Multiplex locked nucleic acid probes for analysis of hepatitis B virus mutants using real-time PCR

Current methods of detecting hepatitis B virus (HBV) mutations are time consuming, labor intensive, and not suitable for screening large numbers of samples. A multiplex real-time PCR approach presented in this article is a hepatitis B virus quantification method that employs the SYBR Green I dye in conjunction with wild-type HBV sequence-specific locked nucleic acid (LNA) probes. The three short LNA probes distinguished the wild-type strain or three groups of mutants (rt173, rt180/rt181, and rt202/rt204) depending on perfect-match hybrids or mismatch within one template simultaneously. Primers labeled with quencher minimized the background signals. This sensitive approach could quantify 10(2) copies of HBV virus, and as low as 1% mutants among 10(4) copies of wild-type HBV could be identified. The technique is handy and convenient, requiring only 3.5 h to analyze 30 hepatitis B surface antigen-positive serum samples. The HBV isolates were confirmed by direct sequencing. Our data indicate that real-time PCR with SYBR Green I dye is a reliable, rapid, and convenient technique for HBV quantification. Furthermore, by incorporating fluorescent LNA probes, this technique becomes handy in identifying and classifying mutations in the HBV polymerase gene. Being sensitive, specific, accurate, rapid, and convenient in nature, this technique could be a suitable diagnostic tool with wide application particularly in cases in which large volumes of clinical samples are handled.     

Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes

Surface plasmon field-enhanced fluorescence spectroscopy (SPFS) was recently developed for PCR product analysis, which allowed for real-time monitoring of hybridization processes and for the detection of trace amounts of PCR products, with a detection limit of 100 fmol on the peptide nucleic acid (PNA) probe surface, and 500 fmol on the DNA probe surface. By selectively labeling the strands of PCR-amplified DNA, it was shown that the heat denaturation process in combination with the application of low-salt condition substantially reduced the interference from the antisense strands and thus simplified the surface hybridization. Furthermore, SPFS was demonstrated to be capable of quantitatively discriminating the difference induced by single nucleotide substitution, even within one minute of contact time.     

Real-time genotyping with oligonucleotide probes containing locked nucleic acids

Oligonucleotide probes containing locked nucleic acid (LNA) hybridize to complementary single-stranded target DNA sequences with an increased affinity compared to oligonucleotide DNA probes. As a consequence of the incorporation of LNA residues into the oligonucleotide sequence, the melting temperature of the oligonucleotide increases considerably, thus allowing the successful use of shorter LNA probes as allele-specific tools in genotyping assays. In this article, we report the use of probes containing LNA residues for the development of qualitative fluorescent multiplex assays for the detection of single nucleotide polymorphisms (SNPs) in real-time polymerase chain reaction using the 5'-nuclease detection assay. We developed two applications that show the improved specificity of LNA probes in assays for allelic discrimination. The first application is a four-color 5'-nuclease assay for the detection of SNPs for two of the most common genetic factors involved in thrombotic risk, factor V Leiden and prothrombin G20210A. The second application is a two-color assay for the specific detection of the A-to-T tranversion in codon 6 of the beta-globin gene, responsible for sickle cell anemia. Both real-time genotyping assays were evaluated by comparing the performance of our method to that of a reference method and in both cases, we found a 100% concordance. This approach will be useful for research and molecular diagnostic laboratories in situations in which the specificity provided by oligonucleotide DNA probes is insufficient to discriminate between two DNA sequences that differ by only one nucleotide.     

Fast quantitative PCR, locked nucleic acid probes and reduced volume reactions are effective tools for detecting Batrachochytrium dendrobatidis DNA

The fungal pathogen Batrachochytrium dendrobatidis threatens amphibian populations around the world. The ability to detect this pathogen on infected animals and in the environment is critical for understanding and controlling this pandemic. We tested several advances in quantitative PCR (qPCR) techniques to detect B. dendrobatidis DNA. We used a fast PCR thermocycler and enzymes that reduced the volume and the duration of the reaction. We also compared a conventional TaqMan minor groove binding (MGB) probe to an identical locked nucleic acid (LNA) counterpart. The fast qPCR reaction had a high degree of sensitivity to B. dendrobatidis DNA. The LNA probe was effective for detecting B. dendrobatidis DNA and produced results -similar to those of the MGB probe. The modifications that we tested can improve the cost, time efficiency and specificity of quantitative PCR as a tool for detecting pathogen DNA.     

锁核酸研究进展

锁核酸(locked nucleic acid,LNA)是一种新型的寡核酸衍生物,结构中β-D-呋喃核糖的2’-O,4’-C位通过缩水作用形成环形的氧亚甲基桥、硫亚甲基桥或胺亚甲基桥,呋喃糖的结构锁定在C3’内型的N构型,形成了刚性的缩合结构。LNA作为一种新的反义核酸,具有与DNA／RNA强大的杂交亲和力、反义活性、抗核酸酶能力、水溶性好及体内无毒性等优点。LNA在基因诊断和基因治疗上有很多优势,如：单链核酸的多态性基因分型、LNA寡聚体具有高效抑制端粒酶活性及LNA修饰的DNA核酶(LNAzymes)高效清除高级结构的RNA等,有良好的应用研究前景。     

Detection of human adenoviruses with real-time PCR assay using TaqMan fluorescent probes

Infections with human adenoviruses are common worldwide and cause a wide range of signs and symptoms. Nowadays in current diagnostics procedures older virological methods, such virus isolation in a cell cultures, are replaced with molecular biology tests. The aim of the study was development of real-time PCR assay for detection of human adenoviruses. DNA isolated from A549 cell line infected with five different HAdV strains was used for development of a qualitative real-time PCR assay for detection of all human adenoviruses using primers targeting a conserved region of the hexon gene and a specific TaqMan probe. The analytical sensitivity of real-time PCR assay was tested using serial dilutions of HAdV7 DNA in range between 10(0) and 10(-6). For comparison typical end-point detected PCR for adenovirus detection with the same DNA dilutions was made. The sensitivity of novel method; was about thousand-fold higher than older one. The conclusion is that real-time PCR is very advisable in diagnostics of diseases caused with adenoviruses. The high level of sensitivity, specificity, accuracy, and rapidity provided by this assay are favorable for the use in the detection of adenoviral DNA in clinical specimens, especially from neuroinfections or immunocompromised hosts.     

High-throughput gender identification of Accipitridae eagles with real-time PCR using TaqMan probes

The objective was to develop high-throughput gender identification of eagles. Based on BLAST and alignment analyses, the CHD-Z and CHD-W sequences of nine species of eagles were highly homologous with Spilornis cheela hoya (S. c. hoya); therefore, TaqMan probes were designed to target their CHD-ZW-common and CHD-W-specific regions. In S. c. hoya, genders were identified using TaqMan-based, real-time PCR (amplified by P2/P8 primers); this method was validated with anatomically confirmed controls (one of each gender). Both genders had high intensities of the HEX-labeled (CHD-ZW-common) probe, whereas only females had high intensity of the FAM-labeled (CHD-W-specific) probe. The sequence of the CHD-W-specific probe designed for S. c. hoya was completely homologous with the CHD-W-specific region in Circaetus gallicus, Gyps indicus, and Gyps bengalensis, and was only one nucleotide different from those of Accipiter nisus, Spizaetus nipalensis, Aquila chrysaetos, Circus spilonotus, and Milvus migrans. For the CHD-ZW-common probe, all species listed were completely conserved. Using real-time PCR software, we established auto-calling of the genders of 15 individuals of S. c. hoya. In conclusion, this method provided accurate, high-throughput gender identification for S. c. hoya, and has considerable potential for identifying the gender of several related species of eagles.     

Alpha-LNA (alpha-D-configured locked nucleic acid)

Two pyrimidine alpha-LNA nucleoside monomers have been synthesised and incorporated into alpha-configured oligonucleotides. A fully modified mixed alpha-LNA sequence displays unprecedented parallel stranded hybridisation with complementary RNA and a remarkable selectivity for RNA over DNA. Modelling shows alpha-LNA:RNA to form an extended duplex with a very broad major groove.     

Detection of mutations in mitochondrial DNA by droplet digital PCR

Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy – a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-todate methods that have not yet been introduced as routine clinical assays. These methods can be used for detecting mutations in mtDNA to verify diagnosis of “mitochondrial disease”, studying dynamics of mutant mtDNA in body tissues of patients, as well as investigating structural features of mtDNAs. Original data on allele-specific discrimination of m.11778G>A mutation by droplet digital PCR are presented, which demonstrate an opportunity for simultaneous detection and quantitative assessment of mutations in mtDNAs.     

Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers

Genomes are becoming heavily annotated with important features. Analysis of these features often employs oligonucleotides that hybridize at defined locations. When the defined location lies in a poor sequence context, traditional design strategies may fail. Locked Nucleic Acid (LNA) can enhance oligonucleotide affinity and specificity. Though LNA has been used in many applications, formal design rules are still being defined. To further this effort we have investigated the effect of LNA on the performance of sequencing and PCR primers in AT-rich regions, where short primers yield poor sequencing reads or PCR yields. LNA was used in three positional patterns: near the 5′ end (LNA-5′), near the 3′ end (LNA-3′) and distributed throughout (LNA-Even). Quantitative measures of sequencing read length (Phred Q30 count) and real-time PCR signal (cycle threshold, C_T) were characterized using two-way ANOVA. LNA-5′ increased the average Phred Q30 score by 60% and it was never observed to decrease performance. LNA-5′ generated cycle thresholds in quantitative PCR that were comparable to high-yielding conventional primers. In contrast, LNA-3′ and LNA-Even did not improve read lengths or C_T. ANOVA demonstrated the statistical significance of these results and identified significant interaction between the positional design rule and primer sequence.     

Detection of Vibrio parahaemolyticus in shellfish by use of multiplexed real-time PCR with TaqMan fluorescent probes

We developed a multiplexed real-time PCR assay using four sets of gene-specific oligonucleotide primers and four TaqMan probes labeled with four different fluorophores in a single reaction for detection of total and pathogenic Vibrio parahaemolyticus, including the pandemic O3:K6 serotype in oysters. V. parahaemolyticus has been associated with outbreaks of food-borne gastroenteritis caused by the consumption of raw or undercooked seafood and therefore is a concern to the seafood industry and consumers. We selected specific primers and probes targeting the thermostable direct hemolysin gene (tdh) and tdh-related hemolysin gene (trh) that have been reported to be associated with pathogenesis in this organism. In addition, we targeted open reading frame 8 of phage f237 (ORF8), which is associated with a newly emerged virulent pandemic serotype of V. parahameolyticus O3:K6. Total V. parahaemolyticus was targeted using the thermolabile hemolysin gene (tlh). The sensitivity of the combined four-locus multiplexed TaqMan PCR was found to be 200 pg of purified genomic DNA and 10(4) CFU per ml for pure cultures. Detection of an initial inoculum of 1 CFU V. parahaemolyticus per g of oyster tissue homogenate was possible after overnight enrichment, which resulted in a concentration of 3.3x10(9) CFU per ml. Use of this method with natural oysters resulted in 17/33 samples that were positive for tlh and 4/33 samples that were positive for tdh. This assay specifically and sensitively detected total and pathogenic V. parahaemolyticus and is expected to provide a rapid and reliable alternative to conventional detection methods by reducing the analysis time and obviating the need for multiple assays.     

Single-nucleotide-polymorphism-specific PCR for quantification and discrimination of Chlamydia pneumoniae genotypes by use of a "locked" nucleic acid

Single-nucleotide polymorphisms (SNPs) are targets to discriminate intraspecies diversity of bacteria and to correlate a genotype with a potential pathotype. Quantification of polygenotypic populations supports this task for in vitro and in vivo applications. We present a novel assay capable of quantifying mixtures of two genotypes differing by only one SNP.     

Methylphosphonate LNA: a locked nucleic acid with a methylphosphonate linkage

Synthesis of an oligonucleotide containing one methylphosphonate locked nucleic acid (LNA) thymine monomer using the phosphoramidite approach is described. The binding affinity of this 9-mer methylphosphonate LNA towards complementary DNA and RNA oligonucleotides was increased compared to the reference DNA, but decreased compared to the reference LNA. In the 9-mer sequence context studied, introduction of a single methylphosphonate LNA monomer, contrary to a single LNA monomer, efficiently inhibits 3'-exonucleolytic degradation.