A rapid two-dimensional fractionation of DNA restriction fragments

Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications

The field of molecular biology was revolutionized by the advent of gel electrophoresis. Restriction landmark genomic scanning (RLGS) is a type of two-dimensional electrophoresis employed in the genome-wide assessment of genomic alterations. RLGS has been used to study genetic and epigenetic changes in normal tissues, primary tumors, cancer cell lines, and various organisms such as mice, rats, hamsters, bacteria, and plants. An RLGS profile displays over 2000 radiolabeled restriction landmark sites in a single assay. When conducted with methylation-sensitive restriction enzymes whose sites are preferentially located in CpG island regulatory regions, RLGS becomes a very versatile tool for the investigation of both normal and aberrant methylation patterns. Early studies performed on tumor DNA were mainly descriptive in nature, essentially a catalogue of loci that were changed to varying degrees in different tumor types. Over time, as investigators have become more proficient with RLGS and have undertaken high-throughput studies, the need for efficient cloning, imaging, and analysis systems has become paramount. Current studies focus on identifying specific genes and pathways involved in deregulated methylation in cancer. As such, RLGS analysis of tumor samples has made tremendous contributions to our understanding of the role of DNA methylation in cancer. Future directions will take advantage of the abundant genomic sequence data available to link all of the RLGS loci to genes and create biologically relevant methylation profiles of cancer. This review discusses practical considerations of using RLGS as a genome scanning tool and the past, present, and future applications in cancer biology.

Selecting and amplifying one fragment from a DNA fragment mixture by polymerase chain reaction with a pair of selective primers

A new method for selecting and amplifying a single DNA fragment from a mixture is proposed. This method is applicable for the rapid classification of DNA fragments from a mixture and for preparation of sequencing templates. DNAs of several to tens of kilobases (kb) are digested with a four-base recognition restriction enzyme to produce smaller fragments. The complementary strand extension reactions are then carried out to produce fluorophore-labeled DNA fragments from the digestion products. These fragments can be rapidly classified according to their terminal-base sequences and their sizes are analyzed by capillary-array gel electrophoresis (CAGE). Electropherograms are used to characterize the fragments and to select polymerase chain reaction (PCR) primers. Any fragment in a digestion mixture can be amplified by PCR with a pair of primers selected from a primer pool by referring to the electropherograms of the fragments. This method was successfully used to compare the electropherograms of two different DNA strands and to sequence a several-kb DNA fragment without subcloning. Combined with CAGE, this method could be used to dramatically simplify DNA fragment analysis.

Genome scanning by two-dimensional DNA typing: the use of repetitive DNA sequences for rapid mapping of genetic traits

The existence of repetitive DNA sequences offers the possibility to assess the mammalian genome for individual variation in its entirety rather than at one or only a few sites. In order to fully explore the various sets of mammalian repeat sequences for this purpose, analytical tools are required which allow many if not all individual members of sets of repetitive elements to be resolved and identified in terms of location and allelic variation. We have applied and further developed an electrophoretic system, two-dimensional DNA typing, which may fulfill these requirements. The two-dimensional system combines separation of DNA fragments by size in a neutral gel, with separation by sequence composition in a denaturing gradient gel. By hybridization with minisatellite- and simple-sequence core probes and by inter-repeat polymerase chain reaction techniques, it is possible to obtain individual--and even chromosome-specific separation patterns that consist of hundreds of spots. Computerized image analysis and matching of such spot patterns allows the rapid assessment of multiple polymorphisms, spread over the genome, to monitor genetic variability in populations. When coupled to databases of polymorphic DNA markers with a known genomic location, two-dimensional DNA typing can greatly accelerate the mapping of genetic traits in humans, animals, and plants.

Mapping genomic organization by field inversion and two-dimensional gel electrophoresis: application to the murine T-cell receptor gamma gene family

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.

Intraplasmid recombination in Streptomyces lividans 66

An Escherichia coli-Streptomyces shuttle plasmid pIF132 containing two direct mel repeats was constructed. While pIF132 replicated relatively stably in E. coli (Rec+ or recA), its structure was unstable in S. lividans: recombination between the mel repeats resulted in a smaller plasmid, pIF138. Furthermore, pIF132 formed oligomers extensively in E. coli but not in S. lividans.

Isolation and characterization of Streptomyces lividans mutants deficient in intraplasmid recombination

Plasmid pIF132 containing two direct repeats of the mel (melanin) sequence was used to monitor intraplasmid recombination. Five mutants of Streptomyces lividans TK64 deficient in intraplasmid recombination were isolated. Four contained additional defects in aerial mycelium formation, pigmentation, and nutrient requirements; among these two showed extensive amplification of chromosomal sequences. Mutant JT46 had no pleiotropic defects but had the most severe blockage in recombination. Only one of the mutants was slightly more sensitive to UV and two were slightly more sensitive to mitomycin C. Plasmid pWCL1 (containing pIJ702, pUC12, and HBVsAg sequences; Lee et al. 1986) could not stably replicate in TK64 without spontaneous deletions. In contrast the mutant JT46 maintained the integrity of pWCL1 much more stably.

Chromosome analysis by two-dimensional fingerprinting

A two-dimensional fingerprinting technique has been developed that allows large, cell genome-size DNA's to be analyzed by restriction endonuclease cleavage and separation of DNA fragments by agarose gel electrophoresis. Equations have been derived to determine the genome size and number of cleavage sites from analysis of the distribution of fragment lengths. Genome sizes of Escherichia coli strain JM101 and two strains of the mycoplasma Acholeplasma laidlawii measured by this method are in agreement with published values. Other uses of two-dimensional fingerprinting for studies of prokaryotic and eukaryotic genome structure and organization are described.

Two-dimensional electrophoretic display of restriction fragments from genomic DNA

We have developed a procedure for the resolution of restriction enzyme digests of mammalian genomic DNA in two dimensions. Fragments from a first digestion are separated on a column of purified agarose containing a second restriction enzyme in the absence of the divalent cation required for enzyme activity. After enzyme activation and digestion, the fragments are resolved on an agarose slab gel. We have digested rat genomic DNA and found in the ethidium-stained pattern a variety of features which have not been described previously.

Mapping of restriction enzyme cuts by a new two-dimensional procedure

A new procedure has been worked out to establish restriction maps. The method is fast, does not in general require labeled DNA and has been applied to map the linear palindromic rDNA of Physarum with the restriction enzyme Bst EII.