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At least 235 records · Page 13Linked to original sources
PubMed1980

Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12.

A hybrid plasmid from the Clarke and Carbon collection has been isolated. This plasmid carries the trmA gene of E. coli, which is necessary for the formation of 5-methyluridine (m5U,ribothymidine) present in all transfer ribonucleic acid (tRNA) chains of the organism so far sequenced. A restriction map of the argCBH-trmA regions is presented. By using cloning in vitro, the trmA gene was located on a 2.9-kilobase pair deoxyribonucleic acid (DNA) fragment. These results and comparison with lambda dargECBH transducing phages established the gene order: argECBH trmA bfe in the 88-min region of the E. coli chromosomal map. Plasmids carrying this 2.9-kilobase pair DNA fragment overproduce the enzyme tRNA(m5U)methyltransferase (EC 2.1.1.35) 20 to 40 times. When this 2.9-kilobase pair chromosomal DNA fragment was expressed in a minicell system, a polypeptide of a molecular weight of 42,000 was synthesized. This polypeptide was tentatively identified as the tRNA(m5U)methyltransferase. These results support the earlier suggestion that the trmA gene is the structural gene for the tRNA(m5U)methyltransferase.

Bacteriophage lambda↗
PubMed1985

The plasmids of Deinococcus spp. and the cloning and restriction mapping of the D. radiophilus plasmid pUE1.

Plasmids were found in strains representing all four species of the genus Deinococcus viz. D. radiodurans, D. radiopugnans, D. radiophilus and D. proteolyticus but were not found in the most intensively-investigated strain of the genus, D. radiodurans R1. Their sizes were calculated from electron micrographs. D. radiophilus yielded three size classes of plasmid while D. radiodurans Sark, D. proteolyticus and D. radiopugnans each yielded two. Attempts to cure D. radiophilus and D. radiodurans Sark of any of their plasmids, using a variety of methods, were unsuccessful. A 10.8 kbase pair (kb) plasmid from D. radiophilus, pUE1, was cloned into the PstI site of pAT153 and propagated in Escherichia coli HB101. The recombinant plasmid, pUE109 was subjected to single and double digestion with various restriction endonucleases and its restriction map constructed. The resistance of E. coli HB101 to ultraviolet radiation was not increased when pUE109 was introduced into it. Attempts to transform D. radiodurans with pUE109 failed to detect tetracycline-resistant transformants.

Chromosome Mapping↗
PubMedDate not supplied

Restriction map of the Casphalia extranea densovirus genome.

A physical map of the Casphalia extranea densovirus genome (CeDNV) was constructed. The size of the intact viral genome was estimated to be 4.9 kilobases or 1.6 MDa (single strand). The double-stranded CeDNV genomic DNA was cleaved with 26 restriction endonucleases and 20 restriction sites were mapped on the genome. The CeDNV DNA restriction map was compared to those of other densoviruses. Southern blotting hybridization experiments failed to reveal any homology between the genomes of CeDNV and Junoniacoenia densovirus (JcDNV).

Blotting, Southern↗
PubMed1986

Restriction mapping and close relationship of the DNA of Streptomyces erythraeus phages 121 and SE-5.

The biological properties and genome structure of two actinophages, 121 and SE-5, infecting Streptomyces erythraeus were characterized. They had the same host range (limited to S. erythraeus) and similar DNA G + C contents (around 60 mol %). Restriction maps of their genomes also showed many similarities. The close relationship between the two phages was confirmed by DNA hybridization experiments: large parts of their genomes were homologous, except for a segment in the middle of the map, where no hybridization was detected.

Bacteriophages↗
PubMed1988

A long range restriction map of the pseudoautosomal region by partial digest PFGE analysis from the telomere.

The analysis of partial digestion products extending from the telomere of the human X and Y chromosomes, visualised by hybridisation to a probe located close to the telomere, was used to establish a restriction map of the pseudoautosomal region. In this highly polymorphic region with a 10-fold elevated recombination frequency in males we identified site or methylation differences between 7 different in male and female cell lines and tissues, and derived an estimate of the size of the pseudoautosomal region of approximately 3 Megabases by comparing X and Y chromosomes. This size correlates well with previous estimates based on genetic arguments and argues against a strongly enhanced rate of exchange near telomeres in general. We identified a CpG rich and hypomethylated region within 500 kbp from the telomere, which might reflect structural features of mammalian telomeres, and a small number of (additional) CpG islands, which might represent candidate genes for the Turner phenotype in XO females.

Animals↗
PubMed1991

Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus.

The use of partial restriction digests for mapping complex genomes by pulsed-field gel electrophoresis has been limited by the difficulty of consistently obtaining these digests in agarose, which is a necessary matrix for high-molecular-weight DNA. Enzyme cleavage in agarose is faster then diffusion for most of the enzymes which cleave infrequently. We have developed a method for the production of partial digests in agarose for the endonuclease NotI (5' . . . GC/GGCCGC . . . 3') which circumvents the diffusion problem by using the blocking methylase M. BspRI (5' . . . GGmCC . . . 3'), which competes for the same sites. Using various ratios of the methylase and endonuclease results in partial digests in any size range desired. We report the successful application of this technique to the production of NotI partial digests of human genomic DNA for the mapping of the ABL locus of human chromosome 9.

Base Sequence↗
PubMed1982

R483 and F plasmid genes promoting RNA degradation: comparative restriction mapping.

The gene promoting nucleic-acid degradation (pnd) on IncIa plasmid R483 was cloned into pBR322. It is located on a 0.85 kilobase (kb) EcoRI-SalI fragment and is close to Tn7. The pnd gene has similar properties to the srnB gene on the F plasmid. A cleavage map of the 0.85 kb pnd fragment was constructed and compared with that of the 1.18 kb EcoRI-BamHI fragment containing the srnB gene. These two regions showed marked heterogeneity as evidenced by their distinctly different restriction maps. This result suggests separate paths of evolution of the two genes for stable RNA degradation.

Base Sequence↗
PubMed1988

A long-range restriction map encompassing the cystic fibrosis locus and its closely linked genetic markers.

The cystic fibrosis (CF) locus has been localized to the long arm of chromosome 7 by linkage analysis, and the genetic relationship between CF and the probes J3.11, met, and 7C22 has been extensively studied. To extend this genetic analysis to higher resolution, to provide information on physical distances underlying the genetic relationships, and to set limits to the position of the cystic fibrosis mutation, we have constructed a partial restriction map covering approximately 5 Mb that defines the physical relationship between these and the more recently isolated markers CS.7, XV-2c, Lcn2, and C2/5. Allelic association indicates that CS.7 and XV-2c are close to the CF locus, and an expressed sequence from this region has been described as a candidate gene for this mutation (X. Estivill et al., 1987, Nature (London) 326: 840-845). Using pulsed-field gel electrophoresis we have determined the physical order of these markers to be cen-7C22-Lcn2-met-C2/5-XV-2c-CS.7-J3.11-tel and have localized the CF mutation to an interval of less than 1500 kb. A (not unexpected) disproportionality was observed between the currently best estimates of genetic and physical distances, with the interval J3.11-met showing an approximately fourfold higher frequency of recombination than the met-7C22 interval.

Chromosome Mapping↗
PubMed1980

Comparison of different rearranged immunoglobulin kappa genes of a myeloma by electronmicroscopy and restriction mapping of cloned DNA: implications for "allelic exclusion".

We have studied the organization and function of different rearranged kappa genes in a myeloma, MOPC-21. Two kappa genes were cloned into Charon 4A and compared with each other and with a cloned germline CK gene by restriction mapping and electron microscopy. One MOPC-21 clone corresponds to the gene coding for the MOPC-21 kappa chain polypeptide; it has the V21 gene joined with the CK gene at the J2 sequence. The other MOPC-21 clone corresponds to a nonfunctional rearranged MOPC-21 kappa gene, except for a lkb deletion, 3' of J4. A similar deletion is also found in a "new" kappa gene present in NS-1, a cellular subclone of MOPC-21. The clone of the "nonfunctional" kappa gene has a V gene which is distinct from V21 which is joined to CK in the vicinity of J2. The undeleted form of this gene codes for a KRNA having the size of mature KmRNA which, however, is not translated into kappa chains. Thus the defect of the "nonfunctional" gene manifests itself at a late step of gene expression. The basis for "allelic exclusion" of antibody genes may simply be the complexity of the processes between genes and gene products, resulting in the expression of only one gene.

Alleles↗
PubMed1989

Long-range restriction map of a region of human chromosome 19 containing the apolipoprotein genes, a CLL-associated translocation breakpoint, and two polymorphic MluI sites.

The apolipoprotein gene cluster on human chromosome 19 (APOC1, APOC2, APOE) has been localised by pulsed-field gel electrophoresis to within 200 kb of a chronic lymphocytic leukemia-associated translocation breakpoint. A restriction map covering 1300 kb around these loci has been constructed and contains two polymorphic MluI sites, which appear to show Mendelian inheritance. The orientation of the map on the chromosome has been established as 19cen - CLL breakpoint - APOC2 - 19qter. Pedigree analysis using APOC2, a probe derived from the CLL breakpoint, and other localised markers on 19q suggests that the myotonic dystrophy locus is distal to APOC2 on 19q.

Apolipoproteins↗
PubMed1982

Restriction map of double-stranded DNA copy synthesized from poliovirus Sabin 1 RNA.

Nearly full-sized double-stranded cDNA was prepared from virion RNA of poliovirus Sabin 1 (LSc, 2ab) strain using reverse transcriptase. The double-stranded cDNa was cleaved at four and two sites by the restriction endonucleases Bam HI and Hind III, respectively. Based on the cleavage patterns of double-stranded cDNA into segments of various lengths, each of which had the sequence corresponding to that of the 3'-end of the viral genome, the location of each restriction fragment was determined. The cDNA fragments were cloned with pBR322 as a vector and some of their nucleotide sequences were determined. The DNA sequence indicated that the restriction map obtained was consistent with the known arrangement of viral RNA fragments (1-3). Comparison of the nucleotide sequences of the cloned Hind III (460 bases) and Pst I (434 bases) fragments with those of the corresponding region of Mahoney type 1 genome (3) revealed 12 point-mutation sites.

Base Sequence↗
PubMed1996

Assembly of high-resolution restriction maps based on multiple complete digests of a redundant set of overlapping clones.

An approach to restriction-site mapping and contig building that uses fragment-size data from multiple complete digests of a set of clones that oversample a genomic region is presented. Maps containing both fragment-length data and clone-end data are maintained for each restriction enzyme. Synchronization between the maps for the different enzymes is achieved by requiring the clone-end maps for all enzymes to be compatible. Basic concepts that underlie multiple-complete-digest mapping--including the match/merge approach to map incorporation, extension vs assimilation, ambiguity, and clone-end compatibility--are presented. An initial application of multiple-complete-digest mapping to real data on a set of cosmid clones suggests that this mapping method has exceptional power to produce accurate maps that are well suited to the needs of large-scale DNA-sequencing projects.

Algorithms↗
PubMed1981

Restriction map of poliovirus type 2 cDNA.

Poliovirus type 1 RNA was reverse-transcribed into c-DNA and inserted at the Pst I site of the plasmid vector pBR322 of E. coli. Resulting recombinant plasmids were analyzed by hybridization with RNase T1-resistant 32P-labeled oligonucleotides, and by restriction enzyme mapping. All of the genome was cloned in a series overlapping cDNA inserts, the longest of which was 3.2 kb. The restriction map of the poliovirus cDNA is presented.

Avian Myeloblastosis Virus↗
PubMed1988

Restriction mapping of Lymantria dispar nuclear polyhedrosis virus DNA: localization of the polyhedrin gene and identification of four homologous regions.

The genome of the multiple-embedded nuclear polyhedrosis virus (MNPV) of Lymantria dispar (LdMNPV) was partially characterized by restriction endonuclease analysis and a physical map was constructed using cosmid cloning and Southern cross blot hybridization. Using BamHI, BglII, EcoRI and HindIII, the size of the genome was estimated to be 88.5 x 10(6) Mr or 134.04 kbp. LdMNPV DNA was also analysed using methylation-sensitive restriction enzymes. The resulting restriction profiles suggested that extensive methylation did not occur at the nucleotide sequence recognized by HpaII and MspI. A BamHI restriction map was constructed by comparing overlapping BamHI fragments between cosmid clones containing partial digests of viral DNA. The positions of the BglII, EcoRI and HindIII sites were determined by Southern cross blot hybridizations and aligned to the BamHI restriction map. At least four homologous regions were identified by cross blot hybridizations of BglII-digested LdMNPV DNA and such regions were found to be interspersed along the genome in a fashion similar to that reported for other baculoviruses. Using recombinant plasmids containing the HindIII-V fragment of Autographa californica MNPV to probe Southern blots of LdMNPV DNA, the restriction fragment(s) that contain the polyhedrin gene were identified. Based on these findings the map was oriented with the polyhedrin gene of LdMNPV as the zero point.

Chromosome Mapping↗
PubMed1985

[Restriction map of maxicircle kinetoplastic DNA of Leishmania gymnodactyli].

Kinetoplast DNA (kDNA) of Leishmania gymnodactyli, as in other Trypanosoma species, is a complicated associate consisting of mini- and maxicircular molecules. Minicircular DNA are presented by the homogeneous in size and heterogeneous in base sequence population. Their size determined by the agarose electrophoretic mobility in gel is 920 pairs of nucleotides. Maxicircular molecules of DNA are homogeneous and contains about 38 thou pairs of nucleotides. The restriction map of maxicircular kDNA molecule of L. gymnodactyli has been made up on the basis of the cleavage data of the whole associate kDNA by restrictases.

Animals↗
PubMed1980

Assembly of the mitochondrial membrane system. Complete restriction map of the cytochrome b region of mitochondrial DNA in Saccharomyces cerevisiae D273-10B.

The cytoplasmic petite (rho-) mutant DS400/A12 has been obtained from the wild type strain of Saccharomyces cerevisiae D273-10B/A21. The DS400/A12 clone has a mitochondrial genome with a 7.6-kilobase pair, tandemly repeated segment of DNA. Genetic tests indicate that DS400/A12 contains all the cob1 and cob2 markers of the cytochrome b gene. The gene has been further dissected by mutagenesis of DS400/A12 and selection of secondary rho- clones with simpler genotypes. Restriction analysis of the mtDNAs of the rho- clones was used to construct the complete restriction map of the cytochrome b region and to map the mutations within narrowly defined physical limits. The cytochrome b mutants scatter over a maximal distance of 3.3 kilobase pairs. All the mutations assigned previously to the cob2 locus are found between 71.6 and 73.2 units. The cob1 mutations are located between 74.6 and 76.3 units. The estimated distance between the two loci is at least 1 kilobase pair.

Cytochrome b Group↗
PubMed1984

Restriction mapping of a chlorobenzoate degradative plasmid and molecular cloning of the degradative genes.

The genes for the degradation of 3-chlorobenzoic acid ( 3Cba ) are present in a 110-kb plasmid pAC27 . A circular map is established using the restriction endonucleases EcoRI, HindIII and Bg/II. The map is derived from the results obtained by partial restriction digestion, complete single and double restriction digestion and finally confirmed with hybridization of the digested fragments using different purified fragments as probes. The 3Cba degradative genes are found to be clustered in one region of the map (EcoRI fragment A) as judged by molecular cloning with a broad host range vector pLAFRI . A portion of the 3Cba degradative gene cluster appears to undergo ready recombination with the chromosome, even in a recA host, suggesting the probable transposable nature of such gene cluster.

Chlorobenzoates↗