Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Restriction Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,261 records · Page 70Linked to original sources
PubMed1979

A restriction enzyme cleavage map of Tn5 and location of a region encoding neomycin resistance.

This paper reports a cleavage site map of Tn5 for restriction enzymes BamHI, Bg/I, Bg/II, Hind II, HindIII, HpaI, Sa/I, Aval, SmaI, XhoI, PstI, PvuII, HaeII and HaeIII that was determined by the analysis of restriction enzyme cleavage patterns of ColEl, two independent ColEl::Tn5 plasmids, and a ColEl::Tn5 deletion derivative. Ba/I, EcoRI, KpnI, and PvuI do not cleave Tn5. Construction and analysis of in vitro-generated deletions of a ColEl::Tn5 plasmid limit the sequences encoding neomycin resistance to a 1500-base-pair-long segment of Tn5. Insertion of DNA at a Bg/II site within this segment results in loss of the neomycin resistance phenotype. Since this Bg/II site lies in an inverted repeat region, sequences within this repeat seem to be involved in the expression of neomycin resistance.

Base Sequence↗
PubMed1998

Identification of linear DNA plasmids of the yeast Pichia pastoris.

Two DNA plasmids, approximately 11 and 8 kb in size, have been identified in a strain of the yeast Pichia pastoris (Northern Regional Research Laboratories No. Y4290). The plasmids are resistant to RNase A and lambda exonuclease, but are sensitive to digestion by DNase I, suggesting that they are linear and double-stranded DNA with 5'-protected ends. A restriction map has been constructed for the 11-kb plasmid, confirming that it is linear.

DNA, Bacterial↗
PubMed1993

Lack of correlation between interspecific divergence and intraspecific polymorphism at the suppressor of forked region in Drosophila melanogaster and Drosophila simulans.

Levels of DNA sequence polymorphism at the suppressor of forked [su(f)] region in natural populations of Drosophila melanogaster and Drosophila simulans are estimated by restriction map analysis. su(f) is located at the base of the euchromatic portion of the X chromosome where the level of crossing-over per physical length is extremely low. In a survey of 55 alleles from three natural populations of D. melanogaster, only 2 restriction sites of 27 hexanucleotide and 108 tetranucleotide restriction sites scored are polymorphic. Among 103 alleles from three natural populations of D. simulans, just one polymorphic restriction site is found in 109 tetranucleotide-recognizing restriction sites scored. The few polymorphisms in these surveys yield estimates of per site heterozygosities (0.00, 0.0002, and 0.0005, respectively) at least a factor of 10 less than the average observed at loci located in regions of the genome with normal levels of crossing-over. Because under a broad category of models of molecular evolution (including the neutral theory) a correlation between levels of polymorphism and interspecific divergence is expected, the DNA sequence divergence is examined for the su(f) region. Contrary to the predicted correlation, the estimated divergence (0.12 substitution per silent site) is, in fact, greater than that observed at loci in regions of normal crossing-over. According to an alternative hypothesis (hitchhiking effect model) intraspecific polymorphism is swept out of the population in regions of the genome closely linked to rare but selectively favored variants as they quickly go to fixation; the rate of divergence is, however, unaffected by these rare hitchhiking events. Thus, the observed paucity of polymorphism and lack of correlation with divergence are in accord with the theory of the hitchhiking effect and several recent reports of polymorphism and divergence in other genomic regions with reduced crossing-over per physical length.

Animals↗
PubMed1990

Characterization of FP22, a large streptomycete bacteriophage with DNA insensitive to cleavage by many restriction enzymes.

Bacteriophage FP22 has a very broad host range within streptomycetes and appeared to form lysogens of Streptomyces ambofaciens ATCC 15154. FP22 shared strong cross-immunity and antibody cross-reactivity with bacteriophage P23, but not with seven other streptomycete bacteriophages. FP22 particles had a head diameter of 71 nm and a tail length of 307 nm. The FP22 genome was 131 kb, which is the largest bacteriophage genome reported for streptomycetes. The G + C content of the genome was 46 mol% and restriction mapping indicated that FP22 DNA had discrete ends. NaCl- and pyrophosphate-resistant deletion mutants were readily isolated and the extent of the deletions defined at least 23 kb of dispensable DNA in two regions of the genome. The DNA was not cleaved by most restriction endonucleases (or isoschizomers) which have been identified in the streptomycetes, including the tetranucleotide cutter MboI (GATC).

Bacteriophages↗
PubMed1990

Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids.

Several linear megaplasmids were detected in the facultatively lithoautotrophic Gram-positive bacterium Nocardia opaca. The wild-type strain MR11 contains, in addition to the cccDNA plasmids pHG31-a and pHG31-b, the linear plasmids pHG201 (270 kb), pHG202 (400 kb) and pHG203 (420 kb). The wild-type strain MR22 contains, in addition to the cccDNA plasmid pHG33, the linear plasmids pHG204 (180 kb), pHG205 (280 kb) and pHG206 (510 kb). After preparation of DNA from cells embedded in agarose, the linear plasmids were demonstrated by pulsed-field electrophoresis. By means of DNA probes for genes of soluble hydrogenase and ribulose-bisphosphate carboxylase, the conjugative plasmids pHG201 and pHG205 were shown to be the carriers of the genetic information for these enzymes. A restriction map of pHG201 for the enzymes AsnI, SpeI, XbaI is presented.

Conjugation, Genetic↗
PubMed1989

Pulsed-field gel electrophoresis determination of the genome size of obligate intracellular bacteria belonging to the genera Chlamydia, Rickettsiella, and Porochlamydia.

The chromosome length of obligate intracellular procaryotes was determined by pulsed-field gel electrophoresis of intact or NotI- and SfiI-restricted genomes. Sizes averaged 2,100, 1,720, 1,550, 2,650, and 1,450 kilobases for Rickettsiella grylli, Rickettsiella melolonthae, Porochlamydia buthi, Porochlamydia chironomi, and Chlamydia psittaci and Chlamydia trachomatis, respectively. An SfiI restriction map of the R. melolonthae genome was derived.

Chlamydia↗
PubMed1990

Mapping of the genes around MEN2A locus using pulsed-field gel electrophoresis.

The gene for multiple endocrine neoplasia type 2A (MEN 2A) is closely linked to RBP3 (retinol-binding protein 3, interstitial, probe IRBP.H4) and the DNA marker D10S15 (probe pMCK2), which have been assigned to the proximal long arm of chromosome 10 by linkage analysis both in Caucasian and Japanese populations. We have constructed a rare-cutting restriction map around the RBP3 and D10S15 loci by pulsed-field gel electrophoresis (PFGE). The RBP3 and D10S15 loci appeared to be within a single 160 kb MluI fragment. In 5 patients with MEN 2A, gene rearrangements, such as a gross deletion, were not found in the 880 kb NruI fragment which covered the closest region to the MEN-2A locus from the RBP3 and D10S15 loci.

Chromosomes, Human, Pair 10↗
PubMed1994

Polymerase chain reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley.

A new strategy has been devised and used for the physical localization of genetically mapped restriction fragment length polymorphism (RFLP) clones to barley chromosomes. Morphologically distinct translocation chromosomes from synchronized root-tip meristems were microisolated and their DNA was used as a template for polymerase chain reaction with sequence-specific primers. Four RFLP clones were assigned to cytologically defined segments of chromosome 5. This related approximately one-third of the map length of linkage group 5 to approximately one-fifth of the mitotic metaphase length of chromosome 5. The technique may substantially contribute to the connection of the RFLP-based genetic linkage maps with cytological markers of the barley chromosomes.

Base Sequence↗
PubMed1998

The number of kringle IV repeats 3-10 is invariable in the human apo(a) gene.

The human apolipoprotein(a) (apo(a)) gene is a member of a family of related genes including plasminogen, apo(a)rg-B and apo(a)rg-C, which are clustered on chromosome 6q 2,7. Apo(a) contains ten different types of plasminogen-like kringle IV repeats (K-IV 1-10) one of which (K-IV 2) varies in number resulting in a remarkable size polymorphism of the protein. Sequence analysis of human apo(a) alleles and indirect evidence have suggested that K-IV 1 and K-IV 3-10 are each present once in individual alleles and that the 3' apo(a) region encompassing kringles IV 3-10, kringle V and the protease domain is invariable. To directly test this, we have constructed a restriction map of the apo(a) gene region from genomic DNA and from a yeast artificial chromosome (YAC) (K-IV 13) which contains the entire apo(a) gene. The presence of a 63 kb ClaI fragment encompassing kringles IV 3-10, kringle V and the protease domain and a 46 kb SwaI fragment, spanning kringles IV 5-10, kringle V and the protease domain was demonstrated by PFGE/Southern blotting in 30 unrelated subjects, who represented a range of apo(a) size alleles containing from 11 to 49 kringles. Our analysis demonstrates that the number of kringles IV 3-10 is invariable in the human apo(a) gene, suggesting that the 3'domain of Apo(a) is functionally important.

Apolipoproteins↗
PubMed1993

Molecular definition of the Prader-Willi syndrome chromosome region and orientation of the SNRPN gene.

The Prader-Willi syndrome and the Angelman syndrome are caused by the loss of function of distinct but closely linked genes on human chromosome 15. Based on a yeast artificial chromosome restriction map and two key patients we have determined that the shortest region of deletion overlap in the Prader-Willi syndrome comprises 320 kb. The region includes the anonymous DNA marker PW71 (D15S63) and the gene for the small nuclear ribonucleoprotein N (SNRPN). The SNRPN gene maps 130 kb distal to PW71 and is transcribed from centromere to telomere.

Autoantigens↗
PubMed1988

Analysis of yeast chromosomal regions carrying members of the glutamate tRNA gene family: various transposable elements are associated with them.

We carried out an analysis on the genomic organisation of the tRNA(Glu) family in S. cerevisiae; eight clones were characterized by restriction mapping, hybridization and sequencing. These data taken together with our earlier findings show that the individual tRNA(Glu3) copies are identical only in their structural part but embedded in entirely different genomic environments. All of the tRNA genes identified here are flanked by elements such as Ty, delta, sigma, and tau. In some cases, sequences from different elements form complex patterns indicating a sophisticated history of these chromosomal regions. A novel observation is that Ty and delta in the regions analyzed are exclusively associated with the tRNA genes. The observed patterns imply that the tRNA genes mark regions of multiple transposition and subsequent excision events, but that these have occurred after the individual tRNA gene copies had been fixed in their present locations. Transcription experiments by the use of micro-injection into Xenopus oocytes suggest that the elements flanking the tRNA genes exert a modulating effect on their expression.

Animals↗
PubMed1997

Genome structure and phylogeny in the genus Brucella.

PacI and SpeI restriction maps were obtained for the two chromosomes of each of the six species of the genus Brucella: B. melitensis, B. abortus, B. suis, B. canis, B. ovis, and B. neotomae. Three complementary techniques were used: hybridization with the two replicons as probes, cross-hybridization of restriction fragments, and a new mapping method. For each type strain, a unique I-SceI site was introduced in each of the two replicons, and the location of SpeI sites was determined by linearization at the unique site, partial digestion, and end labeling of the fragments. The restriction and genetic maps of the six species were highly conserved. However, numerous small insertions or deletions, ranging from 1 to 34 kb, were observed by comparison with the map of the reference strain of the genus, B. melitensis 16M. A 21-kb Spel fragment specific to B. ovis was found in the small chromosome of this species. A 640-kb inversion was demonstrated in the B. abortus small chromosome. All of these data allowed the construction of a phylogenetic tree, which reflects the traditional phenetic classification of the genus.

Brucella↗
PubMed1989

Cloning and characterization of a Bacteroides conjugal tetracycline-erythromycin resistance element by using a shuttle cosmid vector.

The Bacteroides conjugal tetracycline resistance (Tcr) elements appear not to be plasmids. In many cases, resistance to erythromycin (Emr) is cotransferred with Tcr. Using a newly constructed shuttle cosmid, pNJR1, we cloned 44 to 50 kilobase pairs of a conjugal Tcr Emr element on overlapping cosmid clones. Cosmid libraries were made in Escherichia coli with DNA from the original clinical Bacteroides thetaiotaomicron DOT strain containing Tcr Emr-DOT or from a Bacteroides uniformis Tcr Emr-DOT transconjugant strain. The cosmid clones were mobilized from E. coli into B. uniformis in groups of 10 to 20 per filter mating, with selection for Tcr or Emr transconjugants. The Tcr and Emr genes were cloned both separately and together on 30-kilobase-pair fragments. Several of the Tcr clones also contained transfer genes that permitted self-transfer of the cosmid from B. uniformis donors to E. coli or B. uniformis recipients. Neither the Tcr nor the Emr gene conferred resistance on E. coli, and the transfer-proficient clones did not self-transfer out of E. coli. Southern blot analysis was used to compare DNA from independently isolated Bacteroides strains carrying conjugal Tcr or Tcr Emr elements and their respective B. uniformis transconjugants. Results of these analyses indicate that there are large regions of homology, including regions outside the Tcr and Emr genes, but that the elements are not identical. Some Tcr clones contained a region which hybridized to chromosomal DNA from the wild-type B. uniformis recipient strain that did not carry the Tcr Emr-DOT element. This region of homology appeared not to be a junction fragment. It was not required in a Bacteroides recipient for successful transfer of the Tcr Emr element. Although we are not sure we have cloned a junction fragment between the Tcr Emr-DOT element and the B. uniformis chromosome, the preliminary function and restriction map appears to be linear.

Bacteroides↗
PubMed1993

Molecular cloning and restriction endonuclease analysis of 0.4 kb Hin dIII'O' fragment of bovine herpesvirus 1 DNA.

Bovine herpesvirus 1 DNA has been isolated by SDS lysis of the virus purified from potassium tartrate (10-50%) density gradient centrifugation. The quality and quantity of viral DNA was checked by UV spectrophotometry and ethidium bromide stained agarose gel electrophoresis. The 0.4 kb Hin dIII'O' fragment of BHV-1 DNA was selectively cloned into Hin dIII cut pUC9 plasmid DNA (2.665 kb). Recombinants were screened by white/blue colonies as well as Hin dIII restriction enzyme analysis. On restriction endonuclease analysis of recombinant plasmid DNA (p-BH-0) with several restriction enzymes, viz., Sau 3A, Hin fI, Rsa I, Sal I, Dra I, Bgl I, Bgl II, Sma I, Hpa I, Stu I, Mlu I, Xho I, Kpn I, Hae III, Eco RI, Bam HI, Pst I, Pal I, revealed insert viral DNA having sites for Hin fI, Hae III, Rsa I, Sma I, only. Further, the partial restriction map of the recombinant plasmid DNA was constructed using above enzymes.

Animals↗
PubMed1992

Human immunoglobulin genes of the kappa type. The long-range map of an orphon V kappa gene region.

As was previously shown by Zimmer et al. (EMBO J. 9, 1535-1542, 1990 and Biol. Chem. Hoppe-Seyler 371, 939-951, 1990), the so-called W regions comprising 11 V kappa pseudogenes are located on the long arm of chromosome 2, very closely to the centromere. They are probably derived by a pericentric inversion and amplification events from gene regions of the kappa locus, which is located on the short arm of chromosome 2 also very closely to the centromere. The restriction map of the W regions was now extended from the previous 1.2 Mb to 4.3 Mb and, at the same time, revised with respect to certain features. This was made possible by a new hybridization probe specific for the Wc region and by the improved resolution and extended range of pulsed field gel electrophoresis. On the basis of the long-range maps of the W regions and the kappa locus the V kappa genes of the kappa locus have to be at least 2.5 Mb apart. This distance can be taken also as a minimal estimate for the size of the centromere DNA of chromosome 2; it is quite possible that the size is much larger.

Chromosome Mapping↗
PubMed1997

High-resolution mapping by YAC fragmentation of a 2.5-Mb Xp22 region containing the human RS, KFSD and CLS disease genes.

The disease loci for X-linked Retinoschisis (RS), Keratosis follicularis spinulosa decalvans (KFSD), and Coffin-Lowry syndrome (CLS) have been localized to the same, small region in Xp22 on the human X Chromosome (Chr). To generate a high-resolution map of the available contig in this area, we have used the YAC fragmentation vectors pBP108/ADE2 and pBP109/ADE2 and generated fragmented YACs from a 2.5-Mb YAC (y939H7) spanning the mentioned disease gene candidate regions. Forty-seven fragmented YACs were generated and analyzed, ranging in size from 170 kb to over 2400 kb. The resulting YAC fragmentation panel was used to construct a detailed restriction map of the region and has been used to bin clones and markers. As a deletion panel, it will present a valuable resource for further mapping.

Abnormalities, Multiple↗
PubMed1993

Characterization of a small cryptic plasmid from Salmonella enteritidis that affects the growth of Escherichia coli.

We examined the plasmid content of 25 clinical isolates of Salmonella enteritidis, and detected the presence of small plasmids (3-5.3 kb) in 9 of them, alone, or in addition to the large, so-called virulence plasmid. A 5.3-kb plasmid isolated as unique extrachromosomal DNA from a strain responsible for a high-mortality outbreak was characterized by restriction mapping and cloning. The plasmid replicon was localized in a 1.7-kb fragment, that hybridized with three of the small plasmids detected in S. enteritidis, and with another small plasmid from Salmonella typhimurium. A strain of Escherichia coli carrying this plasmid, or a cloned 3.7-kb PvuII restriction fragment, showed a slower growth rate, especially in minimal medium, as well as a noticeable increase in DNA methyltransferase activity.

Blotting, Southern↗
PubMed1993

Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria.

Construction of physical maps of genomes by pulsed-field gel electrophoresis requires enzymes which cut the genome into an analyzable number of fragments; most produce too many fragments. The enzyme I-Ceu I, encoded by a mobile intron in the chloroplast 23S ribosomal RNA (rrl) gene of Chlamydomonas eugametos, cuts a 26-bp site in the rrl gene. This enzyme digests DNA of Salmonella typhimurium at seven sites, each corresponding to one of the rrl genes of the rrn operons, but at no other site. These seven fragments were located on the previously determined Xba I physical map, and the I-Ceu I sites, and thus the rrn genes of S. typhimurium, were mapped on the 4800-kb chromosome. Escherichia coli K-12 also yields seven fragments of sizes similar to those of S. typhimurium, indicating conservation of rrn genes and their location, and a chromosome size of 4600 kb. The sizes of the E. coli fragments are close to the size predicted from restriction maps and nucleotide sequence. The I-Ceu I maps of Salmonella enteritidis, Salmonella paratyphi A, B, C, and Salmonella typhi were deduced after digesting genomic DNA and I-Ceu I and probing with DNA of S. typhimurium; the data indicated strong conservation of rrn gene number and position and genome sizes up to 4950 kb. Digestion of DNA of other bacteria (species of Haemophilus, Neisseria, Proteus, and Pasteurella) suggested that only rrn genes are cut in all these species. I-Ceu I digestion followed by pulsed-field gel electrophoresis is a powerful tool for determining genome structure and evolution.

Base Sequence↗