BACKGROUND: Peptide nucleic acid (PNA) probes are artificial DNA analogues with a hydrophobic nature that can penetrate the mycobacterial cell wall. We evaluated a FISH method for simultaneous detection and identification of Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM) in clinical respiratory specimens using differentially labeled PNA probes. METHODS: PNA probes targeting the mycobacterial 16S ribosomal RNA were synthesized. The cross-reactivity of MTB- and NTM-specific probes was examined with reference strains and 10 other frequently isolated bacterial species. A total of 140 sputum specimens were analyzed, comprising 100 MTB-positive specimens, 21 NTM-positive specimens, and 19 MTB/NTM-negative specimens; all of them were previously confirmed by PCR and culture. The PNA FISH test results were graded by using the United States Centers for Disease Control and Prevention-recommended scale and compared with the results from the fluorochrome acid-fast bacterial stain. RESULTS: The MTB- and NTM-specific PNA probes showed no cross-reactivity with other tested bacterial species. The test results demonstrated 82.9% agreement with the culture results with diagnostic sensitivity of 80.2% and diagnostic specificity of 100.0% (kappa=0.52, 95% confidence interval: 0.370-0.676). CONCLUSIONS: Dual-color PNA FISH showed high specificity for detecting and identifying mycobacteria in clinical specimens. However, because of its relatively low sensitivity, this method could be more applicable to culture confirmation. In application to direct specimens, the possibility of false-negative results needs to be considered.
Cell Wall ; Centers for Disease Control and Prevention (U.S.) ; DNA ; Fluorescence* ; In Situ Hybridization* ; Mycobacterium tuberculosis* ; Nucleic Acid Probes* ; Peptide Nucleic Acids ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; Sputum

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

OBJECTIVETo determine the optimal concentration of c-erbB2 antisense probe labeled with superparamagnetic iron oxide (SPIO) nanoparticles for in vivo tumor imaging in mice using magnetic resonance imaging (MRI).

METHODSThirty BALB/c mice bearing SK-Br-3 tumor were randomized into 5 groups to receive injections of different concentrations of SPIO-labeled c-erbB2 antisense probe (containing 6.0, 9.0, 12.0, 15.0, or 18.0 mg Fe/kg). MRI was performed before and 6 h after the injections, and the signal intensities of the tumor were compared among the groups. The tumor tissues were then dissected for microscopic examination with HE and Prussian blue staining.

RESULTSThe tumor-bearing mice all survived after injections of the probe at doses of 6.0, 9.0 and 12.0 mg, but injections at higher doses (15.0 and 18.0 mg) caused death in some mice. Injections of the probe at the doses of 12.0, 15.0 and 18.0 mg resulted in significant signal enhancement of the tumor (P<0.001) to allow visual identification, but the changes showed no significant differences among the 3 groups (P>0.05). Pathological examination revealed irregular structures of the tumor issue containing numerous heterogeneous tumor cells aligned into cancer nests; Prussian blue staining visualized scattered blue iron particles in the tumor issue, which was especially obvious in mice injected with 12.0, 15.0 and 18.0 mg labeled probe.

CONCLUSIONInjection of 12.0 mg/kg SPIO-labeled c-erbB2 antisense probe allows optimal tumor imaging in BALB/c mice using MRI.

Animals ; Antisense Elements (Genetics) ; Cell Line, Tumor ; Contrast Media ; Dextrans ; Genes, erbB-2 ; Magnetic Resonance Imaging ; Magnetite Nanoparticles ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Nanoparticles ; Nucleic Acid Probes ; genetics ; Xenograft Model Antitumor Assays

OBJECTIVETo develop a rapid duplex Real-time reverse transcription PCR (rRT-PCR) method to detect E119V mutation on neuraminidase (NA) of influenza A(H3N2) subtype with drug resistance to oseltamivir.

METHODSTwenty-six NA genes of influenza A(H3N2) virus between 2000 and 2012 in GenBank database were selected as the target genes, and specific TaqMan-MGB probe was designed to target the E119V amino acid change in neuraminidase protein. rRT-PCR was then performed and evaluated for the sensitivity, specificity and reproducibility using virus with E119V mutation and clinical samples.

RESULTSThis study described the validation of a highly sensitive and specific duplex rRT-PCR for detection of substitutions leading to the E119V amino acid change in NA protein of influenza A(H3N2). Fluorescence signals could be detected even when diluted a A (H3N2) virus (HA = 8) into 10(-5) and linear correlation between the logarithm of the viral titer with the Ct values was observed. In addition, the assay was highly specific in that there was no cross-react with other respiratory viruses, nor did two TaqMan-MGB probes. E119V substitution in quasispecies with both sensitive and resistant viruses could be detected as well. The limit of detection was 5% for quasispecies with high concentrations and 50% for quasispecies with low concentrations. The average coefficient of variation (CV) for within-run assays was 2.32% and 0.57% for H3N2-119E and H3N2-119V primer/probe sets separately, 1.77% and 0.97% for average CV of between-run assays, which exhibited good repeatability. Sequence analysis of twenty NA genes verified glutamic acid (E) at amino acid site 119, which was in consistent with the results from our rRT-PCR method.

CONCLUSIONThe assay developed in this study is highly sensitive and specific, and easy to operate; thereby it could be used for identification of A(H3N2) virus with E119V amino acid change in NA protein.

Amino Acid Substitution ; Drug Resistance, Viral ; Influenza A Virus, H3N2 Subtype ; drug effects ; enzymology ; genetics ; Mutation ; Neuraminidase ; genetics ; Nucleic Acid Probes ; Reverse Transcriptase Polymerase Chain Reaction ; methods

OBJECTIVETo investigate the possibility of applying multiplex ligation-dependent probe amplification (MLPA) to the detection of azoospermia factor (AZF) microdeletion on the Y chromosome in infertile men with azoospermia or severe oligozoospermia.

METHODSDNA samples were obtained from 147 azoospermia or severe oligozoospermia patients and 154 normal controls. After denatured at 95 degrees C, the samples were hybridized to the specific probes designed for the AZF region. With the ligase, the hybrid products were amplified by a pair of universal primers labeled with FAM fluorescence, and then separated by capillary electrophoresis for data analysis. Meanwhile all the samples were subjected to multiplex-PCR (mPCR) analysis for sequence-tagged sites (STS) in the AZF region.

RESULTSSTS deletion was detected in 22 (15.0%) of the 147 patients but not in the normal controls. By MLPA, 40 (27.2%) of the patients were found with specific probe omission in the AZF region, as compared with 20 cases in the control group.

CONCLUSIONCompared with mPCR, MLPA has a better sensitivity in detecting AZF microdeletions, and it provides more precise genetic information on the AZF regions, which may contribute to in-depth exploration into the etiological mechanism of impaired spermatogenesis.

Adult ; Azoospermia ; genetics ; Case-Control Studies ; Chromosome Deletion ; Chromosomes, Human, Y ; genetics ; DNA Probes ; Genetic Loci ; Humans ; Infertility, Male ; Male ; Nucleic Acid Amplification Techniques ; methods ; Oligospermia ; genetics ; Polymerase Chain Reaction ; methods ; Seminal Plasma Proteins ; genetics ; Sequence Tagged Sites ; Sex Chromosome Aberrations ; Sex Chromosome Disorders of Sex Development ; genetics ; Young Adult

BACKGROUND: A peptide nucleic acid (PNA) probe-based real-time PCR (PNAqPCR(TM) TB/NTM detection kit; PANAGENE, Korea) assay has been recently developed for the simultaneous detection of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) in clinical specimens. The study was aimed at evaluation of the performance of PNA probe-based real-time PCR in respiratory specimens. METHODS: To evaluate potential cross-reactivity, the extracted DNA specimens from Mycobacterium species and non-mycobacterial species were tested using PNA probe-based real-time PCR assay. A total of 531 respiratory specimens (482 sputum specimens and 49 bronchoalveolar washing fluid specimens) were collected from 230 patients in July and August, 2011. All specimens were analyzed for the detection of mycobacteria by direct smear examination, mycobacterial culture, and PNA probe-based real-time PCR assay. RESULTS: In cross-reactivity tests, no false-positive or false-negative results were evident. When the culture method was used as the gold standard test for comparison, PNA probe-based real-time PCR assay for detection of MTBC had a sensitivity and specificity of 96.7% (58/60) and 99.6% (469/471), respectively. Assuming the combination of culture and clinical diagnosis as the standard, the sensitivity and specificity of the new real-time PCR assay for detection of MTBC were 90.6% (58/64) and 99.6% (465/467), respectively. The new real-time PCR for the detection of NTM had a sensitivity and specificity of 69.0% (29/42) and 100% (489/489), respectively. CONCLUSIONS: The new real-time PCR assay may be useful for the detection of MTBC in respiratory specimens and for discrimination of NTM from MTBC.
Bronchoalveolar Lavage Fluid/microbiology ; DNA Probes/chemistry/metabolism ; DNA, Bacterial/*analysis ; Humans ; Molecular Typing/*methods ; Mycobacterium tuberculosis/*genetics/isolation & purification ; Nontuberculous Mycobacteria/*genetics/isolation & purification ; Nucleic Acid Hybridization ; Peptide Nucleic Acids/chemistry/*metabolism ; *Real-Time Polymerase Chain Reaction ; Respiratory System/*microbiology ; Sputum/microbiology

Adult ; Aged ; Carcinoma, Squamous Cell ; pathology ; virology ; Cervical Intraepithelial Neoplasia ; pathology ; virology ; Colposcopy ; Cytodiagnosis ; DNA Probes, HPV ; DNA, Viral ; isolation & purification ; Female ; Humans ; Middle Aged ; Nucleic Acid Hybridization ; Papillomaviridae ; genetics ; isolation & purification ; Papillomavirus Infections ; Uterine Cervical Neoplasms ; pathology ; virology ; Vaginal Smears ; Young Adult

The present paper is aimed to detect superparamagnetic iron oxide labeled c-erbB2 oncogene antisense oligonucleotide probe (magnetic antisense probe) connected with SK-Br-3 oncocyte mRNA nucleotide by high resolution atomic force microscope (AFM). We transfected SK-Br-3 oncocyte with magnetic antisense probe, then observed the cells by AFM with high resolution and detected protein expression and magnetic resonance imagine (MRI). The high resolution AFM clearly showed the connection of the oligonucleotide remote end of magnetic antisense probe with the mRNA nucleotide of oncocyte. The expression of e-erbB2 protein in SK-Br3 cells were highly inhibited by using magnetic antisense probe. We then obtained the lowest signal to noise ratio (SNR) of SK-Br-3 oncocyte transfected with magnetic antisense probe by MRI (P<0.05). These experiments demonstrated that the high resolution AFM could be used to show the binding of magnetic antisense probe and SK-Br-3 mRNA of tumor cell nuclear.
Breast Neoplasms ; metabolism ; pathology ; Cell Line, Tumor ; DNA, Antisense ; chemistry ; genetics ; Female ; Ferric Compounds ; chemistry ; Genes, erbB-2 ; genetics ; Humans ; Magnetics ; Microscopy, Atomic Force ; methods ; Molecular Probe Techniques ; Nucleic Acid Probes ; chemistry ; genetics ; Oligodeoxyribonucleotides ; chemistry ; genetics ; Oxyphil Cells ; ultrastructure ; RNA, Messenger ; genetics ; metabolism

We report here a novel membrane transfer-based DNA detection method, in which alkaline phosphatase labeled gold nanoparticle (AuNP) probes were used as a means to amplify the detection signal. In this method, the capture probe P1, complimentary to the 3' end of target DNA, was immobilized on the chip. The multi-component AuNP probes were prepared by co-coating AuNPs with the detecting probe P2, complimentary to the 5' end of target DNA, and two biotin-labeled signal probes (T10 and T40) with different lengths. In the presence of target DNA, DNA hybridization led to the attachment of AuNPs on the chip surface where specific DNA sequences were located in a "sandwich" format. Alkaline phosphatase was then introduced to the surface via biotine-streptavidin interaction. By using BCIP/NBT alkaline phosphatase color development kit, a colorimetric DNA detection was achieved through membrane transfer. The signal on the membrane was then detected by the naked eye or an ordinary optical scanner. The method provided a detection of limit of 1 pmol/L for synthesized target DNA and 0.23 pmol/L for PCR products of Mycobacterium tuberculosis 16S rDNA when the ratio of probes used was 9:1:1 (T10:T40:P2). The method described here has many desirable advantages including high sensitivity, simple operation, and no need of sophisticated equipment. The method can be potentially used for reliable biosensings.
Colorimetry ; methods ; DNA Probes ; chemistry ; genetics ; DNA, Bacterial ; genetics ; Gold ; chemistry ; Humans ; Metal Nanoparticles ; chemistry ; Mycobacterium tuberculosis ; isolation & purification ; Nucleic Acid Hybridization ; methods ; Oligonucleotide Array Sequence Analysis ; methods

Communicable Diseases ; diagnosis ; Humans ; Influenza A Virus, H1N1 Subtype ; genetics ; Influenza, Human ; diagnosis ; virology ; Microspheres ; Nucleic Acid Amplification Techniques ; methods ; Nucleic Acid Hybridization ; methods ; Oligonucleotide Probes ; genetics ; Polymerase Chain Reaction ; methods ; Sensitivity and Specificity