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Protocol- For the meaning in computer science, see Protocol (computing).
A protocol is a rule which guides how an activity should be performed. Formerly used mainly in the diplomatic and government fields of endeavor to denote unwritten guidlines, by the turn of the twenty first century it had come into wide use in the computer and communications fields.
In international law and international relations, a protocol is a treaty or international agreement that supplements a previous treaty or international agreement.
A protocol can amend the previous treaty, or add additional provisions.
Parties to the earlier agreement are not required to adopt the protocol; sometimes this is made clearer by calling it an 'optional protocol', especially where many parties to the first agreement do not support the protocol.
Some examples: the United Nations Framework Convention on Climate Change (UNFCCC) established a framework for the development of binding greenhouse gas emission limits, while the Kyoto Protocol contained the limits later agreed upon.
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Roe Laboratory Protocols
Molecular biological protocols, mostly PCR related used by Bruce A. Roe at the Dept. of Chemistry and Biochemistry, OU, Norman, OK.
http://www.genome.ou.edu/proto.html
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.
http://sciborg.uwaterloo.ca/~mpalmer/silent_mutations.html
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.
http://info.med.yale.edu/genetics/ward/tavi/FISHguide.html
Fidelity of DNA Polymerases for PCR
Article by PN Hengen from TIBS 1995
http://www.lecb.ncifcrf.gov/~pnh/papers/TIBS/aug95.html
PCR protocols
Brief protocols for PCR in use at the Genome Sequencing Center of the Washington University in St Louis Medical School.
http://genome.wustl.edu/tools/protocols/index.php?fin4=1
Thermostable DNA Polymerases
Discussion of their origin and briefly their properties. From the web site of Colorado State University.
http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/hotpolys.html
Optimizing Multiplex and LA-PCR with Betaine
LA-PCR = "long and accurate PCR". Article by PN Hengen in TIBS June 1997.
http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jun97.html
Adjuvants in PCR Reactions
Brief discussion of additives to improve amplification efficiency and specificity of PCR, by Octavian Henegariu, Yale-New Haven Medical Center.
http://info.med.yale.edu/genetics/ward/tavi/p16.html
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.
http://www.info.med.yale.edu/genetics/ward/tavi/Guide.html
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.
http://web.uct.ac.za/microbiology/pcroptim.htm
Optimizing DNA Amplification Protocols using the Eppendorf Mastercycler
Basic discussion of the optimization of PCR, from the web site of Brinkmann Instruments.
http://www.brinkmann.com/PCR_appl_protocolsMC.asp
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.
http://www.bact.wisc.edu/Bact303/b27
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 RÃo and JM Tiedje, Center for Microbial Ecology, Michigan State University, USA
http://rdp.cme.msu.edu/html/t-rflp_jul02.html
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.
http://www.pcrlinks.com/
BioGuide - PCR
Basics of hot start, touchdown, AP and RAPD, primer selection, design programs and references, from the Weizman Institute of Science, Rehovot, Israel.
http://bip.weizmann.ac.il/mb/bioguide/pcr/contents.html
Degenerate PCR
The identification of novel members of gene families by PCR using degenerate primers is described and protocols given. Article by Michael Koelle 1996 on the web site of Dartmouth College.
http://www.dartmouth.edu/artsci/bio/ambros/protocols/other/koelle/degenerate_PCR.html
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
http://twod.med.harvard.edu/labgc/estep/longPCR_protocol.html
DNALC: PCR Animation
An animation explaining how the Polymerase Chain Reaction (PCR) works, from the Dolan DNA learning center, Cold Spring Harbor Laboratory.
http://www.dnalc.org/shockwave/pcranwhole.html
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.
http://info.med.yale.edu/genetics/ward/tavi/Trblesht.html
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 Library, Göttingen.
http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker
Inverse PCR protocol
step by step protocol, from the web site of the Department of Biology, University of Michigan, USA.
http://www.biology.lsa.umich.edu/research/labs/maddock/protocols/PCR/inverse_pcr_protocol.html
Random Arbitrarily Primed PCR
Protocol for RAP-PCR to study prokaryotic gene expression, from the Enterococcus Research Site, University of Oklahoma, USA.
http://www.enterococcus.ouhsc.edu/random_pcr.asp
Rational primer design greatly improves differential display-PCR (DD-PCR)
Article: D Graf, AG Fisher, M Merkenschlager: Nucl. Acids Res. 25:11 2239-2240.
http://nar.oupjournals.org/cgi/content/full/25/11/2239
GenHunter
Manufacturer of material for differential display PCR in Nashville, Tenn USA.
http://www.genhunter.com
Degenerate PCR
An introduction with principle, applications and description of the technique. From the web site of Kebangsaan University, Malaysia.
http://cgat.ukm.my/protease/degpcr.html
What is "Hot-start" PCR?
Principle and description of the technique, from the web site of the Weizmann Institute, Rehovot, Israel.
http://bip.weizmann.ac.il/mb/bioguide/pcr/PCRHot-start.html
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.
http://www.biocan.com/mbio/hot_tag.htm
Inverse PCR and Cycle Sequencing of P Element Insertions for STS Generation
Step by step protocol, by EJ Rehm, Berkeley Drosophila Genome Project, USA.
http://www.fruitfly.org/about/methods/inverse.pcr.html
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.
http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb17/17053-1.pdf
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.
http://imd-www.es.hokudai.ac.jp/~kinjo/fapcr/fapcrout.html
Alu-PCR Hybridization
A report and protocol, from Fondation Jean Dausset.
http://www.cephb.fr/manips_alupcr.html
Standard PCR protocols
From Molecular Biology Techniques Manual, from the web site of the University of Cape Town, South Africa.
http://web.uct.ac.za/microbiology/pcrcond.htm
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.
http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html
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.
http://greengenes.cit.cornell.edu/anchors/
PCR Protocol
Detailed PCR protocol from the web site of the Department of Biology, University of Michigan, USA.
http://www.biology.lsa.umich.edu/research/labs/maddock/protocols/PCR/general_pcr_protocol.html
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.
http://www.genetics.wustl.edu/fish_lab/frank/cgi-bin/fish/prot2.html
Inverse PCR For use with Snyder mTn-lacZ/LEU2 Based Mutagenesis
Protocol by M McMurray, Fred Hutchinson Cancer Research Center, Seattle, Wa. USA.
http://www.fhcrc.org/labs/gottschling/misc/ipcr.html
C. elegans Gene Knockout Project
Protocols including standard nested PCR, from the Biotechnology Laboratory, University of British Columbia.
http://ko.cigenomics.bc.ca/
RFLP Definition
RFLP = Restriction Fragment Length Polymorphism, from FDA
http://vm.cfsan.fda.gov/~frf/rflp.html
Nematode ITS1 Size Variation
Examples of Restriction Fragment Length Polymorphism (RFLP)electrophoresis slabs for different nematodes.
http://nematode.unl.edu/its_id/EXAMPLES/index.htm
Detection of Point Mutations by RFLP of PCR Amplified DNA Sequences
RFLP = Restriction Fragment Length Polymorphism. By Alexander Binder 1997.
http://www-ang.kfunigraz.ac.at/~binder/thesis/node64.html
Cleaved Amplified Polymorphic Sequence
Illustration of principle. CAPS corresponds to RFLP. From Corvallis Forestry Research Community, Corvallis, USA.
http://www.fsl.orst.edu/tgerc/PCRCourse/caps.jpg
Mutation Detection Systems - SSCP Analysis
Discussion of the technique and variations, literature references. By S McQuaid, Institute of Child Health, University College London, UK.
http://www.ich.ucl.ac.uk/cmgs/sscp.htm
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.
http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/R01-013.pdf
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.
http://www.dartmouth.edu/~tjack/
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.
http://www.molecularstaging.com/Pages/RCAToverview_.html
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)
http://www.qiagen.com/literature/brochures/pcr/pdf/pcrcha03.pdf
Multiplex PCR
A new PCR strategy that enables the amplification of multiple DNA targets in one run. From Boston University.
http://www.bu.edu/research/Features/scicoalition_01/twist.html
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.
http://ko.cigenomics.bc.ca/poison1.html
PCR Amplification of cDNA Segments by 2 Stage Nested PCR
Protocol from the method database of NIH, USA.
http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?type=method&method_id=555
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.
http://www.btc-bti.com/pcrelisa.htm
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.
http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/rapd.html
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.
http://www.nottingham.ac.uk/~mbzspd/methods/3RACE_PCR.html
Quantitative PCR Protocol
From the Jackson Laboratory, University of Maine, USA.
http://www.jax.org/cyto/quanpcr.html
Optimizing PCR Protocols
Brief guidelines. From the Jackson Laboratory, University of Maine, USA.
http://www.jax.org/imr/optimize_pcr.html
Innovative Tools for Amplification
Notes about PCR applications, principles, research results, from Roche.
http://www.roche-applied-science.com/sis/amplification/
Biosource molecular methods booklet
56 page booklet on oligonucleotides, PCR and RT-PCR, from Biosource (company).
http://www.biosource.com/content/techCornerContent/methodPDFs/MolecularMethods.pdf
RACE amplification
Rapid Amplification of cDNA Ends. Protocol, from National Institute of Genetics, Japan.
http://www.nig.ac.jp/labs/EarlyEmb/midline/protocol/RACE.html
RAPD's
Brief description of Random Amplified Polymorphic DNA, from Oklahoma State University, USA.
http://opbs.okstate.edu/~melcher/MG/MGW1/MG11127.html
RAPD analysis with P. infestans
Protocol for Randomly Amplified Polymorphic DNA, by H Judelson, University of California, Riverside, USA.
http://www.fgsc.net/methods/Judel.html
PCR Animation
Explaining how Polymerase Chain Reaction (PCR) works. From Dolan DNA Learning Center, Cold Spring Harbor Laboratory, USA.
http://www.dnalc.org/Shockwave/pcranwhole.html
PCR animated
Animation illustrating the principle of PCR, from the University of Ghent, Belgium.
http://allserv.rug.ac.be/~avierstr/principles/pcrani.html
MJ Research
Manufactures and sells products for molecular biology including thermal cyclers and sequencers / genotypers.
http://www.mjr.com/
Attotron Biosensor Corporation
R & D company for development of biosensors and related products for the research and educational markets.
http://www.attotron.com
Protocols Online: PCR Protocols
Extensive collection of PCR protocols and methods from Protocol On Line.
http://www.protocol-online.org/prot/Molecular_Biology/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.
http://www.brinkmann.com/PCR_appl_primer.asp
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.
http://www.hifidna.com/
Kary B. Mullis - Autobiography
The originator of PCR, from the Nobel e-museum web site.
http://www.nobel.se/chemistry/laureates/1993/mullis-autobio.html
PCR method protocols
Protocols for PCR posted by the Helen Donis-Keller Laboratory.
http://hdklab.wustl.edu/lab_manual/pcr/pcrcontents.html
PCR Project
Presentations from the University of California at Berkley on PCR, both current research reports and reviews.
http://sunsite.berkeley.edu/biotech/pcr/
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
http://www.cas.psu.edu/docs/CASDEPT/VET/jackvh/jvhpcr.html
PCR Technology
An introduction by Connie Veilleux from the US National Health Museum website.
http://www.accessexcellence.org/LC/SS/PS/PCR/PCR_technology.html
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.
http://www.faseb.org/opar/bloodsupply/pcr.html
Polymerase Chain Reaction (PCR)
A graphic description of the principle of PCR from the US National Health Museum web site.
http://www.accessexcellence.org/AB/GG/polymerase.html
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.
http://allserv.rug.ac.be/~avierstr/principles/pcr.html
Rep-PCR Genomic Fingerprinting
Bacteria are characterized by Rep-PCR fingerprinting using primers corresponding to naturally occurring repetitive sequences in the interspersed regions.
http://www.msu.edu/user/debruijn/
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.
http://info.med.yale.edu/genetics/ward/tavi/PCR.html
Technical manual of PCR
Intended for specialists planning PCR procedures in their laboratories. From the University of Cape Town updated 2001.
http://web.uct.ac.za/microbiology/pcr.htm
What the Heck is PCR?
Popular description of the PCR technique by John C Brown, University of Kansas 1995.
http://people.ku.edu/~jbrown/pcr.html
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.
http://www.accessexcellence.com/RC/CT/polymerase_chain_reaction.html
Kary Mullis
Inventor Profile of Kary Mullis, the originator of PCR, from the National Inventors Hall of Fame web site.
http://www.invent.org/hall_of_fame/109.html
Wayward PCR primers
Article by PN Hengen from TIBS 1995 on the loss of activity of PCR primers with time.
http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jan95.html
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