Rapid isolation of genes from bacterial lambda libraries by direct polymerase chain reaction screening

Abstract Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) was purified from an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenovibrio marinus MH-110. The protein has a M _r value of approximately 110 000, and is composed of two identical subunits of 55 000. To our knowledge, the existence of L₂-form RubisCO in a chemolithoautotrophic bacterium is first reported in this paper. The N-terminal amino acid sequence determination of the purified enzyme showed high homology with those of the L₂-form RubisCO of Rhodospirillum rubrum and the L _x -form RubisCO from Rhodobacter sphaeroides .     

Use of the polymerase chain reaction for Salmonella detection

J. KWANG, E.T. LITTLEDIKE AND J.E. KEEN. 1996. A primer set of oligonucleotides (S18 and S19) from the _omp C gene of Salmonella has been evaluated for specific detection of Salmonella by polymerase chain reaction (PCR). This primer set successfully amplified 40 Salmonella serovars (60 isolates), but not 24 non-Salmonella bacteria (42 isolates) that have been tested so far. The uniqueness of these primer sequences was also confirmed. The sensitivity of PCR detection in extracted chromosomal DNA for Salm. typhimurium was 1 pg. The sensitivity for boiled whole bacteria was 400 cells. The detection of Salm. typhimurium in ground beef samples required 4–6 h enrichment with an initial inocula of 100 bacteria.     

A general method for introducing a series of mutations into cloned DNA using the polymerase chain reaction

A simple and fast method for introducing a series of mutations in cloned DNA has been developed. The polymerase chain reaction (PCR) has been used for site-directed mutagenesis. Because mutations can be introduced only within the primer sequences used for PCR, a suitable restriction site in the vicinity of the mutated nucleotide is required to permit recloning. Several methods have been devised to overcome this limitation. Our present method is a modification of the overlap extension method [Ho et al., Gene 77 (1989) 51-57], and has some advantages over this and other published methods. In our method, three common primers and a series of primers specific for various mutations are chemically synthesized. Once the proper oligodeoxyribonucleotides are selected as common primers, each mutation requires only one additional primer. Therefore, this method is very useful for introducing many mutations in various sites of the target DNA. We describe our protocol for the site-directed mutagenesis and an example of the introduction of several mutations in the hen egg-white lysozyme-encoding gene.     

Use of polymerase chain reaction catalyzed by Taq DNA polymerase for site-specific mutagenesis

The polymerase chain reaction catalyzed by Taq DNA polymerase has been used for site-specific mutagenesis. The amplification was primed by two oligodeoxyribonucleotides complementary to insulin receptor cDNA. To direct the synthesis of mutant DNA, mismatches were introduced into one of the primers. Six different mutations were constructed by this technique. Of twelve clones whose sequences were determined, ten (83%) had the correct sequence. This technique, which does not require the use of single-stranded DNA templates, provides a simple and efficient approach to site-specific mutagenesis.     

A procedure for rapid isolation of cloned cDNA inserts using the polymerase chain reaction technique

A reproducible and rapid procedure for isolation of cloned cDNA insert from a lambda gt11 cDNA library is described. The procedure relies on the polymerase chain reaction method using forward and reverse primers for lambda gt11, followed by isolation of the cloned cDNA insert by a rapid technique. The procedure should also be applicable to isolation of cDNA inserts cloned in other vectors such as lambda gt10.     

Tagged polymerase chain reaction subtractive hybridization for the enrichment of phage display random peptide libraries

Affinity selection of phage display peptide libraries is routinely used for isolating peptides capable of binding a range of molecules, including antibodies and receptors. This process is most successful when the selecting molecule is relatively pure, for example, a monoclonal antibody. However, isolation of peptides able to bind to target molecules present in a complex mixture is more difficult because the affinity selection process isolates peptides capable of binding to all molecules present in the mixture. Here we describe the development of a tagged polymerase chain reaction (PCR) subtractive hybridization method that is universally applicable for the targeted isolation of peptides able to bind to unique molecules within a complex mixture. We also describe a discriminatory limiting dilution PCR method that can be used to optimize hybridization conditions.     

An optimized recipe for cloning of the polymerase chain reaction-amplified DNA inserts into plasmid vectors

This study compares a number of parameters that are important in the ligation of the polymerase chain reaction-amplified DNA inserts into plasmid vectors and their efficient transformation to bacterial cells. The parameters covered were: T4 polynucleotide kinase treatment followed by either the large fragment of E. coli DNA polymerase or T4 DNA polymerase reactions, the amount of T4 DNA ligase, temperature and duration of ligation, molar ratio of insert to vector as well as the total DNA concentration. The results show that the T4 polynucleotide kinase-treated group without further enzymatic manipulation, at an insert to vector ratio of 3:1 gave the highest recombination efficiency when 10 microg/ml DNA and 20 units T4 DNA ligase were applied for ligation for 12 h at 4 degrees C.     

Optimization strategies for the polymerase chain reaction

The GeneAmp polymerase chain reaction (PCR) process has now become a key procedure in molecular biology research laboratories. The PCR technique is an in vitro method in which genomic or cloned target sequences are specifically enzymatically amplified as directed by a pair of oligonucleotide primers. This technique has been quite robust in the hands of the majority of researchers and is extremely flexible, as evidenced by the increasing number of related PCR formats (i.e., inverse PCR, anchored PCR, asymmetric PCR, labeled primer PCR and RNA-PCR). Today's applications include direct sequencing, genomic cloning, DNA typing, detection of infectious microorganisms, site-directed mutagenesis, prenatal genetic disease research, and analysis of allelic sequence variations. Scientists at Cetus and Perkin-Elmer have collaborated for several years to better understand the interacting biochemical and biophysical parameters which affect PCR optimization. Following are many of the current recommendations, offered with the caveat that our understanding of the PCR process is continually evolving.     

Use of the polymerase chain reaction for homology probing of butyrylcholinesterase from several vertebrates

Genomic blots from man, monkey, cow, sheep, pig, rabbit, dog, rat, mouse, guinea pig, and chicken DNA were hybridized with probes derived from the four exons of the human butyrylcholinesterase gene (BCHE) (Arpagaus, M., Kott, M., Vatsis, K. P., Bartels, C. F., La Du, B. N., and Lockridge, O. (1990) Biochemistry 29, 124-131). Results showed that the BCHE gene was present in a single copy in the genome of all these vertebrates. The polymerase chain reaction was used to amplify genomic DNA from these animals with oligonucleotides derived from the human BCHE coding sequence. The amplified segment contained 423 bp of BCHE sequence including the active site serine of the enzyme (amino acid 198) and a component of the anionic site, aspartate 70. Amplification was successful for monkey, pig, cow, dog, sheep, and rabbit DNA, but unsuccessful for rat, guinea pig, mouse, and chicken DNA. Amplified segments were cloned in M13 and sequenced. The mouse sequence was obtained by sequencing a genomic clone. The highest identity of the human amino acid sequence was found with monkey (100%) and the lowest with mouse (91.5%). The sequence around the active site serine 198, Phe-Gly-Glu-Ser-Ala-Gly-Ala, was conserved in all eight animals as was the anionic site component, aspartate 70. A phylogenetic tree of mammalian butyrylcholinesterases was constructed using the partial BCHE sequences.     

Inhibitors of the polymerase chain reaction

The information on the applied aspects of the polymerase chain reaction (PCR) is updated. In particular, the main inhibitor of PCR, considerably decreasing the sensitivity of the method both at the lysis stage of the tested material and due to the degradation of the DNA matrix and primers and/or to the direct inhibition of the activity of DNA polymerase, are described. The compounds, most frequently distorting the course of the reaction while testing clinical blood samples, bioptic samples, sputum, etc., are characterized. Testing concrete clinical material with the use of PCR was shown to require differentiated approach both at the stage of choosing the adequate method for the preparation of samples and at all other stages, including, e.g., the corresponding DNA polymerases or at the stage of heating for decreasing endonuclease activity or for IgG denaturation. Information on the causes of false negative results of PCR and the variants of their elimination, useful under practical laboratory conditions, is given.     

Specific primer design for the polymerase chain reaction

The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design methods which have been applied in primer design, are also reviewed. In addition, characteristics of population-based methods used in primer design are discussed in detail.     

Use of the polymerase chain reaction for direct detection of Listeria monocytogenes in soft cheese

The polymerase chain reaction (PCR) amplification technique was investigated as a tool for direct detection of Listeria monocytogenes in soft cheeses. Different sets of oligonucleotide primers were used, and parts of the L. monocytogenes Dth18-gene could be amplified specifically when either a plasmid vector carrying the cloned gene or chromosomal DNA was used as a template. The detection limit for L. monocytogenes in dilutions of pure cultures was between 1 and 10 colony-forming units. In extracts from soft cheeses containing L. monocytogenes DNA, the amplification was strongly inhibited. This inhibition could be reduced by an additional purification step. Despite this the detection limit showed a large variation, depending on the brand of cheese used. In some cheeses 10³ cfu/0.5 g could be visualized whereas in others the presence of 10⁸ cfu/0.5 g did not yield a detectable quantity of amplified product.     

Use of the polymerase chain reaction for direct detection of Listeria monocytogenes in soft cheese

The polymerase chain reaction (PCR) amplification technique was investigated as a tool for direct detection of Listeria monocytogenes in soft cheeses. Different sets of oligonucleotide primers were used, and parts of the L. monocytogenes Dth 18-gene could be amplified specifically when either a plasmid vector carrying the cloned gene or chromosomal DNA was used a template. The detection limit for L. monocytogenes in dilutions of pure cultures was between 1 and 10 colony-forming units. In extracts from soft cheeses containing L. monocytogenes DNA, the amplification was strongly inhibited. This inhibition could be reduced by an additional purification step. Despite this the detection limit showed a large variation, depending on the brand of cheese used. In some cheeses 10(3) cfu/0.5g could be visualized whereas in others the presence of 10(8) cfu/0.5 g did not yield a detectable quantity of amplified product.