OBJECTIVETo investigate HLA genotyping by oligonucleotide arrays.

METHODUnsymmetrical PCR was used to amplify HLA-A gene exon 2, 3. The PCR products were used as templates for hybridization. The oligonucleotide probes were spotted on glass to make microarrays. High signal and specific probes were selected. The effects of the length and location of probes on hybridization signal were studied. A set of computer software was designed for scanning and genotype differentiation.

RESULTThe genotypes of 30 samples analyzed by microarray showed concordance to that by SBT and PCR-SSP.

CONCLUSIONHLA-A genotyping by oligonucleotide array is a good method with advantage of high speed, low cost and high flux.

Genotype ; HLA-A Antigens ; genetics ; Humans ; Oligonucleotide Array Sequence Analysis ; methods ; Oligonucleotide Probes ; Sensitivity and Specificity

OBJECTIVETo study the expression pattern of cd99l2 gene during zebrafish development, the RNA probes for whole-mount in situ hybridization were prepared in this study.

METHODSThe cd99l2 fragment obtained by RT-PCR was cloned into pGM-T Easy, then the plasmids were linearized with the restriction enzymes SacII or SalI. Using Sp6 or T(7) RNA polymerase, the digoxingenin-labeled antisense and sense probes were synthesized and confirmed by whole-mount in situ hybridization.

RESULTSThe plasmid cd99l2/pGM-T was constructed. cd99l2 gene expression pattern during embryogenesis of zebrafish was examined using the antisense probe, and intense expression was detected in the central nervous system during zebrafish development.

CONCLUSIONThe antisense probe can be used for study of the spatial and temporal distribution of cd99l2 during zebrafish development using the sense probe as control.

Animals ; Central Nervous System ; embryology ; Cloning, Molecular ; Digoxigenin ; chemistry ; Gene Expression Regulation, Developmental ; Oligonucleotide Probes ; RNA Probes ; Uridine Triphosphate ; chemistry ; Zebrafish ; embryology ; genetics ; Zebrafish Proteins ; genetics

OBJECTIVETo develop a novel real-time PCR for sensitively quantitative detection of JAK2 V617F allele burden in peripheral blood.

METHODSBased on the real-time allele-specific PCR (AS-qPCR), the locked nucleic acid (LNA)-modified oligonucleotide probe was used for selectively blocking amplification of wild-type alleles in AS-qPCR, and then a novel AS-LNA-qPCR method was established. The percentages of sample JAK2 V617F alleles were directly calculated by its threshold cycle (Ct) values according to the standard curve which generated by JAK2 V617F alleles with its Ct values. We validated intra- and inter-assay variability for quantifying JAK2 V617F. We also assayed 623 apparent healthy donors by our method to validate its clinical application value.

RESULTSThe quantitative lower limit of this method for JAK2 V617F was 0.01%, and the intra- and inter-assay average variability for quantifying percentage of JAK2 V617F in total DNA was 6.3% and 8.6%, respectively. Nineteen JAK2 V617F-positive individuals were identified using AS-LNA-qPCR in blood of 623 apparently healthy donors, and the range of percentages of JAK2 V617F alleles were 0.01%-5.49%.

CONCLUSIONThe AS-LNA-qPCR with highly sensitive and reproducible quantification of JAK2 V617F mutant burden can be used clinically for diagnosis as well as evaluation of disease prognosis and efficacy of therapy in patients with myeloproliferative neoplasms.

Alleles ; Humans ; Janus Kinase 2 ; genetics ; Mutation ; Oligonucleotide Probes ; genetics ; Oligonucleotides ; genetics ; Real-Time Polymerase Chain Reaction ; methods ; Sensitivity and Specificity

Two oligonucleotide probes are permitted to anneal to the nucleic acid target of interest so that the ends of two probes immediately become adjacent to each other. The ligase can then efficiently join the two juxtaposed oligonucleotide probes by the formation of a phosphodiester bond if and only if perfectly matched base-pairs at the nick are present. During past 20 years, many ligase-mediated techniques have been developed for analyzing various bio-molecules, such as known/unknown point mutations, small-scale insertions and deletions, CpG islands methylation, large sets of single nucleotide polymorphisms (SNPs), specific proteins and DNA regions with which some other proteins can interact. Since the ligation reaction can be easily integrated into other techniques, certain advances have been already achieved. These novel approaches retain high accuracy through multiple hybridization and enzymatic processing events, and provide inherent quality control checking. In this article, we provide a comprehensive review of the ligase-mediated techniques for bio-molecular analysis.
CpG Islands ; genetics ; DNA Methylation ; Ligases ; metabolism ; Molecular Probe Techniques ; Mutation ; Oligonucleotide Probes ; biosynthesis ; chemical synthesis ; genetics ; Polymorphism, Single Nucleotide

The detection method of gene chip based on SPR principle is a potential high-throughput microanalysis method without labelling. With the use of Self-assembled monolayer (SAM) technology, the gene chip of Neisseria gonorrhoeae probe lattice has been prepared, detected and analyzed using the Surface plasmon resonance (SPR) and SPR imaging (SPRI) gene chip detection system here-in provided for research in the hybridizatin reaction on the probe lattice of gene chip. The result indicates that there is an obvious resonance assimilate peak on the SPR resonance curve. And after hybridization, the refractive index and resonance as well as molecular weight of the probe have increased. So whether a hybridization takes place or whether the wanted ingredient is in the sample under examination can be determined by using SPR to watch the detecting interface or the resonance curve. The SPRI detection system is available for observing the happening of a hybridization on the probe of gene chip in real-time and straighforwardly. The SPR and SPRI system can do analysis qualitatively and quantitatively.
DNA Probes ; genetics ; Neisseria gonorrhoeae ; genetics ; Oligonucleotide Array Sequence Analysis ; instrumentation ; methods ; Surface Plasmon Resonance ; methods ; Surface Properties

OBJECTIVETo establish a method of multiplex ligation-dependent probe amplification (MLPA) for clinical screening of Williams syndrome (WS) and for routine use in WS diagnosis.

METHODSProbes for MLPA were designed according to the frequent deletion regions, and used to screen the two patients suspected with Williams syndrome, and the density of the bands were analyzed with software. Linkage analysis using polymorphic markers was performed to confirm the positive result of MLPA.

RESULTSThe MLPA data indicated that the two children had possible microdeletions in the WS critical region. The deletions were confirmed and both were maternal origin by polymorphism analysis.

CONCLUSIONMLPA is a quick and convenient method for detecting deletion or duplication mutations. It can provide reliable and helpful information for clinical diagnose of Williams syndrome.

Child ; Humans ; Ligase Chain Reaction ; methods ; Male ; Oligonucleotide Probes ; genetics ; Sequence Deletion ; Williams Syndrome ; diagnosis ; genetics ; Young Adult

OBJECTIVETo prepare oligo microarrays for hepatitis virus detection and genotyping.

METHODSBy analyzing the DNA or cDNA of HBV, HDV and 4 different genotypes of HCV with the BLAST program, a group of specific sequences for the candidate probes was specified. Array Designer 3.0 software was applied to analyze the candidates to select probes with high specificity, identical length and similar melting temperature (Tm). Altogether 16, 8 and 68 oligonucleotide probes were designed for diagnosis of HBV, HDV, and genotyping HCV. Following the synthesizing and purification, oligo probes were deposited on oligonucleotide chips as microarrays for hepatitis virus detection and genotyping. The samples were labeled by RD-PCR method. Hybridization results were analyzed to cross out those probes with low specificity and sensitivity, and those with signal to noise ratios (SNR) less than 4.0.

RESULTSTwo types of gene chips were successfully developed: microarrays for HBV and HDV simultaneous detection and for HCV genotyping.

CONCLUSIONUsing oligo probes to construct gene chips for clinical diagnosis of hepatitis virus is a simple and effective method. It may be widely used in detecting hepatitis viruses and their genotyping in clinical settings.

Base Sequence ; DNA Fingerprinting ; DNA, Viral ; genetics ; Genotype ; Hepatitis B virus ; classification ; genetics ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Oligonucleotide Probes ; Sensitivity and Specificity

The aim of this study was to build a gene chip system with surface plasmon resonance (SPR) technique, for which Gamma-peptide nucleic acid (Gamma-PNA) functioned as a probe, in order to improve sensitivity and its specificity. With the use of self-assembled monolayer (SAM) technology, surface chemistry of two-dimensional structure was used. Gamma-PNA was designed according to the bioinformatics, and was plated on the SPR chip modified by SAM. Subsequently, relevant parameters of the experiment were ensured and optimized. The results showed that the performances of Gamma-PNA probe was little affected by the ion concentration of buffer, and it had a strong light signal in a stable state. As the ion concentration was 0, there were still good hybrid reactions; pH value had less influence upon Gamma-PNA probe, and acid environment of buffer could be better. Gamma-PNA probe combined with sensor technologies achieved made the probe with dispensable labels and real-time detection. It also improved the efficiency of the hybridization and the stability, providing the foundation for clinical application.
Nucleic Acid Hybridization ; Nucleic Acid Probes ; Oligonucleotide Array Sequence Analysis ; methods ; Peptide Nucleic Acids ; genetics ; Sensitivity and Specificity ; Surface Plasmon Resonance

Multiplex ligation-dependent probe amplification (MLPA) is a semiquantitative analysis based on polymerase chain reaction (PCR). It possesses many advantages such as high efficiency, simple operation, low cost and has been wildly applied in researches of diseases associated with copy number variation, point mutation and methylation. Recently, MLPA is combined with DNA chip to become a real high-throughput method and get great improvement in reliability. Here, the progresses of methods and application of MLPA, as well as its limitations are reviewed.
DNA Methylation ; DNA Probes ; analysis ; genetics ; Humans ; Nucleic Acid Amplification Techniques ; instrumentation ; methods ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide

OBJECTIVETo investigate the effect of microRNA-205 reduction by antagomirs on adhesion ability of normal human corneal epithelial keratinocytes (NHCEKs).

METHODSAntagomir-205, complementary and inhibitory to microRNA-205, was used to suppress endogenous microRNA-205 in NHCEKs. The adhesion ability of treated NHCEKs was then assessed by cell adhesion assay. Immunoblot and immunohistochemistry were conducted to determine the level of two focal adhesion-related proteins, focal adhesion kinase (FAK) and paxillin (Pax). Phalloidin staining was performed to measure the level of filamentous actin in antagomir-treated NHCEKs.

RESULTSAntagomir-205 markedly reduced the level of microRNA-205 in NHCEKs and significantly enhanced adhesion ability of NHCEKs (P<0.01). Further protein analysis validated that inhibition of microRNA-205 increased the number of phosphorylated FAK and phosphorylated Pax, and decreased filamentous actin.

CONCLUSIONOur findings suggest that microRNA-205 has down-regulating effect on cell motility in NHCEKs.

Base Sequence ; Cell Adhesion ; genetics ; Cells, Cultured ; Epithelium, Corneal ; cytology ; Humans ; Keratinocytes ; cytology ; MicroRNAs ; antagonists & inhibitors ; Oligonucleotide Probes