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There appears a concept called "Tm" in this article, but it is neither linked to an article with such title, or explained in this article itself. Please, define this term in its own article (and link to it), or define it here. Thank you. Pentalis 21 april 2:01 GMT -4:00 winter time.

• It stands for melting temperature, often abbreviated Tm in calculations. Not sure why it is Tm rather than Mt, though capital T usually stands for temperature. CheekyMonkey 12:49, 2 May 2005 (UTC)

• • Thank you very much, I also noticed you added the concept to the disambiguation page too, very kind of your part :-) Pentalis 6:25, 31 May 2005 (GMT -4:00 winter time)

Fixed to T_m. 203.218.136.155 14:39, 11 June 2006 (UTC)

In step 4 of figure 2 is not explained. How is the rest of the DNA past the primers truncated? All we see is a dotted line on the diagram suggesting it is cut somehow.

They don't get replicated, and hence drop out of significance entirely. (Among the millions of DNA molecules that eventually get made.) Its just a diagram to illustrate the concept, the actual reason is in the article. -- Natalinasmpf 13:27, 16 Jun 2005 (UTC)

Contents 1 CATTAGAT 2 Har Gobind Khorana 3 "PCR reaction" 4 History of PCR 4.1 Taq is not a polymerase that is used always 4.2 Bicycle or Car? 4.3 elongation vs extension 4.4 micro-PCR 4.5 Could somebody please include Partial DNA match explanation in this article ? 4.6 possible rephrasing needed 4.7 ile code 4.8 Redirection 4.9 nomenclature 4.10 Is it a good example of PCR elecrtrophoregram 4.11 Use in identification of pathogens

[edit] CATTAGAT

There's a new program being released (under the GNU GPL) to perform primer specificity searches.

http://genome.cs.hi.is/cattagat/

If this looks useful to anyone then perhaps it can be added to the external links. I don't feel right doing it myself since I'm one of the authors of the software. - Haukurth 15:55, 21 July 2005 (UTC)

[edit] Har Gobind Khorana

I don't see how one can attribute the invention of PCR to Khorana. An invention (at least a patentable one) requires a reduction to practice, which he certainly never did. There is no reference cited for this either. In addition, the theromostabile polymerase was not known to Mullis at the time of his invention. Mullis got the Nobel Prize for the invention, not Khorana. I am therefore removing the attribution to Khorana.DonSiano 17:23, 22 August 2005 (UTC)

• Hi DonSiano. I left the actual reference to the paper (which you removed), as well as the actual text from the paper. In the paper, (and in lots of subsequent work), they used the procedure (which I quoted from the original paper) to construct genes in their study tRNA related genes. Some of the other references mentioned in the citations at the bottom of the article also mention Khorana's work. The actual text you removed is below:

• Much of the conceptual work on polymerase chain reaction was carried out in Har Gobind Khorana's lab at MIT ^[1]. Khorana and coworkers published a paper in 1971, describing repair replication and the process by which it could be used to synthetically replicate tRNA genes in E. coli. The major finding is given in this text:

The principles for extensive synthesis of the duplexed tRNA genes which emerge 
from the present work are the following. The DNA duplex would be denatured to 
form single strands. This denaturation step would be carried out in the presence of a 
sufficiently large excess of the two appropriate primers. Upon cooling, 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. (Kleppe et al., 1971)

1. ^ [1]

• I actually redundantly reference the work. If you do not access to the reference, I would be happy to send it to you. In fact, if you read the paper, they actually reduce it to practice not only in the referenced paper, but in much of the subsequent work in synthesizing tRNA related genes. Regardless, the wording I used was being conservative and not attributing an invection to Khorana's lab, just that the conceptual work was laid down over a decade earlier. The quote that I use from the paper (12 years before the invention of PCR) is PCR, they just call it something different. In fact, in the referenced paper, they determine other conditions that are conducive to such amplification, such as minimal primer sizes. I could reference Khorana's subsequent work on amplifying various pieces of genes using the procedure. Granted, Khorana's group did not push automation, thermostable polymerases, et cetera, but it is no reason not to mention and reference the work.

I'll post the information back, unless you can explain to me why this work is not important to the history of PCR. If the wording seems controversial, maybe we could consider rewriting the section?\

--Skosuri 03:46, 9 June 2006 (UTC)

---

Hi Skosuri,

Well, PCR is one of those really big inventions that someone other than the almost universally acknowledged inventor thought of first. And the history of the invention is always more complicated than that which can be accommodated in a in a paragraph or two of an encyclopaedic article. Are there any inventions that don't have that characteristic? Both the courts (and presumably the nobel prize committee) considered this dispute and came down on the side of Mullis. There is no evidence that Mullis was aware of Khorana's work; and others certainly contributed to making it work: including, Henry Erlich, Norman Arnheim, Randall Saiki, Glen Horn, Corey Levenson, Steven Scharf, Fred Faloona and Tom White. And maybe even Kleppe has a claim too. There is, understandably, quite an impulse to knock the hero down a bit. The LSD ref is attributable to this tendency too, I think. I note that the "history" section of the article makes no mention of the others either. Nor is there any note taken that Mullis was a synthetic chemist put out of work by a machine to synthesize oligimers...

The fact is that PCR could have been invented years before Mullis came along, and no doubt a lot of people regret they missed it. One has to wonder, though, how many years would have passed before it was developed if Mullis hadn't done his bit...

The bottom line is, I don't think Khorana deserves all the space you would like to devote to him it this article, which would seem to outweigh Mullis' contribution. I certainly don't dispute that some mention might be made, but it is out of balance. Perhaps you could try some rewording of this: perhaps "like most inventions there are precursors and other actors than the one..." or something along those lines. Please don't just revert--let's try to reach some middle ground that is acceptable to us both.

There has been a lot of interest in PCR as a prototypical invention and it has been the subject of quite a bit of historical work, as I am sure you are aware. Perhaps what is really needed is a separate article on this, perhaps "PCR History"; I'd be willing to work on it with you--it could be interesting and worth doing. We could move a good bit of the history section over there and leave a ref to "main article" here. Which could shorten the PCR article which is already too long besides. What do you think? DonSiano 12:29, 9 June 2006 (UTC)

Call it History of polymerase chain reaction if you do it, to be consistent with other articles 203.218.136.155 14:39, 11 June 2006 (UTC)

[edit] "PCR reaction"

Is it considered acceptable to use the phrase "PCR reaction" or is this considered redundant? The phrase appears a couple of times in this article. (RAS syndrome and the associated discussion page provide an interesting treatment of the issue; a Google search for "'PCR reaction' and 'RAS syndrome'" also reveals some interesting hits).--GregRM 15:17, 21 December 2005 (UTC)

I try and remove the 'reaction' from the 'PCR reaction' whenever I can as it bugs me but maybe I'm just picky! I think it stems from the fact that acronyms such as PCR, ATM, CCTV and so on have become so commonplace it is no longer considered necessary to define them and so people lose sight of the actual meaning and consider the concept as a whole. Thus, when wanting to emphasise the fact that it is a reaction, the 'reaction' tagged onto the end. -luckyluke09

Yes it is redundant, always remove reaction coz this is an encyclopedia 203.218.136.155 14:39, 11 June 2006 (UTC)

Thanks for the replies...I removed references to "PCR reaction" yesterday.--GregRM 22:35, 12 June 2006 (UTC)

[edit] History of PCR

• History of PCR A great review article. Also PCR Protocols, PCR Bioinformatics, and discussion are included.

Links to other PCR topics removed as they are not informative for standard PCR, and should be under Real-time or quantitative PCR. The History of PCR link is much more informative for PCR, yet was removed by [user:Alan Au] -- Bioinformin

[edit] Taq is not a polymerase that is used always

I disagree strongly with the phrase that Taq is used in current practice. Taq is with current standards a bad polymerase and it is not necesary to use Taq. Taq has no proofreading activity and its processivity is not as good as other polymerases, so it is my opinion that wikipedia should take an independent stance and not link PCR to Taq

I also made a very imortant change. It is not nucleotides that are used in the reaction but deoxynucleotides-triphosphate

I think you mean deoxynucleoside-triphosphate. There is no such thing as a nucleotide-triphosphate, since the definition of a nucleotide is a nucleoside + phosphates. 130.243.248.239 14:29, 19 November 2006 (UTC)

Comment:

yes i completly agree to this. while taq polymerase certainly is the most famous and perhaps the one most used, it is far from the only one, nor is it one of the best polymerases available. an elucidation of the other available polymerases would be much appreciated. here assessing their properties, comparing price (relatively, not absolutely), areas of use. where it is appropriate to have a polymerase with high fidelity. 3' nucleases 5' nucleases. and so on and so forth.

thank you -broccolee

[edit] Bicycle or Car?

I was told that Mullis was driving his car and that he was going on vacation with his (first) wife and that he got the idea that he just had to try, so he turned the car around to the lab... Is the motorcycle source reliable?

Several theories abound, ranging from the drugs story to the possibility that Kary Mullis merely reduced to practice the idea that had been given to him by a co-worker who had attended a seminar discussing tRNA synthesis in a manner similar to what we now know as PCR. Another rumour is that Kary Mullis was not going to be named as an inventor on the patents (the glory instead passing to David Gelfand, a co-inventor on the Taq patents, and Randy Saiki), and came to work at Cetus one day with a gun, demanding to be named as the lead inventor. All rumour though, and not suitable for the main page. 159.92.30.11 12:53, 1 June 2006 (UTC)

[edit] elongation vs extension

i observe that one use the term elongation for the polymerase 'elongating' the primer along the dna strand. however the more correct term is extension. also elongation is used regarding protein synthesis.

the analogy is

melting-annealing-extension:PCR-cycle::intiation-elongation-termination:protein synthesis

i am fairly sure these terms are not used over one another. however you may know otherwise.

thats all.

[edit] micro-PCR

In my research on microelectromechanical systems (MEMS) devices, I ran across some information on micro-PCR devices, which are fabricated with MEMS techniques. They consist of arrays of reaction chambers with electric heaters, and their construction allows them to do faster PCR with smaller sample sizes (both DNA and reagents). Does anybody else know the history of micro-PCR (sometimes denoted μPCR) that can help me add some stuff on this topic? Good article: http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TFC-4CPM20J-1-1&_cdi=5223&_user=1238599&_orig=search&_coverDate=01%2F15%2F2005&_qd=1&_sk=999799992&view=c&wchp=dGLbVlb-zSkWz&md5=ded7b4a9d79b6ef6bc883c7d08e00020&ie=/sdarticle.pdf

[edit] Could somebody please include Partial DNA match explanation in this article ?

I think partial DNA match is relevant topic to be included in this article. Could somebody please do that ? I need information about Partial DNA match interpretation. For example, it test is done on 13 alleles, and match is partial (on 10 of them), and reaction has not been succesful on 3 alleles: how should this be interpreted ? As far as I know, there are divided opinions in scientific community about this issue. Please help, this issue is important to me, and at the same time I think it is relevant to be included in this article, because it makes it more complete and understandable.

[edit] possible rephrasing needed

"Primers are short, artificial DNA strands — often not more than fifty and usually only 18 to 25 base pairs long nucleotides that are complementary to the beginning and end of the DNA fragment to be amplified." How can a nucleotide be 18-25 base pairs long, this needs to be rephrased.

removed nucleotide. 203.218.136.155 14:39, 11 June 2006 (UTC)

"Colony PCR - Bacterial clones (E.coli) can be screened for the correct ligation products. Selected colonies are picked with a sterile toothpick from an agarose plate and dabbed into the master mix or sterile water. Primers (and the master mix) are added - the PCR protocol has to be started with an extented time at 95^^C." Would you really use a sterile toothpick, Wouldn't a sterile wire loop be more appropriate? --KX36 10:47, 27 May 2006 (UTC)

[edit] ile code

Can someone explain why the DNA code for ile is AT(A/C/G) when the RNA code is AU(A/C/U)? I thought RNA is complementary to DNA so shouldn't the DNA be TA(A/G/T).

Explanation: If you recall, it is the antisense (noncoding) strand of the DNA that is used as the template strand for the mRNA, meaning that the actual coding DNA strand and the mRNA produced during transcription will be identical except for the G->U nucleotides. Here's a website with a few more diagrams to help: Transcription Amasa walker III 03:48, 23 June 2006 (UTC)

[edit] Redirection

Primer extension is not the PCR reaction! It's a method used in 5'termini mapping!

[edit] nomenclature

Replaced several descriptions "ionic" bonding with hydrogen bonding. Made some other changes. Am very new at Wikipedia editing but have been doing PCR and related technologies for many years. User:Twbeals31 26 July 2006

[edit] Is it a good example of PCR elecrtrophoregram

Why to put such a bad electrophoresis gel photo in the article? It is quite noisy and really bad. There are billions around for example mine. Does this have a some significance? --Araks 13:36, 16 September 2006 (UTC)

I agree. I work in a lab as well, so I can provide a better image.--Roland Deschain 18:41, 16 September 2006 (UTC)

Ok. I've added a gel from my own research. It's reasonably clean and produces one specific band for each reaction.--Roland Deschain 19:06, 16 September 2006 (UTC)

[edit] Use in identification of pathogens

There are several infectious diseases which require the use of PCR for identification of the causative agent as alternative techniques require incubation periods which render them useless. shouldnt this be added to uses?