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PubMed1988

New cloning vectors and techniques for easy and rapid restriction mapping.

We have modified plasmid, phage lambda and cosmid cloning vectors to be of general use for easily and unambiguously determining restriction maps of recombinant DNA molecules. Each vector is constructed so that it contains the rarely found NotI restriction site joined to a short synthetic linker sequence that is followed by a multiple cloning site. DNA cloned into these vectors may be restriction-mapped by either of two methods. In one technique, the cloned DNA is completely digested with NotI, followed by partial digestion with any other restriction enzyme. After electrophoresis and transfer to a nylon membrane, the fragments are hybridized to a labeled probe complementary to the NotI linker. In the second technique, referred to as recession hybridization detection, cloned DNA is digested with NotI and then briefly treated with exonuclease III to recess the 3' ends. After hybridizing a labeled complementary oligodeoxynucleotide to the single-stranded 5' end containing the linker sequence, the DNA is partially digested with another restriction enzyme, electrophoresed and the gel is exposed to x-ray film. With either method the size of each labeled fragment corresponds directly to the distance that a restriction site is located from the NotI linker terminus. Methods for obtaining partial restriction enzyme digests have been devised so that as many as 20 different enzymes may be conveniently mapped on a single gel in little more than a day. The vectors and techniques described may also be adapted to automated or semi-automated devices that read fragment lengths and calculate the resulting restriction map.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophage lambda↗
PubMed1991

Tn5cos: a transposon for restriction mapping of large plasmids using phage lambda terminase.

A method for the rapid restriction mapping of large plasmids has been developed. A 400-bp fragment of phage lambda DNA containing the cos region has been inserted into Tn5. After in vivo transposition of this Tn5cos element into the plasmid of choice, the plasmid is isolated and linearized at its cos site with phage lambda terminase (Ter). Such Ter linearization was about 70% efficient. After partial digestion of the linear molecules with the appropriate restriction enzyme, the products are selectively labelled at the right or left cohesive phage lambda DNA termini by hybridization with digoxygenin (DIG)-11-dUTP-labelled (using terminal transferase) oligodeoxyribonucleotides complementary to the single-stranded cos ends. After pulsed field gel electrophoresis, the labelled fragments are visualized in the dried gel using a DIG-detection kit. The restriction map can be directly determined from the 'ladder' of partial digestion products.

DNA Transposable Elements↗
PubMed1986

Pig mitochondrial DNA: polymorphism, restriction map orientation, and sequence data.

Restriction endonuclease cleavage patterns of mitochondrial DNA (mtDNA) in pigs were analyzed using 18 enzymes which recognize six nucleotides and 1 four-nucleotide-recognizing enzyme. Pigs including Taiwan native breeds and miniature strains maintained in Japan were examined in this study; four commercial breeds of pigs and Japanese wild boars have been investigated earlier [Watanabe, T., et al. (1985). Biochem. Genet. 23:105]. mtDNA polymorphisms were observed in the cleavage patterns of five restriction enzymes, Bg1II, EcoRV, ScaI, StuI, and TaqI. The results support the previous hypothesis that pigs must be derived from two different maternal origins, European and Asian wild boars, and that a breed, Large White, arises from both European and Asian pigs. Two HindIII cleavage fragments were cloned into the HindIII site of M13mp10 and were partially sequenced by the dideoxynucleotide-chain termination method. Furthermore, DraI and StuI cleavage sites were newly determined on the restriction endonuclease map. On the basis of these results, the restriction endonuclease cleavage map of pig mtDNA was rewritten. Comparing sequence data of pig mtDNA at 237 positions with those of cow, human, mouse, and rat mtDNA, the sequence difference, silent and replacement changes, and transitions and transversions among mammalian species were estimated. The relationships among them are discussed.

Animals↗
PubMed1984

Rapid restriction mapping of DNA cloned in lambda phage vectors.

A protocol for the rapid restriction mapping of phage lambda clones has been developed. Partial digestion products are selectively labelled at the right or left cohesive lambda DNA termini by hybridisation with [32P]oligonucleotides complementary to the single-stranded cos ends. After gel electrophoresis and autoradiography, the restriction map can be directly determined from the "ladder" of partial digestion products.

Bacteriophage lambda↗
PubMed1990

[Rapid restriction mapping of DNA cloned in cosmid or lambda phage vectors].

A procedure for rapid restriction mapping of cosmid or lambda phage clones has been developed. The mapping of cosmid is based on linearization of circular cosmid DNA in vitro by the phage lambda terminase. Partial digestion products are selectively labelled at the right or left cos cohesive termini by hybridization with [32P] oligonucleotides complementary to the single-strand cos end. After gel electrophoresis and autoradiography, the restriction map can be directly determined from the "ladder" of partial digestion products of cosmid or lambda clones with computer program or by hand.

Bacteriophage lambda↗
PubMed1993

Construction of cosmid contigs and high-resolution restriction mapping of the Huntington disease region of human chromosome 4.

The gene responsible for Huntington disease (HD) has been localized to a 2.2 million base pair (Mbp) region between the loci D4S10 and D4S98 on the short arm of human chromosome 4. As part of a strategy originally designed to clone the gene based on its chromosomal location, we and others previously identified overlapping yeast artificial chromosome (YAC) clones covering most of this region. While these YAC clones were useful for initially obtaining long-range clone continuity, a number of features of the YACs indicated that smaller clones are generally more useful in the subsequent steps of the positional cloning strategy. In this paper, we use these YAC clones to generate sets of overlapping cosmid clones covering most of the HD region. We isolated a large number of cosmids by screening a chromosome 4-specific cosmid library with labeled DNA from a minimal overlapping set of YAC clones. These cosmid clones were further analyzed by restriction mapping and hybridization experiments, leading to the assembly of 185 cosmids into eleven contigs covering more than 1.65 Mbp and to a fine-structure restriction map of the region. Nine of these contigs cover 90 percent of the 1.7 Mbp subregion between loci D4S125 and D4S98 where the HD gene is now known to lie. The detailed restriction map and the cosmid clones should facilitate the identification and localization of cDNAs and polymorphic markers, and they provide reagents for large scale DNA sequencing of this region of the human genome. Our results suggest that this strategy should be generally useful for converting YAC clones into cosmid contigs and generating high-resolution restriction maps of genomic regions of interest.

Chromosomes, Fungal↗
PubMed1999

A non-radioactive method for mapping restriction fragment length polymorphic genetic markers in Anopheles gambiae.

A non-radioactive method for in situ hybridisation of Restriction Fragment Length Polymorphic (RFLP) markers to the polytene chromosome of Anopheles gambiae, the important malaria vector, which yielded good readable quality of chromosomal bands is reported. The methodology adopted was a Biotin-Streptavidin-Alkaline Phosphatase system which yielded fluorescent signals when stained with dyes such as Nitro Blue Tetrazolium and Bromo Chloro Indolyl Phosphate.

Animals↗
PubMed1990

The virulence plasmid of Salmonella dublin: detailed restriction map and analysis by transposon mutagenesis.

A detailed restriction map of the virulence plasmid of Salmonella dublin has been determined and used for comparison with the virulence plasmid from S. typhimurium. Two regions were identified which appeared to be similar based on blotting and restriction data. One, of about 22 kb, encompassed the virulence region; the other, of about 8 kb, was outside it. The locations of 259 transposon insertions on the S. dublin plasmid were determined and related to their effect on virulence. One gene involved in virulence but outside the essential virulence region was shown to affect citrate metabolism.

Blotting, Southern↗
PubMed1998

Restriction map of a YAC and cosmid contig encompassing the oculopharyngeal muscular dystrophy candidate region on chromosome 14q11.2-q13.

As part of our effort to clone positionally the oculopharyngeal muscular dystrophy (OPMD) gene, we constructed a YAC contig, a cosmid contig, and an EcoRI restriction map of the OPMD candidate region. The YAC contig spans more than 2 Mb and encompasses the loci D14S283 and D14S990 and the cardiac alpha and beta myosin heavy chain genes (MYH6 and MYH7). A 700-kb cosmid contig containing the D14S990 and the myosin genes and a long-range restriction map covering the region between D14S990 and the MYH6 and MYH7 gene cluster were established. A detailed EcoRI restriction map of the cosmid contig was determined, and five putative CpG islands were identified. Based on these data, the four loci were mapped within an approximately 600-kb region with the following centromere to telomere order: D14S283, D14S990, MYH6, and MYH7. The YAC and cosmid contigs will facilitate the identification of genes lying within the OPMD candidate interval.

Chromosome Walking↗
PubMed1990

An algorithm for searching restriction maps.

This paper presents an algorithm that searches a DNA restriction enzyme map for regions that approximately match a shorter 'probe' map. Both the map and the probe consist of a sequence of address-enzyme pairs denoting restriction sites, and the algorithm penalizes a potential match for undetected or missing sites and for discrepancies in the distance between adjacent sites. The algorithm was designed specifically for comparing relatively short DNA sequences with a long restriction map, a problem that will become increasing common as large physical maps are generated. The algorithm has been used to extract information from a restriction map of the entire Escherichia coli genome.

Algorithms↗
PubMed1992

Construction of an EcoRI restriction map of Mycoplasma pneumoniae and localization of selected genes.

A restriction map of the genome of Mycoplasma pneumoniae, a small human pathogenic bacterium, was constructed by means of an ordered cosmid library which spans the complete bacterial chromosome. The positions of 143 endonuclease EcoRI restriction fragments were determined and aligned with the physical map. In addition, restriction sites for the rare-cutting enzymes XhoI (25 sites), ApaI (13 sites), NotI (2 sites), and SfiI (2 sites) were included. The resulting map consists of 185 restriction sites, has a mean resolution of 4.4 kbp, and predicts a genome size of 809 kbp. In addition, several genes were identified and mapped to their respective genomic EcoRI restriction fragments.

Amino Acid Sequence↗
PubMed1985

A fine restriction map of the linear mitochondrial DNA of Tetrahymena pyriformis: genome size, map locations of rRNA and tRNA genes, terminal inversion repeat, and restriction site polymorphism.

A fine restriction map of the linear mitochondrial DNA of Tetrahymena pyriformis strain ST is presented. 1. Based on agarose gel electrophoresis data together with limited nucleotide sequences available on some restriction fragments, we estimate the actual size of this genome to be about 55,000 base pairs. 2. Seven tRNA gene locations have been assigned, which are scattered along the genome length. Six of these locations encode the genes for tRNA(phe), tRNA(his), tRNA(trp), and tRNA(glu), and the duplicate tRNA(tyr) genes which are located at the inverted terminal repeat segments. The tRNA gene(s) encoded in one location has not been identified. We have not yet found the tRNA(leu) and tRNA(met) genes, which were previously shown to be encoded in the genome (Chiu et al. 1974; Suyama 1982). 3. We have mapped the 14S rRNA gene by sequencing the 170 bp segment of EcoRI fragment 8 and by aligning its sequence with E. coli 16S rRNA. From our recent complete sequence data the gene size was found to be about 1,650 bp, which is unexpectedly large for the 14S rRNA which has an estimated size of 1,300 bp. The 14S rRNA is probably a cleavage product of the larger primary transcript of which 200-300 bases of the 5' end are missing. 4. The duplicate copies of the 21S rRNA gene at the terminal duplication inversion segments were analyzed. ClaI fragment 7 (1,500 bp) corresponds in sequence from base position 850 to 2,390 of the 20S rRNA gene of Paramecium mitochondrial DNA (Seilhamer et al. 1984b). The 21S gene is approximately 2,500 bp long. The presence of some restriction site polymorphism is apparent in this segment. 5. Each of the 21S gene copies precedes the tRNA(tyr) gene, but the space flanking one tRNA(tyr) gene differs in size and restriction sites from the space flanking another tRNA(tyr) gene. Thus, this space corresponds to the segment of an imperfect match in the terminal duplication inversion of Goldbach et al. (1978a). 6. Saccharomyces cerevisiae mitochondrial probes including Cob, ATPase VI and IX, and cytochrome oxidase I gene sequences, 21S and 15S rRNAs, and mouse mitochondrial DNA showed no significant hybridization with any restriction fragments of Tetrahymena mitochondrial DNA. The results are in accordance with an extensive sequence divergence previously found in the Tetrahymena mitochondrial genome (Goldbach et al. 1977).

Animals↗
PubMed1992

Restriction mapping and localization of GL-7-ACA acylase gene.

This paper presents the results about the restriction mapping of recombinant plasmids pMR5 and pMR6 containing GL-7-ACA acylase gene from Pseudomonas sp. 130, gene localization and its expression under the control of different promoters, tet, tac or lac/tac, in Escherichia coli. The analysis of gel electrophoresis of pMR5 cleaved with several kinds of restriction enzymes indicated that there is no sites of EcoRI, HindIII and ClaI but the presence of following sites: one HpaI, two XhoI, three EamHI and four PstI on the cloned gene fragment. The restriction maps of pMR5 and pMR6 were determined by comparative digestion of various endonucleases. The gene of GL-7-ACA acylase was localized on a 3.0kb fragment of B2-B3-HpaI from the studies on a serial subcloning. Expression of subclones pMR9, pMR10 and pMR11 in E. coli was compared. Higher yield of acylase was obtained when the gene fragment was placed downstream of the tac promoter. The expression of Pseudomonas gene in E. coli was also discussed.

Amidohydrolases↗
PubMed1989

Restriction-map variation with the yellow-achaete-scute region in five populations of Drosophila melanogaster.

It has been proposed that the degree of recombination for a genomic region will affect the level of both nucleotide heterozygosity and the density of transposable elements. Both features of genomic diversity have been examined in a number of recent reports for regions undergoing relatively normal levels of recombination in Drosophila melanogaster. In this study the genomic variation associated with yellow-achaete-scute loci located at the tip of the X chromosome is examined by six-cutter restriction mapping. In this region, as usual for regions adjacent to telomeres, crossing-over is dramatically reduced, and published studies of visible mutants indicate extremely little restriction-map variation. Eight six-cutter restriction endonucleases were used to locate sequence variation in 14- and 16.5-kb regions in 109 lines sampled from North America, Africa, and Europe. The overall level of heterozygosity is estimated as 0.29%. Nine large insertions, all presumed to be transposable elements, were observed. Base-pair heterozygosity appears to be reduced compared with regions having normal levels of recombination. The estimated heterozygosity is much higher than reported in earlier studies of restriction-map variation among visible mutations in the complex. The incidence of large insertions is not elevated compared with that in other regions of the genome. This suggests that asymmetric synapsis and exchange is not an important mechanism for the elimination of transposable elements.

Animals↗
PubMed1979

Fractionation and identification of spinach chloroplast transfer RNAs and mapping of their genes on the restriction map of chloroplast DNA.

Spinach chloroplast 4S RNAs has been separated by two-dimensional polyacrylamide gel electrophoresis into about 35 species. After extraction from the gel, 27 of these RNA species were identified by aminoacylation as tRNAs specific for 16 amino acids. Individual tRNAs were labeled in vitro with 125I and hybridized to DNA fragments obtained by digestion of spinach chloroplast DNA with KpnI, PstI, SalI and XmaI restriction endonucleases. A minimum of 21 genes corresponding to tRNAs for 14 different amino acids have been localized on the restriction endonuclease cleavage site map of the DNA molecule. Of these, 15 genes corresponding to tRNAs for 12 amino acids are located in the larger of the two single-copy regions which separate the two inverted copies of the repeat region. Each copy of this repeat region contains a set of genes for the ribosomal RNAs and a gene for tRNA2Ile in the "spacer" sequence between the 16S and 23S ribosomal RNAs. The genes for tRNA1Ile, tRNA2Leu and tRNA3Leu also map in the repeat region, but outside the ribosomal DNA unit. At present, two more chloroplast tRNAs (for Pro and Lys) have been identified, but not mapped, while 4 unidentified 4S RNAs have been mapped in the large single-copy region of the DNA molecule. Evidence is presented that isoaccepting tRNA species can be transcripts from different loci.

Amino Acyl-tRNA Synthetases↗
PubMed1993

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

A light microscope-based technique for rapidly constructing ordered physical maps of chromosomes has been developed. Restriction enzyme digestion of elongated individual DNA molecules (about 0.2 to 1.0 megabases in size) was imaged by fluorescence microscopy after fixation in agarose gel. The size of the resulting individual restriction fragments was determined by relative fluorescence intensity and apparent molecular contour length. Ordered restriction maps were then created from genomic DNA without reliance on cloned or amplified sequences for hybridization or analytical gel electrophoresis. Initial application of optical mapping is described for Saccharomyces cerevisiae chromosomes.

Chromosomes, Fungal↗
PubMed1996

Rapid restriction mapping of cosmids by sequence-specific triple-helix-mediated affinity capture.

A simple and rapid strategy for restriction mapping based on sequence-specific triple-helix affinity capture (TAC) was developed. The strategy was applied to the analysis of cosmid clones by the construction of a new cosmid vector, ScosTriplex-II, containing two different triple-helix-forming sequences flanking the cloning site of the original SuperCos-1 cosmid vector. For restriction mapping, the recombinant cosmid DNA is digested with NotI restriction enzyme or with one of four intron-encoded endonucleases for excision of intact inserts followed by controlled partial digestion with a mapping enzyme used in conjunction with the corresponding methyltransferase. The partial digestion products are combined with biotinylated triple-helix-forming oligonucleotides to form a triple-helical complex. The triple-helix complexes are immobilized on streptavidin-coated magnetic beads, washed, and eluted with pH 9 buffer solution. The fragments are separated and directly sized by agarose gel electrophoresis. Bidirectional maps are obtained simultaneously by binding to the two different triple-helix-forming oligonucleotides. No probe labeling, gel drying, blotting to membranes, hybridization, or autoradiography is necessary. Also, TAC conditions that permit gel-free isolation of the terminal restriction fragments from cosmid inserts were found. These advantages afforded by ScosTriplex-II should facilitate the automation of cosmid restriction site fingerprinting needed for large-scale mapping and sequencing projects.

Base Sequence↗