PCR (Methods and Techniques)

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Amplified Fragment Length Polymorphism In Situ PCR RNA to DNA Amplification Real Time PCR Software

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Single tube confirmation PCR protocol Single tube confirmation PCR protocol: For characterization colonies of transformed clones of Saccharaomyces, from the web site of the Stanford Genome Technology Center, Palo Alto, CA, USA. (PCR) http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html A Rapid DNA Minipreparation Method Suitable for AFLP and Other PCR Applications (PDF document) A Rapid DNA Minipreparation Method Suitable for AFLP and Other PCR Applications (PDF document): Preparation of DNA from plant tissues suitable for PCR methods including AFLP, article by DH CHEN and PC RONALD Department of Plant Pathology, University of California, Davis. (PCR) http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb17/17053-1.pdf Alu-PCR Hybridization Alu-PCR Hybridization: A report and protocol, from Fondation Jean Dausset. (PCR) http://www.cephb.fr/manips_alupcr.html Wayward PCR primers Wayward PCR primers: Article by PN Hengen from TIBS 1995 on the loss of activity of PCR primers with time. (PCR) http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jan95.html MJ Research MJ Research: Manufactures and sells products for molecular biology including thermal cyclers and sequencers / genotypers. (PCR) http://www.mjr.com/ T-DNA Generated Enhancer Traps in Arabidopsis T-DNA Generated Enhancer Traps in Arabidopsis: Application of inverse PCR, partial genomic libraries and TAIL-PCR in cloning flanking, at the Department of Biological Sciences, Dartmouth College, Hanover, NH. (PCR) http://www.dartmouth.edu/~tjack/ PCR and multiplex PCR guide PCR and multiplex PCR guide: Discussions of the parameters influencing the PCR reaction and some PCR and multiplex PCR applications, by Octavian Henegariu on the web site of the Yale - New Haven Medical center. (PCR) http://www.info.med.yale.edu/genetics/ward/tavi/Guide.html Protocols Online: PCR Protocols Protocols Online: PCR Protocols: Extensive collection of PCR protocols and methods from Protocol On Line. (PCR) http://www.protocol-online.org/prot/Molecular_Biology/PCR/ Kary Mullis Kary Mullis: Inventor Profile of Kary Mullis, the originator of PCR, from the National Inventors Hall of Fame web site. (PCR) http://www.invent.org/hall_of_fame/109.html Life at High Temperatures Life at High Temperatures: Article by TD Brock from the web site of Department of Bacteriology, University of Wisconsin - Madison on the thermophilic organisms in Yellowstone hot springs, including Thermus aquaticus from which Taq polymerase was obtained. (PCR) http://www.bact.wisc.edu/Bact303/b27 Kary B. Mullis - Autobiography Kary B. Mullis - Autobiography: The originator of PCR, from the Nobel e-museum web site. (PCR) http://www.nobel.se/chemistry/laureates/1993/mullis-autobio.html Adjuvants in PCR Reactions Adjuvants in PCR Reactions: Brief discussion of additives to improve amplification efficiency and specificity of PCR, by Octavian Henegariu, Yale-New Haven Medical Center. (PCR) http://info.med.yale.edu/genetics/ward/tavi/p16.html Improved diagnosis of porcine proliferative enteropathy caused by Lawsonia intracellularis using polymerase chain reaction-enzyme-linked oligosorbent assay Improved diagnosis of porcine proliferative enteropathy caused by Lawsonia intracellularis using polymerase chain reaction-enzyme-linked oligosorbent assay: P Zhang, CJ Gebhart, D Burden, GE Duhamel: Molecular and Cellular Probes, 14(2) 101-108, on the site of BT&C, Inc. (PCR) http://www.btc-bti.com/pcrelisa.htm PCR Animation PCR Animation: Explaining how Polymerase Chain Reaction (PCR) works. From Dolan DNA Learning Center, Cold Spring Harbor Laboratory, USA. (PCR) http://www.dnalc.org/Shockwave/pcranwhole.html RAPD PCR RAPD PCR: RAPD stands for Random Amplification of Polymorphic DNA, where the target sequence(s) (to be amplified) is unknown.Brief description, from Rutgers University, USA. (PCR) http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/rapd.html Effect of PCR Buffer on multiplex PCR (PDF) Effect of PCR Buffer on multiplex PCR (PDF): Multiplex PCR employs different primer pairs in the same amplification reaction. This requires extensive optimization of annealing conditions. From Quiagen (company) (PCR) http://www.qiagen.com/literature/brochures/pcr/pdf/pcrcha03.pdf Detection of Single Nucleotide Mutations in Wheat Using Single Strand Conformation Polymorphism Gels (PDF file) Detection of Single Nucleotide Mutations in Wheat Using Single Strand Conformation Polymorphism Gels (PDF file): P Martins-Lopez, H Zhang, R Koebner, Plant Mol. Biol. Reporter 19(2001): 159-162. From National Research Coouncil Canada. (PCR) http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/R01-013.pdf PCR Protocol PCR Protocol: Detailed PCR protocol from the web site of the Department of Biology, University of Michigan, USA. (PCR) http://www.biology.lsa.umich.edu/research/labs/maddock/protocols/PCR/general_pcr_protocol.html RAPD analysis with P. infestans RAPD analysis with P. infestans: Protocol for Randomly Amplified Polymorphic DNA, by H Judelson, University of California, Riverside, USA. (PCR) http://www.fgsc.net/methods/Judel.html FISH Guide and Troubleshooting FISH Guide and Troubleshooting: Links to pages describing influential parameters, with guides on PCR, RT-PCR and multiplex PCR reactions, Taq, FISH, CM-FISH, TM-FISH, microarrays, CCK, slide prep and labeling, maintained by Octavian Henegariu from Yale University, New Haven, CT. (PCR) http://info.med.yale.edu/genetics/ward/tavi/FISHguide.html The "Poison Primer" Technique for Enhancing Detection of Small Deletions in Mutant Libraries The "Poison Primer" Technique for Enhancing Detection of Small Deletions in Mutant Libraries: This method works because the poison allows the formation of deletion products but titers out full-sized products. From the Biotechnology Laboratory, University of British Columbia. (PCR) http://ko.cigenomics.bc.ca/poison1.html Rep-PCR Genomic Fingerprinting Rep-PCR Genomic Fingerprinting: Bacteria are characterized by Rep-PCR fingerprinting using primers corresponding to naturally occurring repetitive sequences in the interspersed regions. (PCR) http://www.msu.edu/user/debruijn/ Random Arbitrarily Primed PCR Random Arbitrarily Primed PCR: Protocol for RAP-PCR to study prokaryotic gene expression, from the Enterococcus Research Site, University of Oklahoma, USA. (PCR) http://www.enterococcus.ouhsc.edu/random_pcr.asp Tavi's PCR protocols Tavi's PCR protocols: A page describing the main parameters and trouble-shooting in PCR. The page is somewhat dated (updated 1997) but still useful. (PCR) http://info.med.yale.edu/genetics/ward/tavi/PCR.html Polymerase Chain Reaction Polymerase Chain Reaction: Popular survey article by Mark V. Bloom, DNA Learning Center, Cold Spring Harbor Laboratory, from the web site of the US National Health Museum. (PCR) http://www.accessexcellence.com/RC/CT/polymerase_chain_reaction.html BioGuide - PCR BioGuide - PCR: Basics of hot start, touchdown, AP and RAPD, primer selection, design programs and references, from the Weizman Institute of Science, Rehovot, Israel. (PCR) http://bip.weizmann.ac.il/mb/bioguide/pcr/contents.html Mutation Detection Systems - SSCP Analysis Mutation Detection Systems - SSCP Analysis: Discussion of the technique and variations, literature references. By S McQuaid, Institute of Child Health, University College London, UK. (PCR) http://www.ich.ucl.ac.uk/cmgs/sscp.htm Optimizing Multiplex and LA-PCR with Betaine Optimizing Multiplex and LA-PCR with Betaine: LA-PCR = "long and accurate PCR". Article by PN Hengen in TIBS June 1997. (PCR) http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jun97.html PCR Technology PCR Technology: An introduction by Connie Veilleux from the US National Health Museum website. (PCR) http://www.accessexcellence.org/LC/SS/PS/PCR/PCR_technology.html Biosource molecular methods booklet Biosource molecular methods booklet: 56 page booklet on oligonucleotides, PCR and RT-PCR, from Biosource (company). (PCR) http://www.biosource.com/content/techCornerContent/methodPDFs/MolecularMethods.pdf Quantitative PCR Protocol Quantitative PCR Protocol: From the Jackson Laboratory, University of Maine, USA. (PCR) http://www.jax.org/cyto/quanpcr.html The Polymerase Chain Reaction The Polymerase Chain Reaction: A popular description of the way it works, its importance in different connections, legal aspects. Authored by TM Powledge at the Federation of the American Societies of Experimental Biology. (PCR) http://www.faseb.org/opar/bloodsupply/pcr.html Optimizing DNA Amplification Protocols using the Eppendorf Mastercycler Optimizing DNA Amplification Protocols using the Eppendorf Mastercycler: Basic discussion of the optimization of PCR, from the web site of Brinkmann Instruments. (PCR) http://www.brinkmann.com/PCR_appl_protocolsMC.asp PCR Project PCR Project: Presentations from the University of California at Berkley on PCR, both current research reports and reviews. (PCR) http://sunsite.berkeley.edu/biotech/pcr/ Inverse PCR and Cycle Sequencing of P Element Insertions for STS Generation Inverse PCR and Cycle Sequencing of P Element Insertions for STS Generation: Step by step protocol, by EJ Rehm, Berkeley Drosophila Genome Project, USA. (PCR) http://www.fruitfly.org/about/methods/inverse.pcr.html PCR Troubleshooting PCR Troubleshooting: Limited to conventional straight forward PCR. Page designed and maintained by Octavian Henegariu on the web site of the Yale - New Haven Medical Center. (PCR) http://info.med.yale.edu/genetics/ward/tavi/Trblesht.html The web guide of PCR The web guide of PCR: List of links and forum on the subject and related methodology. Set up and maintained by SJ Krivokapich, National University of Misiones, Argentina. (PCR) http://www.pcrlinks.com/ Innovative Tools for Amplification Innovative Tools for Amplification: Notes about PCR applications, principles, research results, from Roche. (PCR) http://www.roche-applied-science.com/sis/amplification/ Inverse PCR for PAC-end sequencing Inverse PCR for PAC-end sequencing: To generate PCR fragments that contain the ends of PAC inserts that can be sequenced. Protocol by B Barbazuk, Washington University Zebrafish Genome Resources Project, USA. (PCR) http://www.genetics.wustl.edu/fish_lab/frank/cgi-bin/fish/prot2.html Which DNA Marker for Which Purpose? Which DNA Marker for Which Purpose?: Compendia of the Research Project "Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees", European Union DGXII Biotechnology FW IV Research Programme. From the web site of the University Libr (PCR) http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker HiFi DNA HiFi DNA: HiFi DNA is a company selling a DNA polymerase for PCR at low temperature giving accurate replication of certain sequences where Taq fails. (PCR) http://www.hifidna.com/ 3' RACE PCR 3' RACE PCR: This technique is used to obtain the 3'end of a cDNA. Protocol by R Hastings, Biochemistry, University of Nottingham Medical School, UK. (PCR) http://www.nottingham.ac.uk/~mbzspd/methods/3RACE_PCR.html Molecular Staging, Inc. Molecular Staging, Inc.: Company promoting diagnostic tests for genetic analysis; rolling circle amplification technology (RCAT), developed for amplifying signals from DNA, RNA and proteins, from Westport, CT. (PCR) http://www.molecularstaging.com/Pages/RCAToverview_.html RACE amplification RACE amplification: Rapid Amplification of cDNA Ends. Protocol, from National Institute of Genetics, Japan. (PCR) http://www.nig.ac.jp/labs/EarlyEmb/midline/protocol/RACE.html Multiplex PCR Multiplex PCR: A new PCR strategy that enables the amplification of multiple DNA targets in one run. From Boston University. (PCR) http://www.bu.edu/research/Features/scicoalition_01/twist.html Optimizing PCR Protocols Optimizing PCR Protocols: Brief guidelines. From the Jackson Laboratory, University of Maine, USA. (PCR) http://www.jax.org/imr/optimize_pcr.html RFLP Definition RFLP Definition: RFLP = Restriction Fragment Length Polymorphism, from FDA (PCR) http://vm.cfsan.fda.gov/~frf/rflp.html Polymerase Chain Reaction (PCR) Polymerase Chain Reaction (PCR): A graphic description of the principle of PCR from the US National Health Museum web site. (PCR) http://www.accessexcellence.org/AB/GG/polymerase.html What the Heck is PCR? What the Heck is PCR?: Popular description of the PCR technique by John C Brown, University of Kansas 1995. (PCR) http://people.ku.edu/~jbrown/pcr.html Detection of Point Mutations by RFLP of PCR Amplified DNA Sequences Detection of Point Mutations by RFLP of PCR Amplified DNA Sequences: RFLP = Restriction Fragment Length Polymorphism. By Alexander Binder 1997. (PCR) http://www-ang.kfunigraz.ac.at/~binder/thesis/node64.html Detection of Asymmetric PCR Products in Homogeneous Solution by Fluorescence Correlation Spectroscopy Detection of Asymmetric PCR Products in Homogeneous Solution by Fluorescence Correlation Spectroscopy: In asymmetric PCR, the low concentration primer is quantitatively incorporated into double stranded DNA after an appropriate number of cycles. If this primer is fluorescent labelled, the dsDNA can be quantitated from the fluorescence. (PCR) http://imd-www.es.hokudai.ac.jp/~kinjo/fapcr/fapcrout.html PCR protocols PCR protocols: Brief protocols for PCR in use at the Genome Sequencing Center of the Washington University in St Louis Medical School. (PCR) http://genome.wustl.edu/tools/protocols/index.php?fin4=1 Fidelity of DNA Polymerases for PCR Fidelity of DNA Polymerases for PCR: Article by PN Hengen from TIBS 1995 (PCR) http://www.lecb.ncifcrf.gov/~pnh/papers/TIBS/aug95.html Hot Start PCR Hot Start PCR: Description of the technique and the reasons to use it, from the web site of Bio Can, a company manufacturing materials for PCR. (PCR) http://www.biocan.com/mbio/hot_tag.htm PCR method protocols PCR method protocols: Protocols for PCR posted by the Helen Donis-Keller Laboratory. (PCR) http://hdklab.wustl.edu/lab_manual/pcr/pcrcontents.html General Notes on Primer Design in PCR General Notes on Primer Design in PCR: Article on the influence of the design of the primer on the outcome of PCR, by Dr Vincent R. Prezioso, published on the domain of Brinkmann Instruments. (PCR) http://www.brinkmann.com/PCR_appl_primer.asp Standard PCR protocols Standard PCR protocols: From Molecular Biology Techniques Manual, from the web site of the University of Cape Town, South Africa. (PCR) http://web.uct.ac.za/microbiology/pcrcond.htm Inverse PCR protocol Inverse PCR protocol: step by step protocol, from the web site of the Department of Biology, University of Michigan, USA. (PCR) http://www.biology.lsa.umich.edu/research/labs/maddock/protocols/PCR/inverse_pcr_protocol.html PCR animated PCR animated: Animation illustrating the principle of PCR, from the University of Ghent, Belgium. (PCR) http://allserv.rug.ac.be/~avierstr/principles/pcrani.html Nematode ITS1 Size Variation Nematode ITS1 Size Variation: Examples of Restriction Fragment Length Polymorphism (RFLP)electrophoresis slabs for different nematodes. (PCR) http://nematode.unl.edu/its_id/EXAMPLES/index.htm Inverse PCR For use with Snyder mTn-lacZ/LEU2 Based Mutagenesis Inverse PCR For use with Snyder mTn-lacZ/LEU2 Based Mutagenesis: Protocol by M McMurray, Fred Hutchinson Cancer Research Center, Seattle, Wa. USA. (PCR) http://www.fhcrc.org/labs/gottschling/misc/ipcr.html Cleaved Amplified Polymorphic Sequence Cleaved Amplified Polymorphic Sequence: Illustration of principle. CAPS corresponds to RFLP. From Corvallis Forestry Research Community, Corvallis, USA. (PCR) http://www.fsl.orst.edu/tgerc/PCRCourse/caps.jpg Rational primer design greatly improves differential display-PCR (DD-PCR) Rational primer design greatly improves differential display-PCR (DD-PCR): Article: D Graf, AG Fisher, M Merkenschlager: Nucl. Acids Res. 25:11 2239-2240. (PCR) http://nar.oupjournals.org/cgi/content/full/25/11/2239 GenHunter GenHunter: Manufacturer of material for differential display PCR in Nashville, Tenn USA. (PCR) http://www.genhunter.com Attotron Biosensor Corporation Attotron Biosensor Corporation: R & D company for development of biosensors and related products for the research and educational markets. (PCR) http://www.attotron.com Anchor Probes for Comparative Mapping of Grass Species Anchor Probes for Comparative Mapping of Grass Species: Article in which probes from different libraries were used to hybridize seven cereals at the Department of Plant Breeding and Biometry, Cornell University, NY. (PCR) http://greengenes.cit.cornell.edu/anchors/ Principle of PCR Principle of PCR: Applications in work on aging of Caenorhabditis elegans and phylogeny of nematodes, by Andy Vierstraete, Department of Biology, University of Ghent, Belgium. (PCR) http://allserv.rug.ac.be/~avierstr/principles/pcr.html Design Oligonunucleotide Primers Design Oligonunucleotide Primers: Interface for scanning DNA sequences for restriction sites, without changing encoded protein created. Includes FAQ, table of enzymes and links to tools, maintained at the University of Waterloo, ON, Canada. (PCR) http://sciborg.uwaterloo.ca/~mpalmer/silent_mutations.html C. elegans Gene Knockout Project C. elegans Gene Knockout Project: Protocols including standard nested PCR, from the Biotechnology Laboratory, University of British Columbia. (PCR) http://ko.cigenomics.bc.ca/ PCR primer design and reaction optimisation PCR primer design and reaction optimisation: Article by Ed Rybicki, Department of Molecular and Cell Biology, University of Cape Town in: Molecular Biology Techniques Manual, on the web site of the University of Cape Town. (PCR) http://web.uct.ac.za/microbiology/pcroptim.htm PCR Amplification of cDNA Segments by 2 Stage Nested PCR PCR Amplification of cDNA Segments by 2 Stage Nested PCR: Protocol from the method database of NIH, USA. (PCR) http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?type=method&method_id=555 PCR Protocols PCR Protocols: Protocols and technical hints, particularly for reverse transcription PCR, somewhat outdated, compiled by Dr Jack Vanden Heuvel, Department of Veterinary Science and Molecular Toxicology Program, Penn State University (PCR) http://www.cas.psu.edu/docs/CASDEPT/VET/jackvh/jvhpcr.html DNALC: PCR Animation DNALC: PCR Animation: An animation explaining how the Polymerase Chain Reaction (PCR) works, from the Dolan DNA learning center, Cold Spring Harbor Laboratory. (PCR) http://www.dnalc.org/shockwave/pcranwhole.html Roe Laboratory Protocols Roe Laboratory Protocols: Molecular biological protocols, mostly PCR related used by Bruce A. Roe at the Dept. of Chemistry and Biochemistry, OU, Norman, OK. (PCR) http://www.genome.ou.edu/proto.html Long PCR Protocol Long PCR Protocol: Protocol and guidelines for choice of conditions for PCR of long sequences (10 kb or larger). From Genetics Dept., Harvard Medical School, Boston, MA, USA (PCR) http://twod.med.harvard.edu/labgc/estep/longPCR_protocol.html RAPD's RAPD's: Brief description of Random Amplified Polymorphic DNA, from Oklahoma State University, USA. (PCR) http://opbs.okstate.edu/~melcher/MG/MGW1/MG11127.html Technical manual of PCR Technical manual of PCR: Intended for specialists planning PCR procedures in their laboratories. From the University of Cape Town updated 2001. (PCR) http://web.uct.ac.za/microbiology/pcr.htm Degenerate PCR Degenerate PCR: An introduction with principle, applications and description of the technique. From the web site of Kebangsaan University, Malaysia. (PCR) http://cgat.ukm.my/protease/degpcr.html Protocol for T-RFLP by Capillary Electrophoresis Protocol for T-RFLP by Capillary Electrophoresis: Detailed protocol for terminal restriction fragment length polymorphism (T-RFLP), which allows the fingerprinting of a community by analyzing the polymorphism of a certain gene. Article by V Grüntzig, B Stres, HL Ayala del Río and JM Tiedje, Center for (PCR) http://rdp.cme.msu.edu/html/t-rflp_jul02.html What is "Hot-start" PCR? What is "Hot-start" PCR?: Principle and description of the technique, from the web site of the Weizmann Institute, Rehovot, Israel. (PCR) http://bip.weizmann.ac.il/mb/bioguide/pcr/PCRHot-start.html Thermostable DNA Polymerases Thermostable DNA Polymerases: Discussion of their origin and briefly their properties. From the web site of Colorado State University. (PCR) http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/hotpolys.html