Rapid detection of K-ras mutations in bile by peptide nucleic acid-mediated PCR clamping and melting curve analysis: comparison with restriction fragment length polymorphism analysis

BACKGROUND: Current methods for detection of K-ras gene mutations are time-consuming. We aimed to develop a one-step PCR technique using fluorescent hybridization probes and competing peptide nucleic acid oligomers to detect K-ras mutations in bile and to compare the efficacy with restriction fragment length polymorphism (RFLP) analysis. METHODS: Bile samples were obtained from 116 patients with biliary obstruction, including gallstones (n = 64), benign biliary strictures (n = 6), pancreatic cancer (n = 20), and cholangiocarcinoma (n = 26). The DNA was extracted and subjected to K-ras mutation analysis by real-time PCR and RFLP analysis. Mutations were confirmed by direct sequencing. The sensitivity and specificity were calculated according to the clinical results. RESULTS: The analysis time for real-time PCR was <1 h, whereas RFLP analysis took more than 2 days. With the sensor probe designed for the GAT (G12D) mutant in codon 12 of the K-ras gene, the real-time PCR method also detected the GTT (G12V) mutant. In contrast, a specific sensor probe for the TGT (G12C) mutant detected GAT (G12D), AGT (G12S), and GTT (G12V) mutants in addition to the TGT mutant. The real-time PCR assay allowed the detection of mutation in a 3000-fold excess of wild-type bile DNA. In bile, K-ras codon 12 mutations were detected in 16 of 46 malignant cases by real-time PCR with the TGT probe and 15 by RFLP analysis. All benign cases were wild type. CONCLUSION: Real-time PCR with a cysteine-specific (TGT) sensor probe can rapidly detect K-ras gene mutations in bile and diagnose malignant biliary obstruction with high specificity.     

Sequence-selective recognition of extended-spectrum beta-lactamase GES-2 by a competitive, peptide nucleic acid-based multiplex PCR assay

Extended-spectrum β-lactamases (ESBLs) in Pseudomonas aeruginosa, such as GES-2, which compromises the efficacy of imipenem, tend to be geographically restricted. The CC-to-AA base pair substitution at positions 493 and 494 of the bla_GES-2-coding region distinguishes this ESBL from bla_GES-1 and the bla_IBC-type genes, making it an ideal target for the development of a novel sequence-specific, peptide nucleic acid (PNA)-based multiplex PCR detection method. By using two primer pairs in conjunction with a PNA probe, this method provided an accurate means of identification of bla_GES-2 compared to standard PCR and gene sequencing techniques when it was used to test 100 P. aeruginosa clinical isolates as well as previously published, well-described control strains encompassing all presently known genes in the bla_GES-IBC ESBL family. This novel method has the potential to be used in large-scale, cost-effective screening programs for specific or geographically restricted ESBLs.     

A locked nucleic acid clamp-mediated PCR assay for detection of a p53 codon 249 hotspot mutation in urine

Hepatocellular carcinoma (HCC) has a 5-year survival rate of <10% because it is difficult to diagnose early. Mutations in the TP53 gene are associated with approximately 50% of human cancers. A hotspot mutation, a G:C to T:A transversion at codon 249 (249T), may be a potential DNA marker for HCC screening because of its exclusive presence in HCC and its detection in the circulation of some patients with HCC. A locked nucleic acid clamp-mediated PCR assay, followed by melting curve analysis (using the SimpleProbe), was developed to detect the TP53 249T mutation. In this assay, the locked nucleic acid clamp suppressed 10(7) copies of wild-type templates and permitted detection of 249T-mutated template, with a sensitivity of 0.1% (1:1000) of the mutant/wild-type ratio, assessed by a reconstituted standard within 2 hours. With an amplicon size of 41 bp, it detects target DNA sequences in short fragmented DNA templates. The detected mutations were validated by DNA sequencing analysis. We then tested DNA isolated from urine samples of patients with HCC for p53 mutations and identified positive TP53 mutations in 9 of 17 samples. The possibility of using this novel TP53 249T assay to develop a urine or blood test for HCC screening is discussed.     

High-sensitivity detection of the A3243G mutation of mitochondrial DNA by a combination of allele-specific PCR and peptide nucleic acid-directed PCR clamping

BACKGROUND: The A3243G mutation of mitochondrial DNA (mtDNA) is involved in many common diseases, including diabetes mellitus and mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS). For detection of this mutation, allele-specific PCR is highly sensitive but requires strict control of PCR conditions; it thus is not adequate for a routine clinical test. We aimed to develop a routinely available PCR method for quantitative detection of low-level heteroplasmy of the A3243G mutation. METHODS: Quantitative allele-specific PCR for the A3243G mutation was performed in the presence of peptide nucleic acid (PNA), in which PNA is complementary to the wild-type mtDNA, with one primer having a 3' end matched to nucleotide position 3243 of the mutant. RESULTS: With our method, amplification of wild-type mtDNA was suppressed 7000-fold compared with amplification of the mutant mtDNA under a broad range of conditions: DNA, 5-100 ng; annealing temperature, 61-66 degrees C; and PNA, 1.5-3.5 micromol/L. Hence, 0.1% heteroplasmy of the A3243G mutation can be reliably quantified by this method. Blood samples form 40 healthy volunteers showed <0.06% heteroplasmy, suggesting that 0.1% is diagnostically significant. CONCLUSIONS: PNA maintains the specificity of allele-specific PCR over a wide range of conditions, which is important for routine clinical testing.     

New real-time PCR assay using locked nucleic acid probes to assess prevalence of ParC mutations in fluoroquinolone-susceptible Streptococcus pneumoniae isolates from France

A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys.     

Targeted delivery of DNA to the mitochondrial compartment via import sequence-conjugated peptide nucleic acid

We report that oligonucleotides can be introduced into the mitochondria of living mammalian cells by annealing them to peptide nucleic acids coupled to mitochondrial targeting peptides. These complexes are imported into the mitochondrial matrix through the outer and inner membrane import channels of isolated mitochondria. They are also imported into the mitochondria of cultured cells, provided that the cytosolic uptake of the complexes is facilitated by using synthetic polycations or membrane permeabilizing toxins. Our method now promises to provide a viable strategy for the genetic modification of the mitochondria in cultured cells, animals and patients.     

Immunological capture of nucleic acid hybrids and application to nonradioactive DNA probe assay

Antibodies specific for DNA:RNA hybrids were coated onto polystyrene test tubes and applied to hybridization assays involving DNA and RNA. Synthetic DNA probes complementary to 16S rRNA of Campylobacter were labeled with biotin and hybridized to ribosomal RNA directly in lysates of bacterial cells. After hybridization, DNA:RNA hybrids were captured with immobilized anti-DNA:RNA antibody, and the biotinylated probe was detected with streptavidin-horseradish peroxidase (EC 1.11.1.7) conjugate. The assay was optimized to detect as few as 70,000 Campylobacter cells in a sample. We compared the utility of this hybridization assay with that of conventional microbiology methods by examination of 1448 stool samples from hospital clinical laboratories. The DNA hybridization assay had a sensitivity of 98.7% (75/76) and a specificity of 98.2% (1347/1372) and overall agreed with 98.2% of the conventional results for a test population that had a 5.2% incidence (76/1448) of Campylobacter infection. The assay is simple to perform and yields results within 2.5 h.     

A one-step dipstick assay for the on-site detection of nucleic acid

Objectives

We have developed a one-step nucleic acid dipstick assay (NADA) for visually detecting polymerase chain reaction (PCR) products within 3 min. “One-step” means that there were no additional procedures between amplification and detection.

Methods

This method was achieved through the use of asymmetric PCR and specially designed probes with appropriate melting temperature values. We initially combined one-step NADA with asymmetric capillary convective PCR (ACCPCR), an easy and rapid nucleic acid amplification technique, to construct an on-site nucleic acid diagnostic platform.

Results

We developed a diagnostic assay for the hepatitis B virus based on the ACCPCR-NADA platform to verify its feasibility. It exhibited an analytical sensitivity of three copies per test and a broad detection spectrum including genotype A–I. It also showed 97.9% sensitivity and 100% specificity based on the results observed using 67 serum samples with the Roche COBAS AmpliPrep/COBAS TaqMan (COBAS) system as the standard for comparison.

Conclusion

The results provide evidence for the feasibility of using an ACCPCR-NADA platform in practical applications, especially in on-site test.     

Mutant-enriched PCR and allele-specific hybridization reaction to detect K-ras mutations in stool DNA: high prevalence in a large sample of older adults

BACKGROUND: Testing for mutant K-ras in stool has been proposed for the detection of pancreatic and colorectal cancer (CRC). Different analytical techniques have been developed, but studies of this biomarker in the general population are lacking. We investigated the prevalence and potential determinants of mutant K-ras in stool in a large sample of unselected older adults and assessed the association with colonoscopic findings. METHODS: In stool samples from 875 older adults (age range 50-75 years) participating in a large-scale population-based cohort study, we used mutant-enriched PCR and allele-specific hybridization reaction to analyze mutations in codons 12 and 13 of the K-ras gene. We assessed the association between mutant K-ras in stool and risk factors for gastrointestinal cancer sites, exocrine pancreatic insufficiency determined by fecal pancreas elastase 1, and colonoscopic findings. RESULTS: The overall prevalence of mutant K-ras in stool was 8% (95% confidence interval 6%-10%). There was a tentative association between increased fecal pancreas elastase 1 and mutant K-ras in stool (P = 0.09). Patients with advanced colorectal neoplasia diagnosed within 2 years after stool collection (24 with advanced adenomas, 7 with CRC) all tested negative. CONCLUSION: The proposed assay identifies mutant K-ras in stool at a higher prevalence than has been reported for other analytical techniques. Our findings do not support the use of this assay for CRC screening, but its potential use for early detection of pancreatic cancer (in combination with other markers) requires further investigation.     

核酸扩增产物的量化酶免疫通用型检测方法

目的以丙型肝炎病毒（ＨＣＶ）ＲＮＡ（ＲＮＡ）核酸扩增产物的量化酶免疫（ＥＩＡ）通用型检测方法及试剂,以准确评价疗效,指导治疗。方法选择合适的扩增循环数使聚合酶链反应（ＰＣＲ）在“平台期效应”出现前即停止;同时将第２次ＰＣＲ所用的引物进行生物素标记,使扩增产物带有生物素标记成分,再通过固相包被的链霉亲合素进行捕获、氢氧化钠解链变性、荧光素标记的ＨＣＶ特异性探针杂交以及辣根过氧化物酶（ＨＲＰ）标记的抗荧光素酶标抗体反应后,ＴＭＢ显色测定,通过显色反应颜色的深浅,反映样品中ＨＣＶＲＮＡ模板的情况。结果ＨＣＶＲＮＡ扩增产物的ＥＩＡ检测结果表明：所建立的方法操作简便、重复性好、特异性强、敏感度高、结果判断客观准确,而且可以反映样品中病原体核酸模板量的多少;干扰素治疗期间,ＨＣＶ感染的慢性丙型肝炎患者不同时间系列血的动态检测结果提示,在临床监测治疗、评价疗效上,本方法具有较大的指导意义。结论所建立的方法可以成为一种通用型检测技术,用于量化分析病毒、细菌等致病因子及人类某些基因（如ＨＬＡＢ２７）的核酸扩增产物的研究,具有广阔的应用前景。     

Recent advances in the development of peptide nucleic acid as a gene-targeted drug

Peptide nucleic acid (PNA) is a non-ionic mimic of DNA that binds to complementary DNA and RNA sequences with high affinity and selectivity. Targeting of single-stranded RNA leads to antisense effects, whereas PNAs directed toward double-stranded DNA exhibit antigene properties. Recent advances in cell uptake and in antisense and antigene effects in biological systems are summarised in this review. In addition to traditional targets, namely genomic DNA and messenger RNA, applications for PNA as a bacteriocidal antibiotic, for regulating splice site selection and as a telomerase inhibitor are described.     

A flexible bioluminescent-quantitative polymerase chain reaction assay for analysis of competitive PCR amplicons

Aequorin-based flash-type bioluminescent methods can detect nucleic acid molecules in the attomolar range (10(-18)) enabling improved monitoring of the polymerase chain reaction (PCR) at cycles previously considered too low for product detection. The high sensitivity of bioluminescence (BL) was used to examine the efficiency of the PCR and to assess the effect of substrate variation during the linear phase of amplification. Primer efficiency was dependent on initial template concentration, in a manner indicative of a two-component reaction. However, the rate of amplicon formation was significantly impaired at low template levels and could not be overcome by excess primer. The PCR was directly dependent upon nucleotide concentration, which was independent of template concentration. Conditions were identified for optimal linear amplification and detection using BL. Accurate quantitative analysis was performed using competitive coamplification of a specific target standard sequence containing identical target primer recognition sites and novel internal sequences. Quantitation was most accurate when target molecule was similar in concentration to the internal standard. The Bioluminescent Quantitative-PCR (BLQ-PCR) assay has the potential to eliminate processing variability. We demonstrated high quantitative potential with a broad dynamic range. Overall, the BLQ-PCR assay is flexible and a viable alternative to contemporary Q-PCR techniques.     

Micromethod for phosphonoformate inhibition assay of hepatitis B viral DNA polymerase

A micromethod for the specific measurement of hepatitis B viral DNA polymerase in serum is presented, based on the phosphonoformate inhibition assay (J Med Virol 12: 61-70, 1983). In the micromethod, sample volume is reduced to 120 microL and the ultracentrifugation step is eliminated. The method allows good discrimination between serum infected with hepatitis B virus and uninfected serum. The cutoff value for rate of nucleotide incorporation, based on assays of 41 serum specimens negative for hepatitis B serological markers, was about 15 nU/L (90th percentile). Serum containing hepatitis B surface and antigens exhibited rates of phosphonoformate-inhibitive nucleotide incorporation of 150 (SD 150) nU/L, with an upper 90th percentile range of 17 to 667 nU/L (n = 41). The micromethod makes use of commercially available [32P]dCTP (specific activity about 7000 kCi/mol). 125I-labeled dCTP was found to be unsuitable for this assay. Human DNA polymerases in serum are detected by this method but are excluded from the phosphonoformate-inhibitive fraction.     

基于磁珠核酸提取方法对现有国产HBV DNA试剂盒分析灵敏度的改进

建立一种基于纳米磁珠为介质的核酸提取和富集方法,提高国产HBV核酸检测试剂的分析灵敏度,用于痕量HBV DNA的测定.方法选择经抗病毒治疗HBV DNA浓度≤1×104 IU/ml的乙型肝炎患者血清标本50份.标准品采用WHO HBV DNA标准品.通过纳米磁珠实现对HBV核酸的吸附浓缩,提高提取的HBV核酸模板的浓度.以瑞士罗氏公司HBV DNA检测试剂和4种国产试剂原有的核酸提取检测方法为对照,评价该方法对国产核酸检测试剂的改进效果.结果纳米磁珠核酸提取方法与国产试剂结合后,国产试剂的分析灵敏度分别达到10和50 IU/ml,与罗氏试剂的分析灵敏度12 IU/ml基本相当.4种国产试剂盒内自带提取试剂检测临床乙型肝炎患者血清中痕量HBV DNA阳性检出率分别为64%(32份)、56%(28份)、62%(31份)和58%(29份),与罗氏试剂阳性检出率88%比较,差异具有统计学意义(x2值分别为7.895、12.698、9.013、11.416,P均＜0.05).纳米磁珠核酸提取方法与国产试剂结合后,阳性检出率分别为88%(44份)、88%(44份)、88%(44份)和86%(43份),与罗氏试剂(88%)比较,阳性检出率差异无统计学意义(x2值分别为0.000、0.000、0.000、0.088,P均＞0.05).HBV核酸浓度为101～103 IU/ml时,病毒核酸浓度对数值与循环阈值呈负相关,但是比103～106 IU/ml浓度范围的相关性下降.结论以纳米磁珠为介质建立的核酸提取方法可显著提高国产HBV DNA检测的分析灵敏度,对监测乙型肝炎患者血液中痕量HBV DNA含量具有重要意义.     

Development of a sensitive PCR inhibition method to demonstrate HBV nucleic acid inactivation

BACKGROUND: The evaluation of pathogen reduction technologies with relevant viruses currently contaminating the blood supply is limited by the availability of high-titer virus inocula and sensitive in vitro or in vivo infectivity assays. Because HBV infectivity can only be assessed by in vivo studies with chimpanzees, a sensitive PCR inhibition assay was developed to measure PEN110 inactivation of HBV. STUDY DESIGN AND METHODS: PCR amplification of 1.1 kb of HBV genome was optimized to determine DNA damage introduced by treatment with PEN110 in RBCs. Inactivation of duck HBV (DHBV) in RBCs, with measurement of the in vitro infectivity, was performed to validate the PCR assay. RESULTS: The PCR was highly specific and sensitive for amplification of the HBV genome and used to demonstrate a reduction of at least 7.2 and 8.1 log geq per mL within the first 18 hours of PEN110 treatment. PEN110 inactivation of DHBV was also achieved within the first 18 hours with a reduction factor of at least 5.0 log tissue culture infectious dose 50 percent per mL, suggesting that PCR inhibition is an alternative to infectivity assays. CONCLUSION: This study establishes PCR inhibition as a reasonable approach to assess the efficiency of PEN110 inactivation of human pathogens with human plasma donations that have been found to contain high titers of relevant agents during different stages of infection.     

人血浆DNA双重实时荧光定量PCR检测法的建立

目的 建立带有内参照的双重实时荧光定量PCR方法检测血浆DNA含量.方法 构建重组质粒DNA作为内参照物,采用共用下游引物的双重实时荧光定量PCR技术同步扩增人看家基因β-actin和重组质粒载体中人工合成DNA序列,定量检测健康成年人血浆DNA含量.结果 本法能在同一个反应管中对目的基因和内参照进行同步扩增,两者的扩增无相互干扰,特异性好;重组质粒DNA的平均扩增效率达90%,β-actin基因的平均扩增效率接近100%;本法批内变异系数（CV）11%,批间CV17%.结论 成功建立含有内参照的双重实时荧光定量PCR方法,可对血浆DNA进行定量检测.