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 595 records · Page 33Linked to original sources
PubMed1996

Restriction endonuclease mapping and molecular cloning of the human herpesvirus 6 variant B strain Z29 genome.

Human herpesvirus 6(HHV-6) variants A and B differ in cell tropism, reactivity with monoclonal antibodies, restriction endonuclease profiles, and epidemiology. Nonetheless, comparative nucleotide and amino acid sequences from several genes indicate that the viruses are very highly conserved genetically, The B variant is the major etiologic agent of exanthem subitum and is frequently isolated from children with febrile illness; no disease has been etiologically associated with HHV-6A. One HHV-6A strain has been cloned and sequenced, but similar information and reagents are not available for HHV-6B. We report here the determination of maps of the restriction endonuclease cleavage sites for BamHI, C1aI, HindIII, KpnI, and Sa1I, and the cloning in plasmids and bacteriophages of fragments representing over 95% of the HHV-6B strain Z29 [HHV-6B(Z29)] genome. Hybridization experiments and orientation of several blocks of nucleotide sequence information onto the genomic map indicate that HHV-6A and HHV-6B genomes are colinear.

Antibodies, Monoclonal↗
PubMed1983

Molecular cloning and restriction endonuclease mapping of the murine cytomegalovirus genome (Smith Strain).

We have cloned EcoRI and HindIII fragments of the Smith strain of murine cytomegalovirus (MCMV) in the plasmid vector pACYC184. These cloned fragments were used to establish a restriction endonuclease map of the genome with respect to the EcoRI and HindIII sites. The map was constructed on the basis of data derived from cross-hybridizations of EcoRI and HindIII cloned fragments, double-digestions of the cloned fragments with EcoRI and HindIII, and hybridization of cloned HindIII fragments to Southern blots of MCMV DNA cleaved with EcoRI. From our mapping data, we have determined that the length of the MCMV genome is approximately 240 kbp. The genome does not appear to undergo inversions and lacks detectable repeated sequences. One HindIII cloned fragment was obtained which contained both HindIII termini. The existence of this fragment may be related to the mode of replication of the MCMV genome.

Animals↗
PubMed1977

Restriction endonuclease mapping and mutagenesis of the F sex factor replication region.

The plasmids pSC138 and pML31 each contain the EcoRI-generated f5 replicator fragment of the conjugative plasmid F in addition to an EcoRI fragment encoding antibiotic resistance: ampicillin resistance derived from Staphylococcus aureus in pSC138 and kanamycin resistance from Escherichia coli in pML31. We have mapped one HindIII and two BamHI restriction sites in the f5 region of these plasmids and one HindIII site in the antibiotic resistance region of each plasmid. The HindIII site in the Km region of pML31 occurs in the kan gene whereas the HindIII site in the Ap region of pSC138 appears to occur in an area important for the regulation of beta-lactamase production. By means of in vitro recombinant DNA manipulation of plasmids pML31 and pSC138, we have shown that approximately 1.9 X 10(6) daltons of the 6.0 X 10(6) dalton f5 fragment can be deleted without disrupting plasmid stability. In addition, we have used these same techniques to isolate a novel F-controlled Ap plasmid cloning vehicle which contains a single restriction site for each of the enzymes EcoRI, HindIII, and BamHI. This cloning vehicle has been linked via either its EcoRI or HindIII site to a ColE1 plasmid replicon to yield stable recombinants.

Conjugation, Genetic↗
PubMed1991

Characterization of the temperate actinophage phi A7 DNA and its deletion derivatives.

A restriction map of phi A7 DNA (46.7 kb) was established for nine endonucleases (BclI, ClaI, EcoRI, EcoRV, HpaI, PvuI, SacII, SphI and XbaI) which cut the phage genome up to 11 times. There was no sites for BamHI, BglII, HindIII, PstI, PvuII, SacI or SalI. phi A7 DNA, circularized through its cohesive ends, could integrate into the genome of several Streptomyces hosts, to form stable lysogens. Integration occurred by recombination between unique attachment sites on the phage (attP) and the host (attB) genomes. The attP site has been located on the phi A7 restriction map. Deletion mutants of phi A7 DNA were obtained by selecting for pyrophosphate- or EDTA-resistant clones. The deletions occurred either near the left-hand end of the conventional restriction map, or about 18 kb from the right-hand end, close to, but not affecting the unique SacII site. Together, the deletions defined at least 7.9 kb of DNA (16.9% of the phage genome) non-essential for plaque formation. phi A7 DNA was introduced into S. lividans protoplasts by liposome-assisted transfection. Since the phage does not adsorb to intact cells of this strain, and therefore does not form plaques, an overlay of S. antibioticus spores was used to detect the infectious progeny released by the protoplasts. Using this technique, phi A7 could be introduced into S. antibioticus with an efficiency of about 6 x 10(6) p.f.u. per micrograms DNA (equivalent to 3 x 10(-4) p.f.u. per DNA molecule).

Attachment Sites, Microbiological↗
PubMed1995

Molecular characterization of two strains of the avian adeno-associated virus (AAAV).

An avian adeno-associated virus (AAAV) was isolated after propagating a field isolate of the CELO virus (fowl adenovirus serotype 1 (FAV1)) in embryonated eggs. The isolated dependovirus was compared with the known AAAV obtained from the American Type Culture Collection (ATCC VR-865). The genomes were analysed by digestion with several restriction endonucleases. Although both DNAs have the same size, most restriction enzymes produced different restriction patterns. Double digests were used to construct for the first time restriction maps for avian dependoviruses. The two DNAs rendered different restriction maps in which the different restriction sites were mainly located in the middle and right part of the genomes. The effect of these differences on the structure proteins was shown by western blot analysis. In the immunoblot, the immunofluorescence and immunodiffusion test the two dependoviruses were serologically indistinguishable and therefore can be regarded as two different strains of the same virus. To differentiate between both strains we named the original one as AAAV VR-865 compared with the isolated AAAV DA-1.

Animals↗
PubMed1993

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein.

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

Amino Acid Sequence↗
PubMed1998

Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules.

New mapping approaches construct ordered restriction maps from fluorescence microscope images of individual, endonuclease-digested DNA molecules. In optical mapping, molecules are elongated and fixed onto derivatized glass surfaces, preserving biochemical accessibility and fragment order after enzymatic digestion. Measurements of relative fluorescence intensity and apparent length determine the sizes of restriction fragments, enabling ordered map construction without electrophoretic analysis. The optical mapping system reported here is based on our physical characterization of an effect using fluid flows developed within tiny, evaporating droplets to elongate and fix DNA molecules onto derivatized surfaces. Such evaporation-driven molecular fixation produces well elongated molecules accessible to restriction endonucleases, and notably, DNA polymerase I. We then developed the robotic means to grid DNA spots in well defined arrays that are digested and analyzed in parallel. To effectively harness this effect for high-throughput genome mapping, we developed: (i) machine vision and automatic image acquisition techniques to work with fixed, digested molecules within gridded samples, and (ii) Bayesian inference approaches that are used to analyze machine vision data, automatically producing high-resolution restriction maps from images of individual DNA molecules. The aggregate significance of this work is the development of an integrated system for mapping small insert clones allowing biochemical data obtained from engineered ensembles of individual molecules to be automatically accumulated and analyzed for map construction. These approaches are sufficiently general for varied biochemical analyses of individual molecules using statistically meaningful population sizes.

Animals↗
PubMed1985

Restriction endonuclease mapping of the hepatitis B viral genome isolated from Taiwan.

The Eco RI fragment of hepatitis B virus (HBV) DNA isolated from human blood plasma Dane particles were inserted into plasmid pUC8 Eco RI site and transformed into E. coli JM103 host. Two recombinants pTWL1 and pTWL2 were found to carry 3.2 kbp fragment and proved to have HBV genome by Southern hybridization method. The 1.4 kbp Bam HI fragment which carried the hepatitis B viral surface antigen (HBsAg) gene, obtained via Bam HI digestion of Dane particles DNA which was made fully double stranded by endogenous DNA polymerase reaction, was also inserted into plasmid pUC8 Bam HI site. Four recombinant clones, pTWS1, pTWS2, pTWS3, and pTWS4 were found. Only one of the clones pTWS1 carried the HBsAg gene in a correct orientation with respect to the lac promoter sequence. The physical mapping of HBV DNA was performed with several restriction endonucleases. Our results indicated that the HBV DNA insert contains unique XbaI and HpaI cleavage sites and lacks the cleavage sites for the HindIII, SmaI, KpnI, SalI, and SstI endonucleases. The locations of Bam HI, BglII, and HincII endonucleases cleavage sites within the cloned HBV DNA of the pTWL1 plasmid were similar to that HBV DNA of adw and adw2 subtypes.

Chromosome Mapping↗
PubMed1990

Computer-assisted analysis of chromosomal locations and transcriptional directions of Escherichia coli genes.

We present a computer-assisted method for locating and orienting nucleotide sequence segments on a large restriction map by comparing restriction fragment lengths. This method is based on the observation that long restriction fragments are rare and, therefore, the longest restriction fragments serve as effective discriminators. The method was applied to Escherichia coli genes, and chromosomal locations and transcriptional directions for more than 500 genes were determined.

Chromosome Mapping↗
PubMed1980

Isolation of DNA from agarose gels using DEAE-paper. Application to restriction site mapping of adenovirus type 16 DNA.

A new method for isolating DNA from agarose gels is described. The method involves the simultaneous transfer of all DNA-fragments from an agarose slab gel onto DEAE-cellulose paper and the elution of the individual fragments from the paper with 1 M NaCl. DNA isolated from agarose gels in this way is susceptible to cleavage with several restriction endonucleases, and can be labeled in vitro with E coli DNA-polymerase I, T4 DNA-polymerase and T4 polynucleotide kinase. We have used the method to construct restriction endonuclease maps of adenovirus type 16 DNA.

Adenoviridae↗
PubMed1994

[RecA-independent induction of the new plasmid rAS1 after introduction of a fragment of the cryptic plasmid p1414 into Bacillus subtilis 168 cells].

Bacillus subtilis 168 was transformed with fragments from the minireplicon of the cryptic plasmid p1414; these fragments were ligated into the cat gene of plasmid pC194. As a result, the 4.6 kb plasmid pAS1 appeared with a low frequency. The plasmid was homologous to the chromosomal DNA of B. subtilis 168, but had no homology with p1414. Plasmid pAS1 had extensive homology (3.2 kb) with plasmid pUB110 and its restriction map in this region of homology correlated well with the restriction map of pUB110. Plasmid pAS1 occurred both in rec+ and recA- cells. We suppose that pAS1 was generated because of the illegitimate recombination between p1414 and the replicon pUB110 incorporated in the chromosome of B. subtilis 168, and the resulting substitution of marker KmR of pUB110 for marker CmR of pC194.

Bacillus subtilis↗
PubMed2004

Molecular characterization and isolation of the F/f gene for femaleness in cucumber ( Cucumis sativus L.).

The biological processes leading to sex expression in plants are of tremendous practical significance for fruit production of many agricultural and horticultural crops. Sex-expression studies in cucumber showed that the different sex types are determined by three major genes: M/m, F/f and A/a. The M/m gene in the dominant condition suppresses stamina development and thus leads to female flowers. The F/f gene in the dominant condition shifts the monoecious sex pattern downwards and promotes femaleness by causing a higher level of ethylene in the plant. To investigate the molecular character of the gene F/f, we used nearly isogenic gynoecious ( MMFF) and monoecious ( MMff) lines (NIL) produced by our own backcross programme. Our investigations confirmed the result of other groups that an additional genomic ACC synthase (key enzyme of ethylene biosynthesis) sequence ( CsACS1G) should exist in gynoecious genotypes. A linkage was also verified between the F/f locus and the CsACS1G sequence with our plant material. After the exploration of different Southern hybridization patterns originating from different CsACS1 probes, a restriction map of the CsACS1 locus was constructed. By using this restriction map, the duplication of the CsACS1 gene and following mutation of the CsACS1G gene could be explained. The promoter regions of the genes CsACS1G and CsACS1 were amplified in a splinkerette PCR and sequenced. An exclusive amplification of the new isolated sequence ( CsACS1G) in gynoecious ( MMFF) and sub-gynoecious ( MMFf) genotypes confirmed that the isolated gene is the dominant F allele.

Base Sequence↗
PubMed1994

Simultaneous detection and typing strategy for human papillomaviruses based on PCR and restriction endonuclease mapping.

The aim of this study was to devise a simple and reliable method for simultaneous detection and typing of genital human papillomaviruses (HPVs). The method comprises three steps (i) amplification of sample DNA with the L1 consensus primers, (ii) digestion of PCR products with restriction endonuclease RsaI and (iii) hybridization of digested PCR products with a unique oligonucleotide probe that detects different fragments of the six most common genital HPV genotypes, namely, HPV types 6, 11, 16, 18, 31 and 33. Seventeen clinical specimens were analyzed by this method and compared to Southern blot using full genomic HPV DNA probes and to PCR using type-specific probes. All three tests agreed with at least one HPV type; however, the new method identified more additional HPV types in cases of mixed infections.

Base Sequence↗
PubMed1978

Map location of the Escherichia coli origin of replication.

Working with restriction fragments obtained directly from the Escherichia coli K12 chromosome, the EcoRI-HindIII restriction map of the section of the chromosome containing the replication origin has been extended by 14 kilobase pairs (kb) to cover 56 kb. Within this newly mapped portion, the ilv and rrnC cistrons have been identified by (1) hybridization of individual restriction fragmanents to the ilv-transducing phage lambdadilv5 and (2) a comparison of the restriction map of this region with the EcoRI map of lambda dilv5 and the Hind III map of the plasmid pJC110, a ColEl-ilv hybrid. The replication origin is located approximately 30 kb from the ilvE gene and 20 kb from the rrnC 16S rRNA cistron. This places the origin near 82.7 min on the genetic map, close to uncA.

Chromosome Mapping↗
PubMed1985

Physical characterization of the genome of the Myxococcus xanthus bacteriophage MX-8.

We have constructed a restriction map for the genome of bacteriophage MX-8 from Myxococcus xanthus using the enzymes PvuII, MboI, and EcoRI. The phage genome size, as determined by restriction analysis, is 51.7 +/- 0.6 Kb. Double digestions, redigestions of isolated fragments, and crossed-contact hybridization of partial digestion products show that the restriction map is circular. Restriction analysis and Southern hybridization show that the phage DNA molecules are packaged sequentially from a concatemer starting from a specific site which we have mapped. The DNA molecules have an average terminal redundancy of approximately 8% and are circularly permuted over at least 40% of the genome.

Bacteriophages↗
PubMed1986

Restriction endonuclease map of endogenous mouse mammary tumor virus loci in GR, DBA, and NFS mice.

Mouse mammary tumor virus (MMTV) is integrated in the genome of most mice as an endogenous provirus. Two of these MMTV proviral loci (Mtv-1 and Mtv-2) are associated with virus expression and tumorigenicity. We prepared restriction endonuclease maps of the endogenous MMTV proviruses in two strains, DBA and GR, which contain the Mtv-1 and Mtv-2 loci, plus a third strain, NFS, which has a low mammary tumor incidence. We find that all these mouse strains have certain MMTV loci in common even though their origins are widely divergent. We also find that some integrated MMTV proviruses appear to have undergone alterations or deletions when compared with MMTV exogenous proviral DNA. We have thus made a comprehensive characterization of MMTV loci in these mouse strains which could serve as a basis for the study of their differences in expression.

Animals↗