History of polymerase chain reaction

:"(This article assumes familiarity with the terms and components used in the PCR process.)"The history of the Polymerase Chain Reaction (or PCR) has variously been described as a classic "Eureka!" moment [http://nobelprize.org/nobel_prizes/chemistry/laureates/1993/mullis-lecture.html Kary Mullis' Nobel Lecture, December 8, 1993] ] , or as an example of cooperative teamwork between disparate researchersRabinow P "Making PCR: A Story of Biotechnology" University of Chicago Press (1996) ISBN 0-226-70147-6] . A list of some of the events before, during, and after its development:

Prelude

* On April 25, 1953 James D. Watson and Francis Crick publish "a radically different structure" for DNA [Watson JD, Crick FHC "A Structure for Deoxyribose Nucleic Acid", Nature vol. 171, pp. 737-738 (1953). [http://www.exploratorium.edu/origins/coldspring/ideas/printit.html] ] , thereby founding the field of Molecular Genetics. Their structure involves two strands of complementary base-paired DNA, running in opposite directions as a double helix. They conclude their report saying that "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material". They are awarded the Nobel Prize in 1962.

* Starting in the mid 1950s, Arthur Kornberg begins to study the mechanism of DNA replication [(Arthur Kornberg's Discovery of DNA Polymerase I) J. Biol. Chem. vol. 280, p. 46. [http://www.jbc.org/cgi/content/full/280/49/e46] ] . By 1957 he has identified the first DNA polymerase [Lehman, IR, Bessman MJ, Simms ES, Kornberg A "Enzymatic Synthesis of Deoxyribonucleic Acid. I. Preparation of Substrates and Partial Purification of an Enzyme from Escherichia coli" J. Biol. Chem. vol. 233(1) pp. 163-170 (1958).] . The enzyme is surprisingly limited, creating DNA in just one direction and requiring an existing primer to initiate copying of the template strand. However, the overall DNA replication process is surprisingly complex, requiring separate proteins to open the DNA helix, to keep it open, to create primers, to synthesize new DNA, to remove the primers, and to tie the pieces all together. He is awarded the Nobel Prize in 1959.

* In the early 1960s H. Gobind Khorana participates in the discovery of the Genetic Code. Afterwards, he initiates a large project to totally synthesize a functional human gene [Khorana HG et al. "Total synthesis of the structural gene for the precursor of a tyrosine suppressor transfer RNA from Escherichia coli. 1. General introduction" J. Biol. Chem. vol. 251(3) pp. 565-70 (1976).] . To achieve this, he pioneers many of the techniques needed to make and use synthetic DNA oligonucleotides. Sequence-specific oligos are used both as building blocks for the gene, and as primers and templates for DNA polymerase. In 1968 Khorana is awarded the Nobel Prize for his work on the Genetic Code.

* In 1969 Thomas Brock reports the isolation of a new species of bacterium from a hot spring in Yellowstone National Park. Naming it "Thermus aquaticus" [Brock TD, Freeze H "Thermus aquaticus, a Nonsporulating Extreme Thermophile" J. Bact. vol. 98(1) pp. 289-297 (1969).] (Taq), it goes on to become a standard source of enzymes able to withstand higher temperatures than those from "E. Coli".

* In 1970 a modified version of DNA Polymerase I from "E. coli" is reported [Klenow H and Henningsen I "Selective Elimination of the Exonuclease Activity of the Deoxyribonucleic Acid Polymerase from Escherichia coli B by Limited Proteolysis" Proc Natl Acad Sci vol. 65 pp. 168-75 (1970).] . Treatment with a protease removes the 'forward' nuclease activity of this enzyme. The overall activity of the resulting Klenow fragment is therefore biased towards the synthesis of DNA, rather than its degradation.

* By 1971 researchers in Khorana's project, concerned over their yields of DNA, begin looking at "repair synthesis" - an artificial system of primers and templates that allows DNA polymerase to copy segments of the gene they are synthesizing. Although similar to PCR in using repeated applications of DNA polymerase, the process they usually describePanet A, Khorana HG "Studies on Polynucleotides" J. Biol. Chem. vol. 249(16), pp. 5213-21 (1974).] employs just a single primer-template complex, and therefore would not lead to the exponential amplification seen in PCR.

* Also by 1971 Kjell Kleppe, a researcher in Khorana's lab, envisions a process very similar to PCR. At the end of a paper on the earlier techniqueKleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana HG "Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA's as catalyzed by DNA polymerases." J. Molec. Biol. vol. 56, pp. 341-61 (1971).] , he describes how a two-primer system might lead to replication of a specific segment of DNA:

:::" "... one would hope to obtain two structures, each containing the full length of the template strand appropriately complexed ":::"with the primer. DNA polymerase will be added to complete the process of repair replication. Two molecules of the original":::"duplex should result. The whole cycle could be repeated, there being added every time a fresh dose of the enzyme." "

:No results are shown there, and the mention of unpublished experiments in another paper may (or may not) refer to the two-primer replication system. (These early precursors to PCR were carefully scrutinized in a patent lawsuit, and are discussed in Mullis' chapters in [Mullis KB, Ferré F, Gibbs RA "The Polymerase Chain Reaction" Birkhäuser Press (1994) ISBN 0-817-63750-8] .)

* Also in 1971, Cetus Corporation is founded in Berkeley, California by Ronald Cape, Peter Farley, and Donald Glaser. Initially the company screens for microorganisms capable of producing components used in the manufacture of food, chemicals, vaccines, or pharmaceuticals. After moving to nearby Emeryville, they take up projects involving the new biotechnology industry, primarily the cloning and expression of human genes, but also the development of diagnostic tests for genetic mutations.

* In 1976 a DNA polymeraseChien A, Edgar DB, Trela JM "Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus" J. Bact. vol. 174 pp. 1550-1557 (1976).] is isolated from "T. aquaticus". It is found to retain its activity at temperatures above 75°C.

* In 1977 Frederick Sanger reports a method for determining the sequence of DNA [Sanger F, Nicklen S, Coulson AR "DNA sequencing with chain-terminating inhibitors" Proc Natl Acad Sci vol. 74(12) pp. 5463-7 (1977).] . The technique involves an oligonucleotide primer, DNA polymerase, and modified nucleotide precursors that block further extension of the primer in sequence-dependent manner. He is awarded the Nobel Prize in 1980.

Thus, by 1980 all of the components needed to perform PCR amplification were known to the scientific community. The use of DNA polymerase to extend oligonucleotide primers was a common procedure in DNA sequencing and the production of cDNA for cloning and expression. The use of DNA polymerase for nick translation was the most common method used to label DNA probes for Southern blotting.

Theme

* In 1979 Cetus Corporation hires Kary Mullis to synthesize oligonucleotides for various research and development projects throughout the companyMullis KB "The Unusual Origins of the Polymerase Chain Reaction" Scientific American, vol. 262, pp. 56-65 (April 1990).] . These oligos are used as probes for screening cloned genes, as primers for DNA sequencing and cDNA synthesis, and as building blocks for gene construction. Originally synthesizing these oligos by hand, Mullis later evaluates early prototypes for automated synthesizers.

* By May 1983 Mullis has synthesized oligo probes for a project at Cetus attempting to analyze a mutation for a human genetic disease. Hearing of problems with their work, Mullis envisions an alternative technique based on Sanger's DNA sequencing method. Realizing the difficulty in making that method specific to a single location in the genome, Mullis considers adding a second primer on the opposite strand. He then generalizes the idea, and realizes that repeated applications of polymerase could lead to a chain reaction of replication for a specific segment of the genome - PCR.

* Later in 1983 Mullis begins to test his idea. His first experiment does not involve thermal cycling - he hopes that the polymerase can perform continued replication on its own. Later experiments that year do involve repeated thermal cycling, and target small segments of a cloned gene. Mullis considers these experiments a success, but is unable to convince other researchers.

* In June 1984 Cetus holds its annual meeting in Monterey, California. Its scientists and consultants present their results, and consider future projects. Mullis presents a poster on the production of oligonucleotides by his laboratory, and shows some of the results from his experiments with PCR. Only Joshua Lederberg, a Cetus consultant, shows any interest. Later at the meeting, Mullis is involved in a physical altercation with another Cetus researcher, over a dispute unrelated to PCR. The other scientist soon leaves the company, and Mullis is removed as head of the oligo synthesis lab. The days of his continued employment at Cetus may be numbered.

Development

* In September of 1984 Tom White, VP of Research at Cetus (and a close friend), pressures Mullis to take his idea to the group developing the genetic mutation assay. Together, they spend the following months designing experiments that could convincingly show that PCR is working on genomic DNA. Unfortunately, the expected amplification product is not visible in agarose gel electrophoresisScharf et al. "Direct Cloning and Sequence Analysis of Enzymatically Amplified Genomic Sequences" Science vol. 233, pp. 1076-78 (1986).] , leading to confusion as to whether the reaction has any specificity to the targeted region.

* In November of 1984 the amplification products are analyzed by Southern blotting, which clearly shows an increasing amount of the expected 110 bp DNA productSaiki RK et al. "Enzymatic Amplification of β-globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia" Science vol. 230 pp. 1350-54 (1985).] . Having the first visible signal, the researchers are able to begin finding optimum conditions for the reaction. Later, the amplified products are cloned and sequenced, showing that only a small fraction of the amplified DNA is the desired target, and that the polymerase then being used only rarely incorporates incorrect nucleotides during replication.

Exposition

* As per normal industrial practice, the results are first used to apply for patents. Mullis prepares an application [Mullis KB "Process for amplifying nucleic acid sequences." U.S. Patent 4,683,202.] for the basic idea of PCR and many potential applications, and is asked by the PTO to include more results. On March 28, 1985 the entire development group (including Mullis) files an application [Mullis, KB et al. "Process for amplifying, detecting, and/or-cloning nucleic acid sequences." U.S. Patent 4,683,195.] that is more focused on the analysis of the SCA mutation via PCR and OR. After modification, both patents are approved on July 28, 1987.

* In the spring of 1985 the development group begins to apply PCR to other targets. Primers and probes are designed for a variable segment of the HLA DQα gene. This reaction turns out to be much more specific than that for the β-hemoglobin target - the expected PCR product is directly visible on agarose gel electrophoresis. The amplification products from various sources are also cloned and sequenced, the first determination of new alleles by PCR. At this same time the original OR assay technique is replaced with the more general ASO methodSaiki et al. "Analysis of enzymatically amplified β-globin and HLA DQα DNA with allele-specific oligonucleotide probes." Nature vol. 324 (6093) pp. 163-6 (1986).] .

* Also early in 1985, the group turns its attention to the use of a thermostable DNA polymerase (the enzyme used in the original reaction is destroyed at each heating step). A literature search reveals that only two have been described, from Taq and Bst. The report on Taq polymerase is more detailed, so it is chosen for testing. A fortuitous decision - the Bst polymerase is later found to be unsuitable for PCRFact|date=April 2008. That summer Mullis tries twice to isolate the enzyme, and a group outside of Cetus is also contracted to make it, all without success. In the Fall of 1985 Susanne Stoffel and David Gelfand at Cetus succeed in making the polymerase, and it is immediately found by Randy Saiki to support the PCR process.

* With patents submitted, work proceeds for reporting PCR to the general scientific community. An abstract for a meeting in Salt Lake City is submitted in April 1985, and the first announcement of PCR is made there by Saiki in October [Saiki, R et al. "A Novel Method for the Prenatal Diagnosis of Sickle Cell Anemia" Amer. Soc. Human Genetics, Oct. 9-13, 1985.] . Two publications are planned - an 'idea' paper from Mullis, and an 'application' paper from the entire development group. Mullis submits his manuscript to the journal Nature, which rejects it for not including results. The other paper, mainly describing the OR analysis assay, is submitted to Science on September 20, 1985 and is accepted in November. After the rejection of Mullis' report in December, details on the PCR process are hastily added to the second paper, which appears on December 20, 1985.

* In May of 1986 Mullis presents PCR at the Cold Spring Harbor Symposium [Mullis KB et al. "Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction." Cold Spring Harbor Symp. Quant. Biol. vol. 51 pp. 263-73 (1986).] , and publishes a modified version of his original 'idea' manuscript much later [Mullis KB and Faloona FA "Specific Synthesis of DNA in vitro via a Polymerase-Catalyzed Chain Reaction." Methods in Enzymology vol. 155(F) pp. 335-50 (1987).] . The first non-Cetus report using PCR is submitted on September 5, 1986 [Verlaan-de Vries M et al. "A dot-blot screening procedure for mutated ras oncogenes using synthetic oligodeoxynucleotides." Gene vol. 50(1-3) pp. 313-20 (1986).] , indicating how quickly other laboratories are implementing the technique. The Cetus development group publishes their detailed sequence analysis of PCR products on September 8, 1986, and their use of ASO probes on November 13, 1986.

* The use of Taq polymerase in PCR is announced by Henry Erlich at a meeting in Berlin on September 20, 1986, is submitted for publication in October of 1987, and is published early the next year'Saiki et al. "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase." Science vol. 239 pp. 487-91 (1988).] . The patent for PCR with Taq polymerase is filed on June 17, 1987, and is issued on October 23, 1990 [Mullis, KB et al. "Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme." U.S. Patent 4,965,188.] .

Variation

* In December 1985 a joint venture between Cetus and Perkin-Elmer is established to develop instruments and reagents for PCR. Complex Thermal Cyclers are constructed to perform the Klenow-based amplifications, but are never marketed. Simpler machines for Taq-based PCR are developed, and on November 19, 1987 a press release announces the commercial availability of the "PCR-1000 Thermal Cycler" and "AmpliTaq DNA Polymerase".

* In the Spring of 1985 John Sninsky at Cetus begins to apply PCR to the difficult task of quantitating the amount of HIV circulating in blood. A viable test is announced on April 11, 1986, and is published in May 1987 [Kwok S et al. "Identification of HIV sequences by using in vitro enzymatic amplification and oligomer cleavage detection." J. Virol. vol. 61(5) pp. 1690-4 (1987).] . Donated blood can now be screened for the virus, and the effect of antiviral drugs can be directly monitored.

* In 1985 Norm Arnheim, also a member of the development team, concludes his sabbatical at Cetus and gets a real job at USC. He begins to investigate the use of PCR to amplifiy samples containing just a single copy of the target sequence. By 1989 his lab runs mutiplex-PCR on single sperm to directly analyze the products of meiotic recombination [Boehnke M et al. "Fine-structure genetic mapping of human chromosomes using the polymerase chain reaction on single sperm." Am J Hum Genet vol. 45(1) pp. 21-32 (1989).] . These single-copy amplifications, which had first been run during the characterization of Taq polymerase, become vital to the study of ancient DNA, as well as the genetic typing of preimplanted embryos.

* In 1986 Edward Blake, a forensics scientist working in the Cetus building, collaborates with Bruce Budowle (of the FBI) and Cetus researchers to apply PCR to the analysis of criminal evidence. A panel of DNA samples from old cases is collected and coded, and is analyzed blind by Saiki using the HLA DQα assay. When the code is broken, all of the evidence and perpetrators match. Blake uses the technique almost immediately in "Pennsylvania v. Pestinikas" [ [http://www.forensicdna.com/Timeline020702.pdf Forensic Science Timeline (PDF).] ] , the first use of PCR in a criminal case. This DQα test is developed by Cetus as one of their "Ampli-Type" kits, and goes on to become part of early protocols for the testing of forensic evidence.

* By 1989 Alec Jeffreys, who had earlier developed and applied the first DNA Fingerprinting tests, uses PCR to increase their sensitivity [Jeffreys A et al. "Amplification of human minisatellites." Nucleic Acids Research vol. 23 pp. 10953-71 (1988).] . With further modification, the amplification of highly polymorphic VNTR loci will become the standard protocol for National DNA Databases such as CODIS. The guilty go to jail, and the ability of PCR to restest old evidence begins to set the innocent free.

* In 1987 Russ Higuchi succeeds in amplifying DNA from a human hair [Higuchi R et al. "DNA typing from single hairs." Nature vol. 332(6164) pp. 543-6 (1988).] . This work expands to develop methods to amplify DNA from highly degraded samples, such as from Ancient DNA and in forensic evidence. On January 30, 1989 an of airs. The ship's doctor is being rapidly aged by a virus attacking her DNA, and is cured when her pre-infection DNA is isolated from a hair found in her cabin. PCR has entered the mainstream media.

Coda

* On December 22, 1989 the journal Science awards Taq Polymerase (and PCR) its first "Molecule of the Year". The 'Taq PCR' paper goes on to become (for several years) the most cited publication in biology.

* After the publication of the first PCR paper, the United States Government sends a stern letter to Randy Saiki, admonishing him for publishing a report on "chain reactions" without the required prior review and approval by the U.S. Department of Energy. Cetus writes back, explaining the differences between PCR and the atomic bomb.

* On July 23, 1991 Cetus announces that it will be sold to its neighboring biotechnology company Chiron. As part of the sale, rights to the PCR patents are sold for USD $300 million to Hoffman-La Roche (who in 1989 had bought limited rights to PCR). Many of the Cetus PCR researchers move to a new subsidiary, Roche Molecular Systems.

* On October 13, 1993 Kary Mullis, who had left Cetus in 1986, is awarded the Nobel Prize in Chemistry. On the morning of his acceptance speech, he is nearly arrested by Swedish authorities for the "inappropriate use of a laser pointer" [Mullis KB "Dancing Naked in the Mind Field" Pantheon Books (1998) ISBN 0-679-44255-3] .

References