TaqMan probes are hydrolysis Hybridization probe probes that are designed to increase the specificity of Real time polymerase chain reaction real time PCR assays . The method was first reported in 1991 by researchers at Cetus Corporation, ref Cite pmid 1871133 ref and the technology was subsequently developed by Roche Molecular Diagnostics for diagnostic assays and by Applied Biosystems for research applications. The TaqMan probe principle relies on the 5 3 exonuclease activity of Taq polymerase to cleave a dual labeled probe during hybridization to the complementary target sequence and fluorophore based detection. ref name taqman1 http www.ncbi.nlm.nih.gov projects genome probe doc ProjTaqMan.shtml TaqMan Gene Expression NCBI Projects ref As in other real time PCR methods, the resulting fluorescence signal permits quantitative measurements of the accumulation of the product during the exponential stages of the PCR however, the TaqMan probe significantly increases the specificity of the detection. TaqMan probes were named after the videogame PacMan Taq Polymerase PacMan TaqMan as its ... 2 0800.htm The Real Time TaqMan PCR and Applications in Veterinary Medicine From PacMan to TaqMan a computer game revisited ref Principle Image Taqman.png thumb 200px Figure 1 TaqMan probe chemistry mechanism TaqMan probes consist of a fluorophore Covalent bond covalently attached to the 5 end of the oligonucleotide probe and a quencher at the 3 end ref name Taqman Probe http premierbiosoft.com tech notes TaqMan.html TaqMan Probes Introduction, functioning and applications ref Figure 1 . Several ..., quenching inhibits any fluorescence signals Figure 1 . TaqMan probes are designed such that they anneal ... of DNA template present in the PCR. Applications TaqMan probe based assays are widely used in real ... for instructions. references External links 1. http www.rt pcr.info taqman rt pcr TaqMan RT PCR resources ..., Taqman Probes, Molecular Beacons. DEFAULTSORT Taqman Category Chemical compounds Category Chemical ... more details
Summary Information Description TaqMan probe chemistry mechanism Source Author Date May 2009 Author User Braindamaged Permission other versions Licensing PD self date May 2009 ... more details
Advert date February 2011 No footnotes date February 2011 Infobox Software name Beacon Designer logo screenshot caption developer Premier Biosoft latest release version 7.9 latest release date 17 June 2010 latest preview version latest preview date operating system Windows, Macintosh platform genre Bioinformatics license commercial website http www.premierbiosoft.com Beacon Designer designs highly specific an efficient primers and probes for real time PCR polymerase chain reaction assays. It is compatible to work on Windows as well as on Mac. The software currently supports the following real time PCR chemistries for efficient primer and probe design. 1. SYBR Green br 2. TaqMan br 3. Molecular beacon br 4. HRMA Primers br 5. Scorpions br 6. FRET br 7. Locked nucleic acid LNA Locked nucleic acid br 8. NASBA molecular biology NASBA br Beacon Designer program has built in support for homology avoidance using the standard web BLAST service or the set up of a desktop BLAST feature for identification of regions that are significantly cross homologous with the target gene sequence. The software designs real time pcr primers and probes for complex differential gene expression and allele discrimination assays. Avoidance of the cross homology renders specificity to the primers in question and they are highly targeted and only amplify the intend sequence and no other targets. Beacon Designer has been used in workshops and conferences related to real time PCR study as a reference software. The author company, Premier Biosoft has also launched a simple version for evaluation of oligos for real time PCR primers and probes support limited to TaqMan and SYBR Green primers by the name Beacon designer free version. External links http www.premierbiosoft.com molecular beacons index.html Beacon Designer Homepage http www.premierbiosoft.com qpcr index.html Beacon Designer Free Edition http www.biocompare.com Articles FeaturedArticle 1167 High Resolution Melt.html High Resolution Melt Ca ... more details
Flap endonucleases FENs, also known as 5 nucleases in older references are a class of nucleolytic enzymes that act as both Directionality molecular biology 5 3 exonucleases and structure specific endonucleases on specialised DNA structures that occur during the biological processes of DNA replication , DNA repair and DNA recombination. Flap endonucleases have been identified in eukaryotes , prokaryotes , archaea and some virus es. Organisms can have more than one FEN Homology biology homologue , this redundancy may give an indication of the importance of these enzymes. In prokaryotes, the FEN enzyme is found as an N terminus N terminal domain of DNA polymerase I, but some prokaryotes appear to encode a second homologue. ref Sayers JR 1994 J Theor Biol, 170 4 415. PMID 7996866 ref The endonuclease activity of FENs was initially identified as acting on a DNA duplex which has a single stranded 5 overhang on one of the strands termed a 5 flap , hence the name flap endonuclease ref Harrington JJ and Lieber MR 1994 EMBO J., 13 , 1235 1246. PMID 8131753 ref . FENs catalyse hydrolytic cleavage of the phosphodiester bond at the junction of single and double stranded DNA. FENs can also act as 5 3 exonucleases on the 5 terminus of the flap strand and on nicked DNA Substrate biochemistry substrate s. Protein structure models based on X ray crystallography data suggest that FENs have a flexible arch created by two helices through which the single 5 strand of the 5 flap structure can thread ref Ceska TA et al., 1996 Nature, 382 , 90 93. PMID 8657312 ref . Flap endonucleases have been used in biotechnology , for example the Taqman PCR assay ref http www.med.unc.edu anclinic Tm.htm Taqman Principles Bot generated title ref and the Invader single nucleotide polymorphism SNP assay ref Olivier M 2005 Mutat. Res. 573 , 103 110. PMID 15829241 ref . For a more detailed reviews of FENs see ref Liu Y et al. , 2004 Annu. Rev. Biochem., 73 , 589 615. PMID 15189154 ref ref Ceska TA and Saye ... more details
Wikify date February 2011 This list of microfluidics related companies gives an overview of companies providing microfluidics products or solutions ref name fluidicMEMS Lily Kim, http fluidicmems.com list of microfluidics lab on a chip and biomems companies List of microfluidics companies ,February 14, 2011. ref ref name microfluidic companies Nathan Blow, http www.nature.com nmeth journal v6 n9 full nmeth0909 683.html Microfluidics the great divide Nature Methods, 2009, 6, 683 686, DOI 10.1038 nmeth0909 683. ref . List by Alphabeta class wikitable sortable Company Name products and services country http www.abbott.com Abbott Laboratories USA http www.liquid logic.com Advanced Liquid Logic Digital Microfluidics NC, USA http www.agilent.com Agilent Technologies Agilent 2100 Bioanalyzer, HPLC Chip MS system USA http www.appliedbiosystems.com Applied Biosystems TaqMan OpenArray Genotyping USA http www.arrayjet.co.uk ArrayJet inkjet microarrayer United Kindom http www.biacore.com Biacore USA http www.bio rad.com Bio Rad USA http www.appliedbiosystems.com absite us en home news announcements biotrove.html BioTrove mid density OpenArray Real Time PCR System USA http www.caliperlifesciences.com Caliper Life Sciences LabChip Systems USA http www.cellixltd.com Cellix Ireland http www.cepheid.com Cepheid USA http www.dionex.com Dionex USA http www.dolomite microfluidics.com Dolomite microfluidic chips, pumps, valves, connectors and system solutions United Kindom http www.eksigent.com Eksigent Technologies California, USA , http www.emeraldbiosystems.com Emerald Biosystems Protein Crystallization Screening WA, USA http www.febit.com febit Germany http www.fluidigm.com Fluidigm Microfluidic based chips and instrumentation for biological research CA, USA http www.fluigent.com Fluigent Paris, FRANCE http www.fluxionbio.com Fluxion Biosciences California, USA http www.gyros.com Gyros Uppsala, Sweden http www.bd.com geneohm english handylab HandyLab Inc. CA, USA http www.helicosbio ... more details
Taq DNA polymerase s 5 nuclease activity is used in the Taqman assay for SNP genotyping. The Taqman ... the nuclease from acting on the probe McGuigan & Ralston 2002 . Since the Taqman assay is based on PCR, it is relatively simple to implement. The Taqman assay can be multiplexed by combining ..., the Taqman assay is limited by the how close the SNPs can be situated. The scale of the assay can be drastically increased by performing many simultaneous reactions in microtitre plates. Generally, Taqman ... detection allelic discrimination using TaqMan . Psychiatr Genet . 12 3 133 6. Oefner, P.J., Underhill ... more details
Viral load is a measure of the severity of a virus viral infection, and can be calculated by estimating the Virus Quantification amount of virus in an involved body fluid. For example, it can be given in ribonucleic acid RNA copies per milliliter of blood plasma. Determination of viral load is part of the therapy monitoring during chronic viral infections, and in immunocompromised patients such as those recovering from bone marrow or solid organ transplant ation. Currently, routine testing is available for HIV 1, cytomegalovirus , hepatitis B virus, and hepatitis C virus. HIV viral load test Several different HIV viral load tests have been developed, and three are currently approved for use in the US COBAS AmpliPrep COBAS TaqMan HIV 1 Test Hoffman La Roche , better known as the polymerase chain reaction PCR test NucliSens HIV 1 QT, or NASBA bioMerieux Versant Quantiplex HIV 1 RNA, or bDNA Chiron Corp. Chiron Bayer These tests have been approved by the Food and Drug Administration in the United States for use in monitoring the health of people with HIV, in conjunction with other markers. Higher numbers in the viral load tests indicate an increased risk of getting sick from opportunistic disease s. These tests are also approved for monitoring the effects of antiretroviral drug anti HIV therapy , to track viral suppression and detect treatment failure. Successful combination antiretroviral therapy should give a fall in viral load of 1.5 to 2 logs 30 100 fold within six weeks, with the viral load falling below the limit of detection within four to six months. ref DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the Use of Antiretroviral Agents in HIV 1 Infected Adults and Adolescents. May 4, 2006. available for download from http www.aidsinfo.nih.gov OrderPublication OrderPubsBrowseSearchResultsTable.aspx?from G&searchString &MenuItem Guidelines AIDSInfo ref An affordable, largely manual test, which has the European regulatory approval ... more details
Essay like date February 2008 A dark quencher is a substance that absorbs excitation energy from a fluorophore and dissipates the energy as heat while a typical fluorescent Quenching fluorescence quencher re emits much of this energy as light ref Osterman, H., The Next Step in Near Infrared Fluorescence IRDye QC 1 Dark Quencher, 2009 Review Article. http biosupport.licor.com docs QC 1DarkQuencher v5.pdf Download PDF ref . Dark quenchers are used in molecular biology in conjunction with fluorophores. When the two are close together, such as in a molecule or protein, the fluorophore s emission is suppressed. This effect can be used to study molecular geometry and motion. An example of its use is in Taqman or invader assay, SNP genotyping methods. For instance, a hairpin loop with a fluorophore and quencher at the base of the stem is used. An unlabeled SNP specific PCR primer one of many with a specific 5 tail binds to the sequence to be probed, and the taq polymerase extends the sequence that will have a specific 5 end dependent on the SNP insensitive to polymorphisms upstream of the SNP in question . In the next run a primer molecular biology primer , complementary to that tail, with a hairpin loop is extended. In the next run the elongation of the complementary strand will linearise the hairpin separating the fluorophore and quencher . An alternative to using quenchers is to use F rster resonance energy transfer FRET where the combination of two dyes gives a signal ref Peng, X., Chen, H., Draney, D.R., Volcheck, W.M., A Non fluorescent, Broad Range Quencher Dye for FRET Assays, Analytical Biochemistry, 2009 Vol. 388 , pp. 220 228. http biosupport.licor.com docs NonfluorQuencherDyePaper09.pdf Download PDF ref . Mode of function Dark quenchers are dyes with no native fluorescence . Until the last few years, quenchers have typically been a second fluorescent dye, for example, fluorescein as the reporter and rhodamine as the quencher FAM TAM probes . However, quencher f ... more details
first6 Masayoshi title Genotyping of triallelic SNPs using TaqMan PCR journal Molecular and Cellular ... base extension SNP array Variome TaqMan Affymetrix International HapMap Project tag SNP Short tandem ... more details
. Real time PCR using Taqman probes 3C qPCR provides a more quantitative measurement of the fragment of interest. The Taqman probe and a constant primer hybridize to the restriction fragment ... more details
realtime PCR Taqman analysis has been developed to diagnose LGV. ref name pmid18447917 cite journal ... L Serovars by TaqMan PCR journal BMC infectious diseases volume 8 issue pages 56 year 2008 pmid ... more details
PCR Real Time PCR index.html ref Sequence specific probes, such as TaqMan i.e. Applied Biosystems , Molecular ... first4 A. title Taqman Technology and Real Time Polymerase Chain Reaction editor last Crocker editor ... more details
Essay like date January 2009 High Resolution Melt HRM analysis is a powerful technique in molecular biology for the detection of mutation s, polymorphism s and epigenetic differences in DNA double stranded DNA samples. It was discovered and developed by Idaho Technology and the University of Utah. ref For academic treatment of the history of HRM see http www.dna.utah.edu Hi Res TOP Hi Res 20Melting.html ref It has advantages over other genotyping technologies, namely It is cost effective vs. other genotyping technologies such as DNA sequencing sequencing and Taqman SNP typing. This makes it ideal for large scale genotyping projects. It is fast and powerful thus able to accurately genotype many samples rapidly. It is simple. With a good quality HRM assay, powerful genotyping can be performed by non geneticists in any laboratory with access to an HRM capable real time PCR machine. Method HRM analysis is performed on double stranded DNA samples. Typically the user will use polymerase chain reaction PCR prior to HRM analysis to amplify the DNA region in which their mutation of interest lies. Essentially the PCR process turns a tiny amount of your region of DNA of interest in to a large amount, so you have quantities large enough for better analysis. In the tube there are now many of copies of your region of DNA of interest. This region that is amplified is known as the amplicon. After the PCR process the HRM analysis begins. The process is simply a precise warming of the amplicon DNA from around 50 C up to around 95 C. At some point during this process, the melting temperature of the amplicon is reached and the two strands of DNA separate or melt apart. Image DNA melting cartoon.jpg 500px The secret of HRM is to monitor this process happening in real time. This is achieved by using a fluorescent dye. The dyes that are used for HRM are known as intercalating dyes and have a unique property. They bind specifically to double stranded DNA and when they are bound they fluore ... more details
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