Endonucleases PvuII Research Articles

Association of restriction fragment length polymorphisms of swine leucocyte antigen class I genes with production traits of Duroc and Hampshire boars

Restriction fragment length polymorphism analyses of swine leucocyte antigen (SLA) class I genes were performed on 70 Duroc and 38 Hampshire boars from the 1986-87 national performance tests of each breed in the USA. Few boars were inbred. Southern blotting and hybridization procedures were performed on genomic DNA, isolated from white blood cells, using PvuII endonuclease and a swine major histocompatibility complex (MHC) class I probe. Durocs had an average of 11 restriction fragments, with the most common being in 63% of the boars and the least common appearing in only one boar. Hampshire boars had an average of 12 restriction fragments, with the most common appearing in 73% of the boars and the least common appearing in only one boar. Least squares procedures and stepwise regression methods were used to examine the association between DNA restriction fragments and the selection index (INDEX), average daily gain (ADG), average backfat thickness (BF), loin muscle area (LEA), and age at 104 kg (DAY104). In the Duroc breed one DNA restriction fragment was associated with decreased INDEX (P less than 0.05) and decreased ADG (P less than 0.05) whereas two other fragments were associated with increased BF (P less than 0.05). In the Hampshire breed two restriction fragments were associated with an increase in INDEX (P less than 0.05). Cluster analyses were used to group pigs of each breed on the basis of similar RFLP patterns. One cluster group in the Duroc breed was associated with lower average INDEX values (P less than 0.05), greater average DAY104 (P less than 0.05), and a larger mean LEA (P less than 0.05). In the Hampshire breed one cluster group was associated with lower INDEX (P less than 0.05). These results suggest there may be an association between swine MHC class I genes and performance traits in swine. The use of SLA class I restriction fragments, as genetic markers, may have potential in the future for improving pig performance.

Multiple Polymorphic Sites in Factor X Locus

The structure of factor X (FX) gene was analyzed in five FX deficient pedigrees with four different variants of the disease, as well as in 50 normal subjects. Genomic DNA from the deficient patients and the normal controls was digested with 12 restriction endonucleases and hybridized with a FX cDNA probe. The results seemingly exclude gross gene deletions or rearrangements in the deficient patients. A variety of polymorphic sites (ie, EcoRI, HindIII, PstI, PvuII, TaqI) was observed within the FX locus and their relative frequency was established. Intriguingly, a highly polymorphic region for the PvuII endonuclease was identified and located approximately 3 kilobases (kb) from the last 3' exon. These polymorphisms allowed us to analyze the allelic segregation in a FX deficient family and to identify a homozygous subject.

Multiple polymorphic sites in factor X locus

The structure of factor X (FX) gene was analyzed in five FX deficient pedigrees with four different variants of the disease, as well as in 50 normal subjects. Genomic DNA from the deficient patients and the normal controls was digested with 12 restriction endonucleases and hybridized with a FX cDNA probe. The results seemingly exclude gross gene deletions or rearrangements in the deficient patients. A variety of polymorphic sites (ie, EcoRI, HindIII, PstI, PvuII, TaqI) was observed within the FX locus and their relative frequency was established. Intriguingly, a highly polymorphic region for the PvuII endonuclease was identified and located approximately 3 kilobases (kb) from the last 3′ exon. These polymorphisms allowed us to analyze the allelic segregation in a FX deficient family and to identify a homozygous subject.

Detection of human leukocyte interferon-alpha A and -alpha 2 genes in genomic DNAs by the use of deoxyoctadecyloligonucleotide probes.

Two deoxyoctadecyloligonucleotides complementary to the sequence spanning a single base substitution between human leukocyte interferon (HuIFN) alpha A and alpha 2 genes were efficiently used as probes to distinguish between HuIFN-alpha A and -alpha 2 genes. At 37 degrees C or 42 degrees C under aqueous conditions (0.9 M NaCl), hybridization between both probes and the alpha A and alpha 2 genes without any mismatch was strong, whereas the hybridization with one base mismatch (alpha A probe-alpha 2 gene and alpha 2 probe-alpha A gene) was very weak or negligible. Because the single base substitution of G in the alpha 2 gene for A in the alpha A gene provides an extra HinfI site in the alpha 2 gene at the center of the sequence hybridizing to the alpha 2 probe, digestion with HinfI restriction endonuclease caused complete loss of the hybridization between the alpha 2 probe and the alpha 2 gene. PvuII digestion provides 298-bp fragments hybridizing to the probes only from the alpha A and alpha 2 genes among the known HuIFN-alpha genes. Thus, with the use of these oligonucleotide probes in combination with PvuII and PvuII-HinfI restriction endonuclease digestion, the existence of the sequences corresponding to both IFN-alpha A and IFN-alpha 2 genes in human genomic DNAs was demonstrated. The results also surprisingly indicate that these genes, formerly considered alleles because of their essential identity (1 base pair difference in the coding sequence), are not likely to be alleles, but represent closely related distinct genes.

Mapping of a restriction fragment length polymorphism within the human aldolase B gene.

Peripheral blood DNA was hybridized to the full-length cDNA and the cloned structural gene of human aldolase B. With PvuII endonuclease a restriction fragment length polymorphism was detected that was present in the heterozygous state in about 21% of the individuals tested. A map of the human aldolase gene was constructed for the two groups of individuals found to produce different fragments after PvuII digestion. This allowed the localization of the polymorphic site within the gene, which was found to be due to the loss of a PvuII site in the last intron upstream from the 3' end. This polymorphism may be used as a genetic marker to study individuals affected by hereditary fructose intolerance.

Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli

A 4.84-kilobase-pair plasmid was isolated from Proteus vulgaris (ATCC 13315) and cloned into the plasmid vector pBR322. Plasmid pBR322 contains substrate sites for the restriction endonucleases PvuI and PvuII. The recombinant plasmids were resistant to in vitro cleavage by PvuII but not PvuI endonuclease and were found to cause production of PvuII endonuclease or methylase activity or both in Escherichia coli HB101. The approximate endonuclease and methylase gene boundaries were determined through subcloning, Bal 31 resection, insertional inactivation, DNA-dependent translation, and partial DNA sequencing. The two genes are adjacent and appear to be divergently transcribed. Most E. coli strains tested were poorly transformed by the recombinant plasmids, and this was shown by subcloning and insertional inactivation to be due to the PvuII methylase gene. At a low frequency, stable methylase-producing transformants of a methylase-sensitive strain were obtained, and efficiently transformed cell mutants were isolated from them.

High copy number plasmid vectors for use in lactic streptococci

A 3.8 kb DNA fragment from plasmid pBD64 which encoded chloramphenicol and kanamycin resistance genes, but had no replication region, was used as a replicator probe to select for the replication region of the cryptic lactic streptococcal plasmid pSH71 using Bacillus subtilis as host. Three of the resultant recombinant plasmids, pCK1, pCK17 and pCK21 are described. They are vectors in Streptococcus lactis and can be used to clone BglII-compatible fragments into their kanamycin resistance gene. All the plasmids have single sites for restriction endonucleases AvaI, BamHI, EcoRI, PvuII and XbaI, while plasmids pCK17 and pCK21 have single sites for ClaI.

Relaxation of PvuII recognition sequence

The substrate specificity of PvuII endonuclease is relaxed in the presence of dimethyl sulfoxide. The new recognition sequences cleaved in pBR322 DNA have been found to be CCGCTG, CATCTG, CAGATG, CAGGTG and CAGCGG.

Molecular cloning in streptococci: Physical mapping of the vehicle plasmid pSM10 and demonstration of intergroup DNA transfer

The streptococcal resistance plasmid pSM10 (8.3 kb), a deletion derivative of pSM10419 (22.9 kb) determining constitutive erythromycin and lincomycin resistance, was physically mapped with the restriction endonucleases AvaI, AvaII, EcoRI, HpaI, KpnI, PvuII (one site each), HindIII, HaeII (three sites each), HincII (four sites), and HhaI (five sites). Using the cryptic plasmid pVA318 as cloning vehicle, the largest HindIII fragment of pSM10 (3.3 kb) was shown to contain the erythromycin/lincomycin resistance gene(s) of the plasmid. The AvaII site of pSM10 proved to be suitable as a site for cloning AvaII-generated chromosomal DNA fragments from a group C streptococcal strain in the Challis strain of Streptococcus sanguis (group) H). A detailed physical map of the chimeric plasmid pSM10221 (12.8 kb), a fusion product of pSM10 and the staphylococcal chloramphenicol resistance plasmid pC221 (4.5 kb), is also presented. The plasmid chimera has properties making it potentially useful in development of a doubly selective streptococcal cloning vehicle by searching for insertional inactivation.

Megacinogenic plasmid from Bacillus megaterium 216

Ability to produce megacin A, a bacteriocin of B. megaterium, was transferred from the strain B. megaterium 216 into auxotrophic derivatives of the strain B. megaterium KM via protoplast fusion and polyethylene-glycol-induced protoplast transformation by plasmid DNA, respectively. A 30.9 megadalton plasmid was detected in cells with MegA phenotype, and the loss of this phenotype was accompanied in each case with the elimination of that plasmid. The megacinogenic plasmid pBM309 has a single site for both BamHI and XhoI. It is cleaved by the endonucleases SalI, BglII, PstI, PvuII, and EcoRI into 3, 3, 4, 4, and 9 fragments, respectively. The physical map of this plasmid is presented.

Restriction endonuclease mapping of Co1E2-P9 and Co1E3-CA38 plasmids

Using single and double restriction-endonuclease digestions, 16 and 17 cleavage sites have been mapped for the ColE2-P9 and ColE3-CA38 plasmids, respectively. One or more sites for AvaI, BglI, EcoRI, HincII, PvuI, PvuII, SmaI and XhoI endonucleases were found in both plasmids, two BglII sites were found only in ColE2-P9, and one KpnI site was unique to ColE3-CA38. ColE2-P9 was found to be slightly smaller than ColE3-CA38,4.4 Md compared to 4.6 Md. Eleven restriction sites are common to both plasmids in that they are identically placed relative to each other. These sites define a continuous DNA segment equal to over 60% of each plasmid. The remaining portions of the plasmids, which contain the non-homologous regions identified by Inselburg and Johns (1975) have no restriction sites in common, and differ in size by about 0.2 Md.