Rare-cutting Enzymes Research Articles

Detection of mutations and DNA polymorphisms using whole genome Southern Cross hybridization

We report a general method for the detection of restriction fragment length alterations associated with mutations or polymorphisms using whole genomic DNA rather than specific cloned DNA probes. We utilized a modified Southern Cross hybridization to display the hybridization pattern of all size-separated restriction fragments from wild-type Caenorhabditis elegans to all the corresponding fragments in a particular mutant strain and in a distinct C. elegans variety. In this analysis, almost all homologous restriction fragments are the same size in both strains and result in an intense diagonal of hybridization, whereas homologous fragments that differ in size between the two strains generate an off-diagonal spot. To attenuate the contribution of repeated sequences in the genome to spurious off-diagonal spots, restriction fragments from each genome were partially resected with a 3' or 5' exonuclease and not denatured, so that only the DNA sequences at the ends of these fragments could hybridize. Off-diagonal hybridization spots were detected at the expected locations when genomic DNA from wild-type was compared to an unc-54 mutant strain containing a 1.5 kb deletion or to a C. elegans variety that contains dispersed transposon insertions. We suggest that this modified Southern Cross hybridization technique could be used to identify restriction fragment length alterations associated with mutations or genome rearrangements in organisms with DNA complexities as large as 10(8) base pairs and, using rare-cutting enzymes and pulse-field gel electrophoresis, perhaps as large as mammalian genomes. This information could be used to clone fragments associated with such DNA alterations.

A cassette with seven unique restriction sites, including octanucleotide sequences: extension of multiple-cloning-site plasmids

A 27-bp synthetic DNA cassette was constructed which contains the restriction sites of the two rare-cutter enzymes Not I and Sfi I and, in an overlapping arrangement, those of five enzymes with 6-bp recognition sequences: Apa, BalI, NdeI, SacII, XmaIII. The protruding termini of the fragment allow its insertion into any Eco RI-cut DNA creating a new EcoRI site at one side of the cassette only. This fragment was integrated into the pUC18-like multiple-cloning-site (MCS) plasmids pTZ18R and pTZ19R, producing a set of vectors which carry seven additional unique restriction sites (giving a total of 17) within their MCS. They still provide the capabilities of simple recombinant selection by blue/white coloured colonies, creation of single-stranded DNA in the presence of a helper phage, and in vitro transcription of cloned DNA using T7 RNA-polymerase. Plasmids with two copies of the DNA cassette inserted into their MCS were also constructed. Beside the advantages they provide in some cloning procedures, these latter plasmids, which carry a tandem repeat, are valuable sources of related 27-bp fragments, with features similar to the original but with different cloning termini.

Characterization of DNA rearrangements of N-myc gene amplification in three neuroblastoma cell lines by pulsed-field gel electrophoresis

We characterized N-myc gene amplification in three human neuroblastoma cell lines (IMR-32, TGW, GOTO). Rearrangements in long-range regions surrounding amplified N-myc genes were examined by pulsed-field gel electrophoresis. Since rare-cutting enzymes completely digested DNA at the middle of the N-myc gene, we were able to construct a physical map upstream and downstream of the germline N-myc gene, and to obtain information on restriction sites surrounding amplified N-myc genes. This method enables us to envisage the organization of amplified units over a long range. Digestion patterns differed considerably among the germline and the three cell lines, but were simple in each case. We estimated that the minimal distance between neighboring N-myc genes is at least several hundred kilobases. Our data suggest that amplification units contain several DNA fragments derived from ditterent loci, but that they are homogeneous.

Plasmid and bacteriophage vectors for excision of intact inserts

Plasmid (pPolyIII) and bacteriophage λ (EMBL301) vectors are described in which sites for the rare-cutting enzymes SfiI and NotI (8-bp, recognition sequences) flank the Polylinker cloning region. Intact DNA inserts for introduction into cultured cells or into the early embryo are readily excised from the vectors. General-purpose miniplasmid cloning vectors pPolyI and pPolyII are also described, and the utility of the bacteriophage λ vector is demonstrated in the construction of a bovine genomic library.