Real-time PCR fluorescent chemistries.

There are more than a dozen formats available for the fluorescent detection of amplified DNA in kinetic (real-time) PCR. These chemistries are adaptable to most real-time PCR instruments and may offer benefits over the usual manufacturer-recommended chemistries for the instrument. The most popular chemistries are the generic dye, SYBR Green I, TaqMan, and hybridization probes. However, there are now new dyes being reported with superior fluorescent detection and product resolution; as well as new probe formats that may offer advanced multiplexing opportunities for quantification and genotyping.

[1]  K. Livak,et al.  Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. , 1995, PCR methods and applications.

[2]  F. A. van den Bergh,et al.  Rapid single-tube genotyping of the factor V Leiden and prothrombin mutations by real-time PCR using dual-color detection. , 2000, Clinical chemistry.

[3]  Fred Russell Kramer,et al.  Multicolor molecular beacons for allele discrimination , 1998, Nature Biotechnology.

[4]  J. Comet,et al.  Biological detection of low radiation doses by combining results of two microarray analysis methods. , 2004, Nucleic acids research.

[5]  O. Landt,et al.  Genotyping of the triallelic variant G2677T/A in MDR1 using LightCycler with locked-nucleic-acid-modified hybridization probes. , 2004, Analytical biochemistry.

[6]  A. Fiander,et al.  Novel Method for Detection, Typing, and Quantification of Human Papillomaviruses in Clinical Samples , 2001, Journal of Clinical Microbiology.

[7]  C. Heid,et al.  A novel method for real time quantitative RT-PCR. , 1996, Genome research.

[8]  N. Thelwell,et al.  Mode of action and application of Scorpion primers to mutation detection. , 2000, Nucleic acids research.

[9]  P. Lohse,et al.  Fluorescence-based detection of the CETP TaqIB polymorphism: false positives with the TaqMan-based exonuclease assay attributable to a previously unknown gene variant. , 2001, Clinical chemistry.

[10]  N. Thelwell,et al.  Duplex Scorpion primers in SNP analysis and FRET applications. , 2001, Nucleic acids research.

[11]  D. Whitcombe,et al.  Detection of PCR products using self-probing amplicons and fluorescence , 1999, Nature Biotechnology.

[12]  S. Read,et al.  LightCycler Multiplex PCR for the Laboratory Diagnosis of Common Viral Infections of the Central Nervous System , 2001, Journal of Clinical Microbiology.

[13]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[14]  Thomas R Gingeras,et al.  Fifty years of molecular (DNA/RNA) diagnostics. , 2005, Clinical chemistry.

[15]  V. Leb,et al.  Parallel detection of five human herpes virus DNAs by a set of real-time polymerase chain reactions in a single run. , 2003, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[16]  R. Abramson,et al.  Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[17]  D. Whiley,et al.  Detection of Human Respiratory Syncytial Virus in Respiratory Samples by LightCycler Reverse Transcriptase PCR , 2002, Journal of Clinical Microbiology.

[18]  C. J. Di Como,et al.  Effects of ethidium bromide and SYBR Green I on different polymerase chain reaction systems. , 2000, Journal of biochemical and biophysical methods.

[19]  H. Einsele,et al.  Quantification of Fungal DNA by Using Fluorescence Resonance Energy Transfer and the Light Cycler System , 2000, Journal of Clinical Microbiology.

[20]  F. Mayall,et al.  The detection of Simian virus 40 in mesotheliomas from New Zealand and England using real time FRET probe PCR protocols , 2003, Journal of clinical pathology.

[21]  M. Kubista,et al.  Detection of PCR products in real time using light-up probes. , 2000, Analytical biochemistry.

[22]  S. Dowell,et al.  Development and Evaluation of Real-Time PCR-Based Fluorescence Assays for Detection of Chlamydiapneumoniae , 2002, Journal of Clinical Microbiology.

[23]  C. Wittwer,et al.  Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. , 2004, Clinical chemistry.

[24]  Fred Russell Kramer,et al.  Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. , 2002, Nucleic acids research.

[25]  T. Hadfield,et al.  Real-Time PCR Detection of Brucella abortus: a Comparative Study of SYBR Green I, 5′-Exonuclease, and Hybridization Probe Assays , 2003, Applied and Environmental Microbiology.

[26]  P. Bernard,et al.  The LightTyper: high-throughput genotyping using fluorescent melting curve analysis. , 2003, BioTechniques.

[27]  F. A. van den Bergh,et al.  Genotyping of HLA-B27 by real-time PCR without hybridization probes. , 2000, Clinical chemistry.

[28]  O. Landt,et al.  Direct Detection and Differentiation of Legionella spp. and Legionella pneumophila in Clinical Specimens by Dual-Color Real-Time PCR and Melting Curve Analysis , 2002, Journal of Clinical Microbiology.

[29]  P. Höllsberg,et al.  A Sensitive Quantification of HHV-6B by Real-time PCR , 2002, Biological Procedures Online.

[30]  T. Deguchi,et al.  Quantitative Detection of Mycoplasma genitalium from First-Pass Urine of Men with Urethritis and Asymptomatic Men by Real-Time PCR , 2002, Journal of Clinical Microbiology.

[31]  H. Blom,et al.  Molecular beacons: colorful analysis of nucleic acids , 2002, Expert review of molecular diagnostics.

[32]  Kendall W. Cradic,et al.  Substitution of 3'-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays. , 2004, Clinical chemistry.

[33]  W. Tan,et al.  Real-time monitoring of intracellular mRNA hybridization inside single living cells. , 2001, Analytical chemistry.

[34]  R. Steffensen,et al.  Rapid genotyping of MBL2 gene mutations using real-time PCR with fluorescent hybridisation probes. , 2003, Journal of immunological methods.

[35]  Shuming Nie,et al.  Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells. , 2004, Nucleic acids research.

[36]  J. D. de Vries,et al.  Rapid genotyping of the OATP1B1 polymorphisms A388G and T521C with real-time PCR FRET assays. , 2005, Pharmacogenomics.

[37]  M. Rajeevan,et al.  Copyright © American Society for Investigative Pathology and the Association for Molecular Pathology Validation of Array-Based Gene Expression Profiles by Real-Time (Kinetic) RT-PCR , 2022 .

[38]  A. Bhagwat,et al.  Application of a molecular beacon-real-time PCR technology to detect Salmonella species contaminating fruits and vegetables. , 2004, International journal of food microbiology.

[39]  Combined Immunomagnetic Separation-Molecular Beacon-Reverse Transcription-PCR Assay for Detection of Hepatitis A Virus from Environmental Samples , 2004, Applied and Environmental Microbiology.

[40]  F. Plummer,et al.  Improved mRNA Quantitation in LightCycler RT-PCR , 2003, International Archives of Allergy and Immunology.

[41]  H. Einsele,et al.  Automated RNA extraction by MagNA Pure followed by rapid quantification of cytokine and chemokine gene expression with use of fluorescence resonance energy transfer. , 2003, Clinical chemistry.

[42]  J. J. Hyldig-Nielsen,et al.  Self-reporting PNA/DNA primers for PCR analysis. , 2001, Genome Research.

[43]  D. Dittmer,et al.  SYBR Green-Based Real-Time Quantitative PCR Assay for Detection of West Nile Virus Circumvents False-Negative Results Due to Strain Variability , 2004, Journal of Clinical Microbiology.

[44]  D. Corella,et al.  Validating a rapid method for detecting common polymorphisms in the APOA5 gene by melting curve analysis using LightTyper. , 2005, Clinical chemistry.

[45]  K. Livak,et al.  Allelic discrimination using fluorogenic probes and the 5' nuclease assay. , 1999, Genetic analysis : biomolecular engineering.

[46]  P. Walsh,et al.  Simultaneous Amplification and Detection of Specific DNA Sequences , 1992, Bio/Technology.

[47]  T. Mygind,et al.  Evaluation of real-time quantitative PCR for identification and quantification of Chlamydia pneumoniae by comparison with immunohistochemistry. , 2001, Journal of microbiological methods.

[48]  Qiuping Guo,et al.  A new class of homogeneous nucleic acid probes based on specific displacement hybridization. , 2002, Nucleic acids research.

[49]  M. Oellerich,et al.  Genotyping of eight thiopurine methyltransferase mutations: three-color multiplexing, "two-color/shared" anchor, and fluorescence-quenching hybridization probe assays based on thermodynamic nearest-neighbor probe design. , 2000, Clinical chemistry.

[50]  C. Saint,et al.  Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. , 2005, Analytical biochemistry.

[51]  Thomas C. Quinn,et al.  Quantitative Multiprobe PCR Assay for Simultaneous Detection and Identification to Species Level of Bacterial Pathogens , 2002, Journal of Clinical Microbiology.

[52]  A new minor groove binding asymmetric cyanine reporter dye for real-time PCR. , 2003, Nucleic acids research.

[53]  J. Vázquez-Boland,et al.  Quantitative Detection of Listeria monocytogenes and Listeria innocua by Real-Time PCR: Assessment of hly, iap, and lin02483 Targets and AmpliFluor Technology , 2004, Applied and Environmental Microbiology.

[54]  Alan W. Stitt,et al.  Retinal VEGF mRNA measured by SYBR green I fluorescence: A versatile approach to quantitative PCR. , 2000, Molecular vision.

[55]  A. Pingoud,et al.  Comparison between Taq DNA polymerase and its Stoffel fragment for quantitative real-time PCR with hybridization probes. , 2001, BioTechniques.

[56]  S. Klaschik,et al.  Real-Time PCR for Detection and Differentiation of Gram-Positive and Gram-Negative Bacteria , 2002, Journal of Clinical Microbiology.

[57]  A. Heim,et al.  Quantitative multiplex real-time PCR for the sensitive detection of interferon beta gene induction and viral suppression of interferon beta expression. , 2003, Cytokine.

[58]  Christian Drosten,et al.  Rapid Detection and Quantification of RNA of Ebola and Marburg Viruses, Lassa Virus, Crimean-Congo Hemorrhagic Fever Virus, Rift Valley Fever Virus, Dengue Virus, and Yellow Fever Virus by Real-Time Reverse Transcription-PCR , 2002, Journal of Clinical Microbiology.

[59]  P. Ikonomi,et al.  Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. , 2002, Nucleic acids research.

[60]  D. Hodgson,et al.  Development of a Facile Fluorescent Assay for the Detection of 80 Mutations Within the p53 Gene , 2002, Molecular medicine.

[61]  Thomas D. Schmittgen,et al.  Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. , 2000, Analytical biochemistry.

[62]  C. Wittwer,et al.  Fluorescein-labeled oligonucleotides for real-time pcr: using the inherent quenching of deoxyguanosine nucleotides. , 2001, Analytical biochemistry.

[63]  T. B. Morrison,et al.  Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. , 1998, BioTechniques.

[64]  Carl T Wittwer,et al.  High-resolution genotyping by amplicon melting analysis using LCGreen. , 2003, Clinical chemistry.

[65]  Frank Vitzthum,et al.  Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. , 2004, Nucleic acids research.

[66]  E Schütz,et al.  Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. , 1999, BioTechniques.

[67]  G. Dusheiko,et al.  Monitoring the Emergence of Hepatitis B Virus Polymerase Gene Variants during Lamivudine Therapy Using the LightCycler , 2001, Journal of Clinical Microbiology.

[68]  K. Elenitoba-Johnson,et al.  High-resolution melting analysis for detection of internal tandem duplications. , 2004, The Journal of molecular diagnostics : JMD.

[69]  Kirk M. Ririe,et al.  Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. , 1997, Analytical biochemistry.

[70]  E. Lukhtanov,et al.  3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. , 2000, Nucleic acids research.

[71]  M. Kubista,et al.  Light-up probes: thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. , 2000, Analytical biochemistry.

[72]  E. Lyon,et al.  Mutation detection using fluorescent hybridization probes and melting curve analysis , 2001, Expert review of molecular diagnostics.

[73]  Russell Higuchi,et al.  Kinetic PCR Analysis: Real-time Monitoring of DNA Amplification Reactions , 1993, Bio/Technology.

[74]  Elaine Lyon,et al.  Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. , 2004, Clinical chemistry.

[75]  A. V. van Loon,et al.  Rapid and Sensitive Routine Detection of All Members of the Genus Enterovirus in Different Clinical Specimens by Real-Time PCR , 2002, Journal of Clinical Microbiology.

[76]  C. Heath,et al.  Real-time automated polymerase chain reaction (PCR) to detect Candida albicans and Aspergillus fumigatus DNA in whole blood from high-risk patients. , 2003, Diagnostic microbiology and infectious disease.

[77]  A. Bahrmand,et al.  PCR hot start using primers with the structure of molecular beacons (hairpin-like structure). , 2000, Nucleic acids research.

[78]  Ru Chen,et al.  Development of a novel real-time RT-PCR assay with LUX primer for the detection of swine transmissible gastroenteritis virus , 2004, Journal of Virological Methods.

[79]  Sanjay Tyagi,et al.  Wavelength-shifting molecular beacons , 2000, Nature Biotechnology.

[80]  D. Pillay,et al.  Use of Real-Time PCR and Fluorimetry To Detect Lamivudine Resistance-Associated Mutations in Hepatitis B Virus , 1999, Antimicrobial Agents and Chemotherapy.

[81]  C. Wittwer,et al.  Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. , 1997, Clinical chemistry.

[82]  U. Reischl,et al.  Algorithm for the identification of bacterial pathogens in positive blood cultures by real-time LightCycler polymerase chain reaction (PCR) with sequence-specific probes. , 2004, Diagnostic microbiology and infectious disease.

[83]  M. Mimmack,et al.  Quantitative polymerase chain reaction: validation of microarray results from postmortem brain studies , 2004, Biological Psychiatry.

[84]  C. Saint,et al.  Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR. , 2003, Nucleic acids research.

[85]  R. Clegg Fluorescence resonance energy transfer and nucleic acids. , 1992, Methods in enzymology.

[86]  Amalio Telenti,et al.  Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis , 1998, Nature Biotechnology.

[87]  J. Roehrig,et al.  Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay , 2000, Journal of Clinical Microbiology.