On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases

A fully integrated system has been developed for genetic analysis based on direct sequencing of polymerase chain reaction (PCR) products. The instrument is based on a serially connected fused-silica capillary assembly. The technique involves the use of microreactors for small-volume PCR and for dye-terminator cycle-sequencing reaction, purification of the sequencing fragments, and separation of the purified DNA ladder. Four modifications to the normal PCR protocol allow the elimination of post-reaction purification. The use of capillaries as reaction vessels significantly reduced the required reaction time. True reduction in reagent cost is achieved by a novel sample preparation procedure where nanoliter volumes of templates and sequencing reaction reagent are mixed using a micro- syringe pump. The remaining stock solution of sequencing reaction reagent can be reused without contamination. The performance of the whole system is demonstrated by one-step sequencing of a specific 257-bp region in human chromosome DNA. Base calling for the smaller fragments is limited only by the resolving power of the gel. The system is simple, reliable and fast. The entire process from PCR to DNA separation is completed in ~4 h. Feasibilities for development of a fully automated sequencing system in the high-throughput format and future adaptation of this concept to a microchip are discussed.     

Detection of multiple β-casein (CASB) alleles by amplification created restriction sites (ACRS)

Direct sequencing of polymerase chain reaction (PCR) amplified DNA has been used to detect the DNA sequences for bovine beta-casein (CASB) A3 and B variants. Based on these sequences we have designed primers which create allele-specific restriction sites in the PCR product. Restriction analysis of PCR product generated in one reaction enable us to identify the A1, A2, A3 and B alleles of CASB rapidly without the use of radioactivity.     

一种快速提取植物病毒DNA的方法

介绍在PCR检测体系中一种快速提取病毒DNA的方法。利用高盐缓冲液溶液释放病毒DNA,同时利用葡聚糖凝胶微柱纯化提取液,有效消除样品中PCR抑制物质并直接作为PCR反应模板扩增检测病毒。该法无需任何特殊设备,适合对大量植株进行大通量的检测分析。     

A new quantitative polymerase chain reaction-high performance ion exchange liquid chromatographic method for the detection of fibroblast growth factor-beta (FGF-beta) gene amplification.

A method for the quantitative determination of fibroblast growth factor-beta (FGF-beta) genomic amplification based on the use of optimized polymerase chain reaction (PCR) procedures and high performance ion exchange (HPIEX) liquid chromatography has been developed. Co-amplification of a second genomic species permits internal standardization of the techniques during optimization of the reaction conditions, the PCR cycle number and the PCR cycle efficiency, as well as during the analytical HPIEX chromatographic determination of the PCR products. These investigations confirm the versatility of these procedures to quantitatively analyse FGF-beta gene amplification in various cells and tissues.     

PNA-based light-up probes for real-time detection of sequence-specific PCR products.

The aim of this study was to introduce the use of a peptide nucleic acid (PNA)-thiazole orange conjugate for real-time monitoring of PCR. When the so-called light-up probes hybridize sequence-specifically to the PCR product, an increase in the fluorescent signal is obtained. It was found that the light-up probe can quantitatively measure the amount of DNA or intact bacterial cells in the reaction mixture, without interfering with the PCR amplification. A linear detection range of at least 4 log units was obtained without optimization of the system. The detection limit of this light-up assay per reaction mixture was 0.4 pg genomic Yersinia enterocolitica DNA.     

Use of activated carbon coated with bentonite for increasing the sensitivity of pcr detection of Escherichia coli O157:H7 in Canadian oyster (Crassostrea gigas) tissue

A novel method for directly increasing the recovery of Escherichia coli O157:H7 and efficiently eliminating PCR inhibitors in oyster tissue without preenrichment was developed with the use of activated carbon coated with bentonite. The recovery of E. coli O157:H7 was significantly affected by the amount of bentonite used to coat the activated charcoal and the pH value of sample preparations. When 4.2 g of activated carbon were coated with 0.4 g of bentonite and seeded oyster samples were adjusted to a pH of 5.0, a high recovery of E. coli O157:H7 (91.6+/-4.4%) was obtained. Activated carbon, coated with bentonite, allowed the PCR detection of 1.5 x 10(2) CFU/g of oyster tissue which was equivalent to 30 genomic targets per PCR reaction. Without the use of activated carbon coated with bentonite, the minimum level of detection was 1.5 x 10(5) CFU/g of oyster tissue, which is equivalent to 3.0 x 10(4) genomic targets per PCR reaction. Three commercial DNA purification systems were used for comparison. The limit of detection with the Wizard DNA Clean-Up System and the Chelex(R)100 Resin was 1.5 x 10(3) CFU/g of oyster tissue which was equivalent to 3.0 x 10(2) CFU/PCR reaction. The QIAamp DNA Mini Kit resulted in a detection limit of 5 x 10(2) CFU/g of oyster tissue which was equivalent to 5 x 10(2) genomic targets per PCR reaction. The use of activated carbon coated with bentonite is an inexpensive method for removal of PCR inhibitors from tissue samples prior to the release of DNA from target cells resulting in relatively low numbers of target cells detected without enrichment.     

Reduction of heteroduplex formation in PCR amplification

Heteroduplex formation is known to occur during mixed-template polymerase chain reaction (PCR) using universal primers, and may represent a serious problem in several PCR-based analyses. A common way to eliminate heteroduplex formation is to use reconditioning PCR. Because we detected that reconditioning PCR was not always sufficient to prevent heteroduplex formation, we focused on developing methods for the elimination of heteroduplexes during PCR. We detected that the heteroduplex to homoduplex ratio can be decreased by the addition of Taq polymerase and by a decrease in the number of PCR cycles. An appropriate combination of both of these approaches can be a method generally applicable to decrease the formation of heteroduplexes.     

Preparing of single-stranded DNA in single-stage PCR with low-melt excess primer for hybridization on biochips

A method for fluorescently labeled single-stranded DNA (ssDNA) production during single-stage polymerase chain reaction (PCR) for subsequent hybridization on a biochip was described. This approach, whose efficiency was confirmed in the case of DARC gene, is considered as an alternative to two-stage nested PCR, consisting of two separate reactions: symmetric and asymmetric. Implementation of PCR in a single stage was achieved due to the use of a truncated excess primer in the second stage that does not anneal on the matrix during the cycles of symmetric stage of PCR and that enters the reaction after decrease of the annealing temperature in asymmetric stage. As a result, high efficiency of genotyping by means of hybridization on biochips is maintained. The suggested approach will allow us to reduce the time, working hours, and risk of contamination when researching biochips.     

Modification of gDNA extraction from soil for PCR designed for the routine examination of soil samples contaminated with Toxocara spp. eggs

A modification of gDNA extraction was developed for the polymerase chain reaction (PCR) technique, intended for the detection and differentiation of Toxocara spp. eggs in soil or sediments. Sand samples from sandpits confirmed as being contaminated with Toxocara spp. eggs by the flotation technique were analysed by PCR. The use of proteinase K made it possible to obtain genomic DNA from the sample without needing to isolate eggs using flotation or to inactivate PCR inhibitors present in the sand. Specific primers in the PCR reaction allowed discrimination between T. canis and T. cati eggs. The modification simplified the procedure, thanks to eliminating the step of gDNA isolation from eggs, which is both laborious and difficult.     

A simple and fast method for cloning and analyzing polymerase chain reaction products

A method describing a fast and efficient way for cloning polymerase chain reaction (PCR) products is presented that involves end repair and purification of the PCR product, followed by kinasing and ligation to the vector with the use of a temperature gradient. Efficiency of ligation was estimated to be 50%–70%. Following transformation, cells are plated on MacConkey agar. Bacteria from selected colonies are used directly from the plates for screening without any subsequent purification. Using this protocol, PCR products can be efficiently cloned quickly and economically.     

Restriction fragment length polymorphism species-specific patterns in the identification of white truffles

A molecular method for the identification of ectomycorrhizae belonging to five species of white truffle is described. The polymerase chain reaction (PCR) and universal primers were used to amplify internal transcribed spacers and 5.8S rDNA, target sequences present in a high number of copies. The amplified products were digested with restriction enzymes in order to detect interspecific polymorphisms. Species-specific restriction fragment length polymorphism patterns were determined for all five species. The use of PCR in conjunction with restriction enzymes provides a sensitive and efficient tool for use in distinguishing ectomycorrhizal species and monitoring inoculated seedlings or field mycorrhizal populations.     

Evaluation of mass spectrometric techniques for charaterization of engineered proteins

A simple and versatile method of in vitro site-specific mutagenesis based on polymerase chain reaction (PCR) is described. The complete method required the use of three oligonucleotide primers and two PCRs. The product of the first PCR was used as one of the primers (megaprimer) in the second PCR. Essentially 100% of the final product incorporated the desired mutation. The various aspects of the procedure and its application is described in detail.     

Enhancing PCR amplification and sequencing using DNA-binding proteins

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.     

Detection of influenza viruses in throat swab by using polymerase chain reaction

An assay protocol based on exploiting the polymerase chain reaction (PCR) for the direct detection of influenza virus in throat swab is described. By use of the mixture of H1 and H3 primers, it was possible to determine the subtype of the influenza A viruses simultaneously. No visible band was detected after PCR of influenza B or A (H2N2) viruses with a pair of H1 or H3 primers. The dilution experiment showed that the influenza viruses, as few as 1.3-6 plaque-forming units, were sufficient for detecting the HA gene by PCR. All throat swab samples from which influenza viruses had been isolated by conventional method were also positively detected by PCR method.     

Site-specific mutagenesis using asymmetric polymerase chain reaction and a single mutant primer.

A method is described for preparing site-specific mutants using a polymerase chain reaction (PCR) based protocol. The protocol requires a single mutant primer, and has been used to introduce mutations into DNA fragments ranging in size from 200 bp to 1569 bp in length in the GM-CSF, beta-actin, human growth hormone and erythropoietin genes. Sequence analysis of PCR derived mutant fragments shows an error rate of less than one bp change per 1500 bp incorporated. Single base pair mutations have been introduced into these genes which create unique restriction sites. We demonstrate that these mutant templates may be used for competitive PCR to quantitate mRNA and DNA. This method thus offers a rapid means for producing competitive templates for use in quantitative PCR.     

Characterization and organization of gene families at the Gli-1 loci of bread and durum wheats by restriction fragment analysis

Summary The polymerase chain reaction (PCR) can be used to detect polymorphisms in the length of amplified sequences between the annealing sites of two synthetic DNA primers. When the distance varies between two individuals then the banding pattern generated by the PCR reaction is essentially a genetic polymorphism and can be mapped in the same way as other genetic markers. This procedure has been used in a number of eukaryotes. Here we report the use of PCR to detect genetic polymorphisms in cereals. Known gene sequences can be used to design primers and detect polymorphic PCR products. This is demonstrated with primers to the -amylase gene family. A second approach is to use semi-random primers to target diverse regions of the genome. For this purpose the consensus sequences at the intron-exon splice junctions were used. The targeting of the intronexon splice junctions in conjunction with primers of random and defined sequences, such as -amylase, provides a source of extensive variation in PCR products. These polymorphisms can be mapped as standard genetic markers.     

Typing of toxic strains of Clostridium difficile using DNA fingerprints generated with arbitrary polymerase chain reaction primers

Clostridium difficile is the causative agent for pseudomembranous colitis in humans. Toxic strains of C. difficile produce two toxins, toxin A and toxin B. A reliable and definitive method of typing the toxic strains of C. difficile is needed since nosocomial cross infection is a primary concern in hospitals and other health care facilities. A method for typing toxic strains of Clostridium difficile using arbitrary polymerase chain reaction (PCR) primers is presented in this study. The C. difficile strains were initially characterized for the toxin A genetic determinant using specific PCR primers which differentiate toxin positive from toxin negative strains. These toxic strains were then PCR typed using six arbitrary primers which generated DNA patterns that were unique for all toxic strains examined. The use of this typing scheme in clinical applications is discussed.     

PCR REACTION PARAMETER TITRATION AS AN APPROACH TO DEVELOP SHORTENED REACTION TIMES IN A CONVENTIONAL THERMAL CYCLER

A shortened PCR procedure was developed in a conventional thermal cycler. Overnight cultures of E. coli were used for PCR to amplify fragments of the uidA and slxII genes. A standard PCR program (30 cycles of 1 m denaturation at 94C, 1 m annealing at 54C or 60C, and 2.5 m elongation at 72C) required 3.5 h to complete and was able to detect a product from 1 × 10³ PCR template cells in an agarose gel. The shortened PCR program (35 cycles of 17 s denaturation at 94C, 20 s annealing at 54C or 60C and 23 s elongation at 72C) required 1.5 h time and was able to detect PCR product from 5×10 PCR template cells. The results show that it is possible to shorten the time of each PCR cycle producing a more rapid method for the detection of E. coli while still using a conventional thermal cycler. This approach was successful using different primer pairs, indicating other researchers could use this approach to significantly shorten their PCR reaction times.     

Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence

In samples where the amount of DNA is limited, the polymerase chain reaction (PCR) can amplify specific regions of the DNA. A quantitative analysis of the PCR product would be desirable to ensure sufficient DNA is available for analysis. In this study, we examine the use of capillary electrophoresis (CE) with laser fluorescence detection for quantitation of PCR products. A coated open tubular capillary was used with a non-gel sieving buffer and a fluorescent intercalating dye to obtain results within 20 minutes. Using an internal standard, peak migration time was below 0.1% relative standard deviation (R.S.D.) with a peak area precision of 3% R.S.D. In comparison to quantitation by hybridization, (i.e., slot blot) and spectrophotometric analysis, capillary electrophoresis shows distinct advantages due to its ability to separate unincorporated primers and PCR byproducts from the targeted PCR product. The results demonstrate that CE can be used to monitor the quality and quantity of the PCR product.