Polymerase chain reaction techniques

Rapid and sensitive PCR-dipstick DNA chromatography for multiplex analysis of the oral microbiota

A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria, Streptococcus mutans, Streptococcus sobrinus, Scardovia wiggsiae, Actinomyces species, and Veillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.

Real-time PCR Assay for Ultrasensitive Quantification of DNA-Binding Proteins

Background: The specific binding of proteins to DNA is a key step for many cellular activities, such as transcription regulation, DNA replication, recombination, repair, and restriction. The detection of DNA-binding proteins, as well as the identification of specific binding sites, is therefore important to understand gene expression mechanisms and cellular function. We describe an ultrasensitive method for quantification of DNA-binding proteins.

Methods: We combined the common exonuclease III (ExoIII) footprinting assay and real-time PCR for quantification of DNA-binding proteins, for an assay that does not require antibodies against the target proteins. Double-strand DNA probes were designed to monitor the activities of DNA-binding protein. The protein-binding site is at the 5′ end of the forward primer. When a target protein is present, it will specifically bind to the protein-binding site and produce a physical hindrance to ExoIII, which protects the reverse DNA strand from digestion by ExoIII. The remaining single-strand DNA template can be quantitatively detected by real-time PCR. Conversely, in the absence of the target protein, the naked primer regions will be degraded by ExoIII, which then cannot be amplified by real-time PCR.

Results: We detected the binding of 10 different transcription factors in crude cell extracts. The assay quantitatively detected binding at femtomolar concentrations of protein.

Conclusions: This technique is customizable and easy to establish. It has potential applications in research, medical diagnosis, and drug discovery.

New Trends in Immunoassays

This article takes a special focus on signal amplification technologies in immunoassays and new generations of lateral-flow assays. Novel signal amplification technologies based either on new classes of biofunctional nanocrystals consisting of releasable fluorophores or on aggregation-induced emission (AIE) can improve the sensitivity and the limits of detection in immunoassays. A bio-barcode assay also allows signal amplification by utilizing antibody-coated magnetic beads to concentrate the analytes and antibody-coated gold nanoparticle probes to carry with a large number of oligonucleotides. These innovative technologies boost the development of immunoassays. Growth in rapid immunoassay is fueled by the increasing number of diabetics, the globalization of infectious diseases and the surge in cardiovascular and other chronic diseases as well as other chronic conditions. Rapid, near patient, decentralized, point-of-care (POC) tests are emerging as a tool for more efficient diagnosis and patient evaluation. Technological innovations in lateral-flow assays have enabled a move to bring testing closer to the patient. A novel "digital-style" lateral-flow assay provides semi-quantitative results by simply counting the number of red lines in the test without any expensive reading instrument. An immuno-threshold-based assay can give a signal directly proportional to the concentration of a hapten to prevent confusion on interpretation of the test results. In addition, POC tests become more meaningful to healthcare professionals by combining the benefits of new technologies to provide quantitative results. A molecular compact disc provides a high-resolution imaging capability that can identify and quantify many different antigens simultaneously in highly complex immunoassays. Further advances in immunoassays will bring diagnostic testing even closer to the patient, and can help physicians to monitor diseases that require immediate test results, thereby enhancing the quality of patient care.

Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins

An ultrasensitive method for detecting protein analytes has been developed. The system relies on magnetic microparticle probes with antibodies that specifically bind a target of interest [prostate-specific antigen (PSA) in this case] and nanoparticle probes that are encoded with DNA that is unique to the protein target of interest and antibodies that can sandwich the target captured by the microparticle probes. Magnetic separation of the complexed probes and target followed by dehybridization of the oligonucleotides on the nanoparticle probe surface allows the determination of the presence of the target protein by identifying the oligonucleotide sequence released from the nanoparticle probe. Because the nanoparticle probe carries with it a large number of oligonucleotides per protein binding event, there is substantial amplification and PSA can be detected at 30 attomolar concentration. Alternatively, a polymerase chain reaction on the oligonucleotide bar codes can boost the sensitivity to 3 attomolar. Comparable clinically accepted conventional assays for detecting the same target have sensitivity limits of approximately 3 picomdar, six orders of magnitude less sensitive than what is observed with this method.

A method for examining expression of homologous genes in plant polyploids

One of the essential issues regarding evolution of polyploid species is how duplicate genes are expressed. Most studies on gene expression in polyploids have been based on isozyme analyses; RNA analysis has not been widely used partially due to difficulties in distinguishing homologous transcripts which usually have the same length and similar or almost identical sequences. In this study, a method combining RT-PCR with RFLP was used to analyze transcripts of homologous genes in natural and synthetic Brassica amphidiploids. Sequences coding for several known genes were selected and used to synthesize gene-specific primers. Total RNAs were used as templates for RT-PCR to amplify homologous transcripts in three diploid parental species, three cultivated amphidiploid species and six synthetic amphidiploids. For each gene, initial PCR products amplified in all species had identical length; however, homologous transcripts in the diploid and amphidiploid species could be distinguished after digesting the PCR products with restriction enzymes. Preliminary results based on three genes indicated that both transcripts from the diploid parents were expressed in the synthetic and natural amphidiploids. This study represents the first application of RT-PCR and RFLP analysis to investigate expression of homologous genes in higher plants. The technique is a sensitive, simple and efficient method for distinguishing homologous transcripts in a mixed RNA population and can be applied to many types of studies on expression of homologous genes.

Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates

An antigen detection system, termed immuno-polymerase chain reaction (immuno-PCR), was developed in which a specific DNA molecule is used as the marker. A streptavidin-protein A chimera that possesses tight and specific binding affinity both for biotin and immunoglobulin G was used to attach a biotinylated DNA specifically to antigen-monoclonal antibody complexes that had been immobilized on microtiter plate wells. Then, a segment of the attached DNA was amplified by PCR. Analysis of the PCR products by agarose gel electrophoresis after staining with ethidium bromide allowed as few as 580 antigen molecules (9.6 x 10(-22) moles) to be readily and reproducibly detected. Direct comparison with enzyme-linked immunosorbent assay with the use of a chimera-alkaline phosphatase conjugate demonstrates that enhancement (approximately x 10(5)) in detection sensitivity was obtained with the use of immuno-PCR. Given the enormous amplification capability and specificity of PCR, this immuno-PCR technology has a sensitivity greater than any existing antigen detection system and, in principle, could be applied to the detection of single antigen molecules.

Applications of polymerase chain reaction methods in genome mapping

Important new polymerase chain reaction-based techniques have been developed to assist in genome analysis. Applications range from genetic and physical mapping of DNA to sequence analysis. The polymerase chain reaction has played a significant role in increasing the feasibility of many aspects of genome analysis and positional cloning.