Since the last compilation of restriction enzymes, (1) 442 new entries have been added including 13 new specificities. A complete list of these new enzymes can be found in Table I. With the growing size of the restriction enzyme database and the recognition that the most widespread use of the information is as a database for computer programs predicting restriction enzyme cleavage patterns, Tab...

Siml, a type II restriction endonuclease, has been isolated from Staphylococcus iniermedius 6H using heparin and hydrooxyapatite chromatographic steps. The crude extract contained -3000 U Siml per gram of cells. Three cleavage positions of Siml on pUC19 DNA (-999, 1480 and 1768) have been mapped by double digests with enzymes Bgll, /tccl 131 (isoschizomer of Seal), Sail, Pvul, NmGl (isoschizome...

Sequence-specific binding to DNA in the presence of competing non-sequence-specific ligands is a problem faced by proteins in all organisms. It is akin to the problem of parking a truck at a loading bay by the side of a road in the presence of cars parked at random along the road. Cars even partially covering the loading bay prevent correct parking of the truck. Similarly on DNA, non-specific l...

Borrelia burgdorferi, the etiologic agent of Lyme disease, was recently shown to contain plasmid DNA. Two plasmid species have been described in strain CT1, a Wisconsin tick isolate: a 9.2-kilobase entity; and a larger, 70-kilobase entity. Characterization of the 9.2-kilobase entity by using DNase I and restriction endonucleases demonstrated that the plasmid is supercoiled and exists as a stabl...

We have proposed that the ability of T4 to produce non-glucosylated progeny after a single cycle of growth on a galU rglA rglB+ mutant of Escherichia coli is due to the initiation of the rglB+ function by a phage-coded, anti-restriction endonuclease protein. Based on this hypothesis, we screened T4 deletion mutants for failure to give a burst in this host. The absence of an arn gene in phage mu...

the enzyme DpnII, produced by another strain of D. pneumoniae, recognizes the same sequence, but is inhibited by this same methylated base. The significance of the occurrence of modified nucleotides in eukaryotic DNA is not as yet understood, although a relationship between modification and gene expression has been proposed by several workers (Waalwijk & Flavell, 1978; Bird et al., 1979). By us...

Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Our results confirm that hsp65 PRA must no longer be used for Nocardia species i...

A procedure was developed for cloning (anonymous) DNA sequences whose primary structures differ between two DNA samples. The procedure is based upon in-gel competitive DNA reassociation after electrophoresis of a mixture of restriction enzyme-digested target DNA (from which clones are to be isolated) and a large excess of unclonable reference DNA (competitor DNA). Inclusion of polyethylene glyc...

Chromosome conformation capture (3C) and derivative experimental procedures are used to estimate the spatial proximity between different genomic elements, thus providing information about the 3D organization of genomic domains and whole genomes within the nucleus. All C-methods are based on the proximity ligation-the preferential ligation of joined DNA fragments obtained upon restriction enzyme...

An improved procedure for preparing PCR cloning vectors was developed. This procedure includes the incorporation of adapters to create XcmI restriction enzyme sites in pBluescript II SK(+) vectors, digestion with XcmI followed by further digestion of the small fragment produced by XcmI digestion with additional enzymes, and purification with PCR purification kits. Using this procedure, PCR clon...