: 25 August 1989 Published: 11 October 1989

Quantitative measurement of DNA migration in gel electrophoresis requires precisely controlled homogeneous electric fields. A new electrophoresis system has allowed us to explore several parameters governing DNA migration during homogeneous field pulsed field gel (PFG) electrophoresis. Migration was measured at different switch times, temperatures, agarose concentrations, and voltage gradients. Conditions which increase DNA velocities permit separation over a wider size range, but reduce resolution. We have also varied the angle between the alternating electric fields. Reorientation angles between 105 degrees and 165 degrees give equivalent resolution, despite significant differences in DNA velocity. Separation of DNA fragments from 50 to greater than 7000 kilobases (Kb) can easily be optimized for speed and resolution based on conditions we describe.

A new instrument has been developed for the electrophoretic separation of large DNA molecules that can independently regulate the voltage of each of 24 electrodes and allow the magnitude, orientation, homogeneity, and duration of the electric field to be precisely controlled. Each parameter can be varied at any time during the electrophoretic process. Thus distinct sets of conditions can be combined to optimize the separation of various fragment sizes in a single run. Independent control of electrode voltage allows all of the fields to be generated with electrodes arranged in a closed contour, independent of a particular geometry. This device increases both the resolution in any size range and the speed of separation, especially for DNA molecules larger than 3 megabases.

A new two-dimensional gel electrophoresis technique has been developed for the mapping of multigene families. Resolution in the first dimension is based on the generation of large size DNA fragments by infrequently-cutting restriction enzymes, and separation of these fragments by field inversion gel (FIG) electrophoresis. A second restriction enzyme digestion is then carried out with the separated DNA fragments in the agarose gel. Standard gel electrophoresis in the second dimension allows one to estimate the number of hybridizing genes contained in each large DNA fragment. We have also developed a novel method to increase the separation, resolution and hybridization signal in the second dimension by condensing the bands from the first dimension into spots. As an example, we have applied these techniques to determine the organization of the murine T-cell receptor gamma locus. The murine gamma gene family was found to be contained on two DNA fragments encompassing 195 kilobases of DNA. The two-dimensional gel electrophoresis method is particularly useful in the analysis of the organization of multigenic families where single copy probes are not readily available, and should extend the potential usefulness of field inversion gel electrophoresis in gene mapping.