sybr-green-i and Neoplasms

Cancer development and progression frequently involve nucleotide mutations as well as amplifications and deletions of genomic segments. Quantification of allele-specific copy number is an important step in characterizing tumor genomes for precision medicine. Despite advances in approaches to high-throughput genomic DNA analysis, inexpensive and simple methods for analyzing complex nucleotide and copy number variants are still needed. Real-time polymerase chain reaction (PCR) methods for discovering and genotyping single nucleotide polymorphisms are becoming increasingly important in genetic analysis. In this study, we describe a simple, single-tube, probe-free method that combines SYBR Green I-based quantitative real-time PCR and quantitative melting curve analysis both to detect specific nucleotide variants and to quantify allele-specific copy number variants of tumors. The approach is based on the quantification of the targets of interest and the relative abundance of two alleles in a single tube. The specificity, sensitivity, and utility of the assay were demonstrated in detecting allele-specific copy number changes critical for carcinogenesis and therapeutic intervention. Our approach would be useful for allele-specific copy number analysis or precise genotyping.

Topics: Alleles; Animals; Benzothiazoles; Cell Line, Tumor; Diamines; DNA; DNA Copy Number Variations; Fluorescent Dyes; Gene Dosage; Genotyping Techniques; Humans; Mice; Neoplasms; Nucleic Acid Denaturation; Organic Chemicals; Polymorphism, Single Nucleotide; PTEN Phosphohydrolase; Quinolines; Real-Time Polymerase Chain Reaction

MicroRNAs (miRNAs) are a kind of small molecules that involve in many important life activities. They have higher expression levels in many kinds of cancers. In this study, we developed an isothermal enzyme-free amplification (EFA) and label-free graphene oxide (GO)-based SYBR Green I fluorescence platform for detection of miRNA. MiRNA-21 was used as an example to demonstrate the feasibility of the method. Results show that the sensitivity of miRNA-21 is 1pM, and the linearity range is from 1pM to 1nM. The method can specifically discriminate miRNA-21 from miRNA-210 and miRNA-214. Three tumor cell lines of A549, HepG2 and MCF7 were detected by the method. The sensitivities of them were 10(2) cells, 10(3) cells and 10(3) cells respectively. Clinical tumor samples were also tested by this method, and 29 of 40 samples gave out positive signals. The method holds great promise in miRNA detection due to its convenience, rapidness, inexpensive and specificity.

Topics: Benzothiazoles; Biosensing Techniques; Cell Line, Tumor; Diamines; Fluorescent Dyes; Graphite; Humans; Limit of Detection; MicroRNAs; Models, Molecular; Neoplasms; Nucleic Acid Amplification Techniques; Organic Chemicals; Oxides; Quinolines; Spectrometry, Fluorescence; Temperature

Conditional gene deletion using Cre-lox recombination is frequently used in mouse genetics; however recombination is frequently incomplete, resulting in a mixture of cells containing the functional (2lox) allele and the truncated (1lox) allele. Conventional analysis of 1lox/2lox allele ratios using Southern Blotting is time consuming, requires relatively large amounts of DNA and has a low sensitivity. We therefore evaluated the utility of Real-Time PCR to measure 1lox/2lox allele ratios.. We show that SYBR Green based Real-Time PCR analysis of 1lox/2lox allele ratios can generate erroneous peaks in the melting curve that are possibly caused by alternate hybridization products promoted by the palindromic loxP sequence motif. Since abnormal melting curves frequently contribute to dismissal of SYBR Green based data, we developed a convenient method with improved specificity that avoids such erroneous signals. Our data show that probe based Real-Time PCR, using a universal probe directed against the loxP site, can accurately detect small differences in 1lox/2lox allele ratios. We also validated this method in Fabpl4× at -132-Cre transgenic mice, measuring 1lox/2lox allele ratios that are in agreement with published data. Our Real-Time PCR protocol requires the use of one probe only for all reactions. Also the universal probe established in our assay is generally applicable to any experiment analyzing Cre-lox recombination efficiency, such that only primer sequences have to be adapted.. Our data show that 1lox/2lox allele ratios are detected with high accuracy and high sensitivity with Real-Time PCR analysis using a probe directed against the loxP site. Due to the generally applicable probe the assay is conveniently adapted to all models of Cre-lox mediated gene deletion.

Topics: Animals; Benzothiazoles; Diamines; DNA (Cytosine-5-)-Methyltransferases; DNA Methyltransferase 3A; Gene Deletion; Genetic Techniques; Integrases; Mice; Mice, Transgenic; Neoplasms; Organic Chemicals; Polymerase Chain Reaction; Quinolines; Recombination, Genetic; Sensitivity and Specificity

Photodynamic therapy is a recently developed anticancer treatment that utilizes the generation of singlet oxygen and other reactive oxygen species in cancer tissue. Nrf2, an NF-E2-related transcription factor, plays a pivotal role in transcriptional upregulation of many target genes, including those for metabolizing enzymes and transporters essential for cellular defense in response to oxidative stress. In the present study, we examined the potential involvement of Nrf2 in the induction of human ABC transporter ABCG2 and heme oxygenase-1 (HO-1). When HepG2 cells were incubated with non-toxic concentrations of delta-aminolevulinic acid, protoporphyrin IX, or pheophorbide a and then exposed to visible light for 90 min, the mRNA level of HO-1 began increasing markedly, reaching the maximal level in 4 h. Following the transient induction of HO-1, the mRNA level of ABCG2 gradually increased in a time-dependent manner, whereas the ABCB6 mRNA level was little affected. Nrf2-specific siRNA treatments suppressed the induction of both ABCG2 and HO-1 after the photoactivation of porphyrins, suggesting that Nrf2 is a common regulator for transcriptional activation of the ABCG2 and HO-1 genes. On the other hand, the mRNA level of HO-1 was remarkably enhanced by Zn(2+)-protoporphyrin IX or hemin even in the absence of light. This induction may be attributed to inactivation of Bach1, a repressor for the HO-1 gene, by those compounds. Since patients have demonstrated individual defferences in their response to photodynamic therapy, transcriptional activation of the ABCG2 and HO-1 genes in cancer cells may affect patients' responses to photodynamic therapy.

Topics: Aminolevulinic Acid; ATP Binding Cassette Transporter, Subfamily G, Member 2; ATP-Binding Cassette Transporters; Benzothiazoles; Blotting, Western; Cell Line, Tumor; Chlorophyll; Chromatography, High Pressure Liquid; Diamines; Electrophoresis, Polyacrylamide Gel; Fluorescent Dyes; Heme Oxygenase-1; Humans; Neoplasm Proteins; Neoplasms; NF-E2-Related Factor 2; Organic Chemicals; Oxidative Stress; Photochemistry; Photochemotherapy; Photosensitizing Agents; Porphyrins; Protoporphyrins; Quinolines; RNA, Messenger; RNA, Small Interfering; Transfection

The aim of this study is to assess a real-time PCR technique on the LightCycler 2.0 with SYBR-Green I detection as compared to another real-time PCR method based on detection with FRET (fluorescence resonance energy transfer) probes for the quantification of CMV DNA.. The two real-time PCR methods were used to test plasma samples from immunocompromised patients with clinically suspected CMV disease, patients under follow-up without symptoms, and healthy adults. A standard curve for quantitative analysis by the SYBR-Green I method was performed with 10-fold diluted solutions of DNA from the CMV Towne strain (ATCC VR-977) cultured in MRC-5 monolayer. In addition, frozen samples from patients positive for CMV pp65 antigenemia were also analyzed and results compared using the two real time PCR methods.. The real-time PCR technique using SYBR-Green I on the LightCycler 2.0 was a highly specific, fast, simple and reliable test to quantify CMV; moreover, it was cost-effective.. Quantification of CMV DNA in plasma using this sensitive, fast, low-cost method was advantageous for the diagnosis and follow up of patients with opportunistic CMV infection, which are increasingly more frequent in our daily hospital clinical practice.

Topics: Adult; AIDS-Related Opportunistic Infections; Antigens, Viral; Benzothiazoles; Bone Marrow Transplantation; Cell Line; Child; Computer Systems; Cytomegalovirus; Cytomegalovirus Infections; Diamines; DNA, Viral; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Humans; Immunocompromised Host; Infant, Newborn; Neoplasms; Neutrophils; Opportunistic Infections; Organic Chemicals; Phosphoproteins; Polymerase Chain Reaction; Postoperative Complications; Quinolines; Reagent Kits, Diagnostic; Reference Standards; Sensitivity and Specificity; Viral Matrix Proteins; Viremia

Double-strand breaks (DSBs) are the most lethal form of DNA damage. They can be repaired by one of two pathways, homologous recombination and non-homologous end joining (NHEJ). A NHEJ assay has previously been reported which measures joining using cell-free extracts and a linearised plasmid as DNA substrate. This assay was designed for 3 x 10(9) cells grown in vitro and utilised radioactively labelled substrate. We have scaled down the method to use smaller cell numbers in a variety of cell lines. Altering the cellular extraction procedure decreased background DNA contamination. The cleaner preparations allowed us to use SYBR Green I staining to identify joined products, which was as sensitive as 32P-end-labelled DNA. NHEJ was found in established tumour cell lines from different originating tissues, though actual levels and fidelity of repair differed. This method also allowed end joining to be assessed in clinical specimens (human blood, brain and bladder tumours) within 24 h of receiving samples. The application of this method will allow investigation of the role of DSB DNA repair pathways in human tumours.

Topics: Benzothiazoles; Cell Extracts; Cell-Free System; Cells, Cultured; Diamines; DNA Repair; Fluorescent Dyes; Genetic Techniques; Humans; Neoplasms; Organic Chemicals; Quinolines; Recombination, Genetic; Time Factors; Tumor Cells, Cultured