The polymerase chain reaction

Evolution of the cytochrome b gene of mammals

With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.

Amplification of nucleic acids by polymerase chain reaction (PCR) and other methods and their applications

The in vitro replication of DNA, principally using the polymerase chain reaction (PCR), permits the amplification of defined sequences of DNA. By exponentially amplifying a target sequence, PCR significantly enhances the probability of detecting target gene sequences in complex mixtures of DNA. It also facilitates the cloning and sequencing of genes. Amplification of DNA by PCR and other newly developed methods has been applied in many areas of biological research, including molecular biology, biotechnology, and medicine, permitting studies that were not possible before. Nucleic acid amplification has added a new and revolutionary dimension to molecular biology. This review examines PCR and other in vitro nucleic acid amplification methodologies--examining the critical parameters and variations and their widespread applications--giving the strengths and limitations of these methodologies.

Restriction fragment length polymorphism in plants and its implications

In the last decade RFLP analysis has evolved from an idea that seemed promising to a well-established tool that has led to fundamental advances in several fields. Construction of genetic maps has now become feasible in many organisms where it would previously have been impractical. Since genetic maps are of general utility for many sorts of biological research, they cannot fail to have a significant impact in the immediate future. As genetic maps become reconciled with physical maps in several plants, it will become possible to clone virtually any gene. For a plant breeder this will have the effect of broadening the gene pool available for plant improvement to include virtually all organisms, including animals and microorganisms. Much remains to be done, however. We need basic studies of the biochemistry, physiology, and genetics of plants and the insects and pathogens infesting them to be able to identify target genes for cloning. We need basic studies of transformation and gene expression to be able to have introduced genes expressed in transformed plants in the proper amounts and in the desired tissues. It must also be kept in mind that the best of our present technologies only suffice to clone and transform single genes. We will have to make another large jump in capabilities to be able to transfer QTL between plants. Since the most important agronomic traits are controlled by QTL, this effort will have to be undertaken. However, the future looks promising for plant breeding and RFLP analysis. The molecular genetic revolution now has every indication of being transferrable to practical problems such as plant breeding, and the first steps in this transferral have already occurred through the medium of RFLP analysis.

Phenotypic and molecular biological analysis of human butyrylcholinesterase variants

Our laboratory has recently shown that several variant forms of human butyrylcholinesterase, associated with unusual sensitivity to succinylcholine, are caused by specific mutations within the structural DNA coding for this enzyme. Atypical (dibucaine-resistant) butyrylcholinesterase is caused by a point mutation at nucleotide position 209(GAT-- greater than GGT), which changes aspartate 70 to glycine. One fluoride-resistant variant family has a point mutation at nucleotide 728(ACG-- greater than ATG), which changes threonine 243 to methionine. Another type of fluoride-resistant variant has a point mutation at nucleotide 1169(GGT-- greater than GTT), which changes glycine 390 to valine. One type of silent phenotype is due to a frame-shift mutation at nucleotide position 351(GGT-- greater than GGAG). A polymorphic site at nucleotide position 1615 (GCA/ACA), coding for Ala/Thr, accounts for the quantitative K-variant, which causes an approximate one-third reduction of activity, if Thr occupies that position at codon 539. Examples are given to illustrate the advantages of using a combination of the new DNA analytical techniques, including: the use of allele-specific probes, with the standard serum cholinesterase phenotyping methods. More accurate typing of patients with certain variants is now possible; pedigree analysis will be aided by the improved methodology.

General colorimetric method for DNA diagnostics allowing direct solid-phase genomic sequencing of the positive samples

A system for rapid colorimetric detection of specific genome DNA fragments amplified by the polymerase chain reaction (PCR) is described that has been designed to allow direct solid-phase sequencing of positive samples. The amplified material is immobilized on magnetic beads by using the biotin streptavidin system. An Escherichia coli lac operator DNA sequence is incorporated in the amplified material during the second step of a nested primer procedure. This 21-base-pair sequence is used for a general colorimetric detection with a fusion protein consisting of the E. coli Lac repressor and beta-galactosidase. Positive samples can be treated subsequently with alkali to obtain a single-stranded DNA template suitable for direct genomic sequencing. This method to detect immobilized amplified nucleic acids (DIANA) is well adapted for automated or semiautomated clinical assays. Here, we show that it can be used to detect and sequence Chlamydia trachomatis genomic DNA in clinical samples.

Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species

Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.

The 60- to 90-kDa parietal cell autoantigen associated with autoimmune gastritis is a beta subunit of the gastric H+/K(+)-ATPase (proton pump)

Autoantibodies in the sera of patients with pernicious anemia recognize, in addition to the alpha subunit of the gastric H+/(+)-ATPase, an abundant gastric microsomal glycoprotein of apparent Mr 60,000-90,000. Herein we have colocalized the glycoprotein and the alpha subunit of the gastric H+/K(+)-ATPase to the tubulovesicular membranes of the parietal cell by immunogold electron microscopy. Moreover, the glycoprotein and the alpha subunit were coimmunoprecipitated, and copurified by immunoaffinity chromatography, with an anti-glycoprotein monoclonal antibody. The pig glycoprotein was purified by chromatography on tomato lectin-Sepharose, and five tryptic peptides from the purified glycoprotein were partially sequenced. The complete amino acid sequence, deduced from the nucleotide sequence of overlapping cDNA clones, showed 33% similarity to the sequence of the beta subunit of the pig kidney Na+/K(+)-ATPase. We therefore propose that the 60- to 90-kDa glycoprotein autoantigen is the beta subunit of the gastric H+/K(+)-ATPase and that the alpha and beta subunits of the proton pump are major targets for autoimmunization in autoimmune gastritis.

Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens

The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo rat Dipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.

At the crossroads of developmental genetics: the cloning of the classical mouse T locus

The discovery, more than 60 years ago, of a mutant mouse with a short tail led to the birth of the new field of developmental genetics. Over the years since, numerous investigators have probed the biology of the original short-tail mutation at the T locus, as well the naturally-occurring t haplotypes that were uncovered as a result of their interaction with this mutation. Although the T locus ranks among the best characterized developmental loci in the mouse, it was not among the first to be cloned. This situation has now been rectified with two recent reports from Herrmann, Lehrach and their colleagues. While the T locus is expressed uniquely in the embryonic tissues predicted from the mutant phenotype, the gene itself, as well as the predicted amino acid sequence of the T product, show no strong homology to any known sequence. For the moment, at least, the mystery behind the function of the T locus still awaits definitive resolution.

PCR cloning and sequence of gastrin mRNA from carcinoma cell lines

The hypothesis that a gastrin-like peptide is acting as an autocrine growth factor in gastric and colonic carcinoma cell lines requires that the cells should synthesize a gastrin-like mRNA. Although no gastrin mRNA was observed in the gastric line Okajima or the colonic lines HCT 116 or LIM 1215 by Northern blotting, gastrin mRNA was detected by application of the polymerase chain reaction. Two products were observed corresponding to mRNA with and without a 130 bp intron. The sequences of both products were identical to the sequences predicted from the normal human gastrin gene.

Brain alpha-bungarotoxin binding protein cDNAs and MAbs reveal subtypes of this branch of the ligand-gated ion channel gene superfamily

alpha-Bungarotoxin (alpha Bgt) is a potent, high-affinity antagonist for nicotinic acetylcholine receptors (AChRs) from muscle, but not for AChRs from neurons. Both muscle and neuronal AChRs are thought to be formed from multiple homologous subunits aligned around a central cation channel whose opening is regulated by ACh binding. In contrast, the exact structure and function of high-affinity alpha Bgt binding proteins (alpha BgtBPs) found in avian and mammalian neurons remain unknown. Here we show that cDNA clones encoding alpha BgtBP alpha 1 and alpha 2 subunits define alpha BgtBPs as members of a gene family within the ligand-gated ion channel gene superfamily, but distinct from the gene families of AChRs from muscles and nerves. Subunit-specific monoclonal antibodies raised against bacterially expressed alpha BgtBP alpha 1 and alpha 2 subunit fragments reveal the existence of at least two different alpha BgtBP subtypes in embryonic day 18 chicken brains. More than 75% of all alpha BgtBPs have the alpha 1 subunit, but no alpha 2 subunit, and a minor alpha BgtBP subtype (approximately 15%) has both the alpha 1 and alpha 2 subunits.

Selective cloning of B cell hybridoma-specific rearranged immunoglobulin gene loci using the polymerase chain reaction

The use of conventional DNA cloning procedures to obtain productively rearranged Ig genes from B cell hybridomas for structure/function analysis of immunoglobulins is tedious and time-consuming. Here we describe a procedure based on PCR which permits rapid, selective isolation of DNA segments containing individual hybridoma-specific Ig gene rearrangements. The method, an adaptation of the so-called 'inverted PCR' technique (IPCR), can be applied most efficiently to specific genes where a preliminary restriction map is available from Southern blot analysis of the hybridoma genomic DNA. To achieve amplification of a given rearranged Ig locus, small amounts of total hybridoma DNA are digested to completion with a chosen restriction endonuclease and the fragments circularised by DNA ligase. Cleavage of the DNA circles using a second restriction enzyme, chosen specifically to cut 3' to a rearranged V-(D)-J exon, leads to linear DNA segments where the rearranged gene is now flanked by segments of known nucleotide sequence derived originally from the 3' region of the Ig H or L chain gene locus. This permits the selection of oligonucleotides that provide convergent primers for specific amplification of DNA segments containing the required gene rearrangement. Amplified DNA fragments can be cloned and rapidly characterised by sequence analysis.

Application of the polymerase chain reaction to the diagnosis of human genetic disease

In vitro DNA amplification by means of the polymerase chain reaction is currently revolutionizing human molecular genetics. Since its inception in 1985, a wide variety of different methods and their applications in the diagnosis of disease have been described. This review is intended to serve as a brief guide to current and emerging possibilities in this rapidly expanding field.

Clinical applications of the polymerase chain reaction

The polymerase chain reaction (PCR) is a technique that allows a million-fold, or greater, amplification of defined regions of DNA or RNA. It is potentially capable of detecting a single copy of a gene, present only once in 105 eukaryotic cells. This remarkable level of sensitivity has allowed the development of many diagnostic assays for human pathogens and disease states. These include: the detection of viral, bacterial and protozoal agents; diagnosis and genetic analysis of inherited diseases such as β-thalassaemia, sickle cell disease, haemophilia, Tay-Sachs disease and many others; diagnosis and analysis of neoplastic disorders such as, chronic myelogenous leukaemia (CML), acute lymphocytic lymphoma (ALL), follicular lymphomas and various other cancers, including the detection of activated oncogenes; prenatal and pre-implantation diagnosis; and the development of genetic risk prediction.

The PCR can greatly simplify diagnostic processes that were previously difficult to perform, particularly where the initial amounts of biological material were very limited. In other cases, PCR provides the only method available for detection and diagnosis. However, although simple in theory, the PCR technique remains, for routine clinical diagnostic purposes, currently in the domain of the specialist laboratory. This is because of its sensitivity to nucleic acid contamination from other sources that can cause misleading results. Procedures and precautions are being developed to minimize this problem and there is little doubt that, in many instances, the PCR will be the diagnostic method of choice within the next few years.

Reverse transcription and direct amplification of cellular RNA transcripts by Taq polymerase

We report the ability of Taq polymerase to directly transcribe RNA templates in vitro. We have made use of this finding to develop a single-step protocol for amplification of RNA transcripts. The method was shown to require only subnanogram amounts of total cellular RNA as starting material. A microassay was developed in which RNA can be extracted from one drop of blood or 1000 cultured cells, and analyzed for the expression of a specific gene.

Cloning of two additional catecholamine receptors from rat brain

An approach based on the polymerase chain reaction (PCR) was used to isolate additional members of the G-linked receptor family from a rat striatal lambda gtII cDNA library. Priming with one degenerate probe corresponding to highly conserved consensus sequences in the third transmembrane (TM) domain of 15 G-linked receptors and sequences in the phage vector resulted in one clone (G-13) encoding a dopamine D2 receptor variant with a 29 amino acid insert in the third cytoplasmic loop. In addition, the amino acid sequence encoded by clone G-36 contained conserved sequences characteristic of the G-linked class of receptors and displayed sequence homology in TM domains with the beta 2-adrenergic receptor (48%). Two conserved serine residues in TM5 postulated to be part of a ligand binding site in the adrenergic receptor, suggests that G-36 encodes a catecholaminergic receptor. Northern blot analysis confirmed the expression of G-36 in rat brain, but not in kidney, heart and lung. Several strong hybridizing bands to G-36 were obtained in both human and rat genomic DNA. The general PCR strategy employed here should prove to be extremely useful for the isolation of other members of the G-linked receptor family.

The nucleotide sequence of the bovine MHC class II alpha genes: DRA, DOA, and DYA

The nucleotide sequence of the exons 2, 3, and 4, and parts of the intervening sequences of a BoLA-DRA and -DQA gene and one other class II BoLA-A gene have been determined. The structure of the BoLA-DRA and -DQA gene was found to be very similar to that of the corresponding human HLA class II genes. An analysis of the structure of the other class II BoLA-A gene showed that this A gene was clearly very different from both the human A genes and the bovine DRA and DQA genes. The results indicate that this other type of class II A gene probably represents the class II gene that has already been identified in restriction fragment length polymorphism (RFLP) studies as BoLA-DYA. Since no clear homologue of this presumed BoLA-DYA gene was found among the human HLA class II genes, these results indicate that, at least as far as the A genes are concerned, a distinct class II gene is present in cattle.

The nucleotide sequence of bovine MHC class II DQB and DRB genes

The nucleotide sequences of most of the exons and parts of the introns of two BoLA-DQB genes and two BoLA-DRB genes have been determined. The structure of these genes is very similar to that of human major histocompatibility complex (MHC) class II genes. The two DQB genes probably represent true alleles. Based on the exons sequenced, both DQB genes and one of the DRB genes seem to be functional. The other DRB gene is a pseudogene; stopcodons are found in the exons encoding the second and transmembrane domain and, furthermore, a 2 base pair (bp) deletion has occurred in the leader exon which places the initiation start codon out of frame. Also in this pseudogene, an almost perfect inverted repeat of 200 bp is found flanking the exon encoding the first domain, which might have been the result of a duplication/inversion event. The sequences presented in this paper do not contain any repetitions. Therefore, DNA fragments containing these sequences can be used as homologous bovine probes in restriction fragment length polymorphism (RFLP) analysis to study disease associations in cattle.

The polymerase chain reaction: current and future clinical applications

The polymerase chain reaction has undergone rapid improvement since its initial development, such that the technique currently permits rapid, accurate, predictive tests to be made in the field of prenatal diagnosis and has greatly aided forensic medicine. It is anticipated that the polymerase chain reaction will also facilitate advances in other fields, in particular preimplantation diagnosis, virology, bacteriology, and cancer therapy.

Incomplete primer extension during in vitro DNA amplification catalyzed by Taq polymerase; exploitation for DNA sequencing

Polyacrylamide gel electrophoresis of DNA fragments obtained by the polymerase chain reaction using Taq polymerase revealed the presence of multiple fragments shorter than the expected product. These abortive extension products were observed even when analysis by agarose gel electrophoresis showed only a single band. The production of prematurely terminated fragments can be exploited for the sequencing of PCR products if phosphorothioate groups are incorporated base specifically during the reaction in the presence of two oligonucleotide primers, one of which is 5'-32P-labeled. The addition of snake venom phosphodiesterase to the reaction mixture after completion of the amplification cycles digests each fragment from the 3'-end to a phosphorothioate group so that the sequence can be read by polyacrylamide gel electrophoresis.

Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR

We have devised a strategy to extend the use of the polymerase chain reaction (PCR) to amplify double-stranded DNA when sequence information is available only at one extremity. The only information required is a short stretch of sequence used to design a gene-specific primer, which is then used in combination with a second generic vector primer at the unknown end. The primers are used in a PCR reaction after ligating the unknown end to a generic vector. Restriction, ligation, amplification and sequencing of the products can be achieved within three days. This method eliminates the laborious steps of shotgun cloning, colony screening and culturing of cells. We have used this method to take two contiguous steps beyond the histidine transport operon in Salmonella typhimurium. We also demonstrate the usefulness of this technique to do chromosome walking in the absence of any restriction data.

Mitochondrial DNA sequences in single hairs from a southern African population

Hypervariable parts of mitochondrial DNA (mtDNA) were amplified enzymatically and sequenced directly by using genomic DNA from single plucked human hairs. This method has been applied to study mtDNA sequence variation among 15 members of the !Kung population. A genealogical tree relating these aboriginal, Khoisan-speaking southern Africans to 68 other humans and to one chimpanzee has the deepest branches occurring amongst the !Kung, a result consistent with an African origin of human mtDNA. Fifteen cases of unrelated individuals having identical sequences in the most variable parts of the mtDNA control region were found within populations of !Kung, Western Pygmies, and Eastern Pygmies, but no cases of identity were evident among these populations. This and other evidence of geographic structuring of the mitochondrial diversity in Africa, together with knowledge of the rate of accumulation of base changes in human mtDNA, implies that the average rate at which female lineages have moved their home bases during hunter-gatherer times could be as low as 13 meters per year. The technique of enzymatic amplification and direct sequencing applied to readily collected, highly stable biological materials such as hairs makes it possible to examine with high resolution many representatives of virtually any population.

PCR amplification of DNA microdissected from a single polytene chromosome band: a comparison with conventional microcloning

A novel alternative to microcloning for the production of region specific chromosomal DNA is described. In this method, 'microamplification', single bands are dissected from polytene chromosomes and digested with Sau3A. Oligonucleotide adaptors are ligated to these fragments to provide convenient priming sites for polymerase chain reaction amplification. In this way, as much as 1 microgram of DNA can be amplified from a single band. Probes made from PCR amplified DNA from two such dissections have been used to probe cloned DNA form a 100 kb chromosome walk. Whereas conventional microcloning has generated cloned EcoRI fragments corresponding to 3-4 kb of the walk, the PCR probes cover greater than 90% of this chromosomal region. Thus microamplification is significantly more effective than microcloning in providing probes for establishing chromosomal walks.

In vivo footprinting of a muscle specific enhancer by ligation mediated PCR

In vivo protein-DNA interactions at the developmentally regulated enhancer of the mouse muscle creatine kinase (MCK) gene were examined by a newly developed polymerase chain reaction (PCR) footprinting procedure. This ligation mediated, single-sided PCR technique permits the exponential amplification of an entire sequence ladder. Several footprints were detected in terminally differentiated muscle cells where the MCK gene is actively transcribed. None were observed in myogenic cells prior to differentiation or in nonmuscle cells. Two footprints appear to correspond to sites that can bind the myogenic regulator MyoD1 in vitro, whereas two others represent muscle specific use of apparently general factors. Because MyoD1 is synthesized by undifferentiated myoblasts, these data imply that additional regulatory mechanisms must restrict the interaction between this protein and its target site prior to differentiation.

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.