Species-specific recombinant DNA probes for Mycoplasma meleagridis

Two recombinant DNA probes (pMM-2 and pMM-13) were isolated from a Mycoplasma meleagridis strain 17529 genomic library prepared in plasmid pUC8, and Escherichia coli strain JM83. In dot blot assays, 32P-labeled pMM-13 with a DNA insert of 3.5 kbp, hybridized with 18 isolates of M. meleagridis but not with 16 other known species of avian mycoplasmas. Except for weaker signals on hybridization with the M. meleagridis cultures, pMM-2 with an DNA insert of 0.85 kbp, showed a similar reaction pattern. The minimal concentration of M. meleagridis strain 17529 chromosomal DNA that pMM-13 and pMM-2 detected were 1 and 8 ng, respectively. Neither probe hybridized with chromosomal DNA of M. gallisepticum strain S6, M. synoviae strain WVU-1853, or M. iowae strain I-695 at concentration of 256 ng.

Plasmid rescue from transgenic mouse DNA using LacI repressor protein conjugated to magnetic beads

A method for the efficient rescue of lac operator containing plasmids from transgenic mouse genomic DNA is described. The method is based on the high affinity of the LacI repressor protein for the lac operator sequence. Using the LacI repressor protein conjugated to magnetic beads, more than 95% of plasmid sequences could be purified from restriction enzyme digested genomic DNA. After circularization, the plasmids were introduced into Escherichia coli by means of electroporation. Since the plasmid was cloned into a bacteriophage lambda vector, the efficiency of plasmid rescue could easily be compared with in vitro packaging. Our results indicate that plasmid rescue is about 25 times more efficient. Application of this method should be especially useful with transgenic mouse models harboring LacZ plasmid shuttle vectors for studying spontaneous or induced mutations in vivo.

Tri-primer PCR can distinguish free and cloned viral DNA in a single reaction

A polymerase chain reaction based method is described which distinguishes free and cloned JC virus (JCV) DNA in a single reaction. The method utilizes three primers and amplifies DNA fragments of two different sizes, one specific for free and another specific for pBR322 cloned viral DNA. The procedure was used to simultaneously detect the presence of free and contaminating cloned JCV DNA in brain tissues.

Chemiluminescent restriction fragment length polymorphism analysis (DNA fingerprinting) to identify keratinocytes from two donors in co-culture

The transplantation of allogeneic cells such as pancreatic islet cells, bone marrow, and keratinocytes for skin replacement is in growing use clinically. Present techniques which are used to distinguish transplanted allogeneic cells from phenotypically identical host cells in chimeric tissue have serious limitations. This study assesses the feasibility of using chemiluminescent restriction fragment length polymorphism (RFLP) analysis to distinguish between keratinocyte cell lines from 2 different donors grown in co-culture. We evaluated the sensitivity of this technique in tissue cultured cells in order to define its usefulness in clinical situations. RFLP analysis readily detects heterologous DNA comprising only 10% of a 5 micrograms sample. This was a detection threshold of 500 ng of high molecular weight DNA. With standard extraction methods, this represents the DNA obtained from 4000 cells. This new chemiluminescent technique is as sensitive as older techniques which employ radioactive probes, but avoids the hazards of handling radioactive material. Using this RFLP analysis, the presence of transplanted allogeneic cells can be readily detected in small biopsy specimens. This technique has wide potential application in allogeneic cellular transplantation investigations.

Automated fluorescent DNA sequencing of polymerase chain reaction products

The methods described in this chapter provide some useful approaches for DNA sequencing of templates produced by PCR. These procedures have been employed successfully for large-scale DNA sequencing of cosmid fragments subcloned in plasmid or M13 vectors, and for sequence analysis of cDNAs cloned in bacteriophage lambda vectors. In addition, the method describing direct sequencing from PEG-precipitated PCR product has been used successfully for analysis of Caenorhabditis elegans genomic and cDNA sequences. It is important to reiterate that for every combination of amplification primer pair and target DNA, there is an optimal method for PCR amplification; the ability to sequence the products of any PCR experiment directly will also vary. A coupled PCR/DNA sequencing method that works well for one experimental system may work quite poorly with others. Hence, a few days or hours spent optimizing PCR amplification conditions and selecting the best DNA sequencing method for the target DNA of interest will be time well spent.

High-yield recovery of recombinant DNA from poorly growing cosmid and lambda genomic clones

Certain genomic sequences cannot be recovered efficiently in cosmid or lambda bacteriophage clones, presenting a barrier to efforts to construct a contiguous cloned library of a genome. We have encountered such sequences during our efforts to isolate cosmid and bacteriophage lambda clones carrying members of the human type 2 cystatin gene family. Several cosmid clones constructed in the pWE 15 vector did not survive purification, and using standard techniques, we were unable to obtain significant amounts of cosmid DNA from those clones we could purify. Similarly, several lambda bacteriophage clones constructed in the lambda DASH II vector could not be purified, and those lambda clones we were able to isolate gave low titers in liquid lysates. In this paper, we describe generally applicable methods for preparing high yields of recombinant DNA from such recalcitrant cosmid and lambda clones constructed in these vectors.

A novel method for isolation of large insert DNA from recombinant lambda DNA

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