Talk:Restriction fragment length polymorphism

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This article is lacking moleular level details in describing riflips. more examples and relevant ideas should be given. it's a good start but much could be added.

from wikien-l

From:

Date: Mon, 26 Apr 2004 15:53:37 -0400

To: jwales at bomis.com

Subject: wikipedia and RFLP

Just a quick note to tell you that you need to have the content of the page dealing with RFLP corrected. One of my students used it as a source and found that RFLP is referred to as a property of DNA (it is a technique) and that the DNA is first usually amplified by pcr - it is NOT usually done in this manner. PLEASE check content - the page is mis-informative.

name omitted PhD

Assistant Professor of Biology

university name omitted

• The article has been changed to address what were primarily infelicities of expression rather than gross misinformation. [1] Certainly DNA displays restriction fragment length polymorphism. Is it therefore wrong to describe this polymorphism as a property? Apparently it was misleading to at least one person, probably because they are used to RFLP meaning the test rather than the property being tested for. [2] RFLP can be (and is) performed on PCR-amplified DNA but "usually" is indeed an overstatement.
  I hope that name omitted has been duly notified that we would welcome her participation in actually editing out and clarifying anything else she finds wrong or unclear! - Nunh-huh 21:57, 26 Apr 2004 (UTC)

• Oh well, I partially disagree with Dr. Omitted (though I lack a Ph.D.). It seems pretty clear from Griffiths et al An introduction to Genetic Analysis (7th edition; pp. 404-406) that RFLPs are indeed a property of DNA, or at least a property of the individual with that DNA. This textbook considers RFLPs as a kind of allele.

I just did a PubMed search for RFLP. Ignoring articles that are trying to do something better than RFLP, the first article my school has a subscription for says in Materials & Methods "Alleles were distinguished on the bases of restriction fragment length polymorphism (RFLP) using Hph1". This seems to establish RFLP as a property. However, the following sentence in an abstract of another article does make it sound more like a technique: "Between 1993 and 1998 DNA fingerprints of mycobacterial isolates from TB patients were determined by restriction fragment length polymorphism (RFLP)." I'm somewhat confused myself.

Zashaw 00:09, 27 Apr 2004 (UTC)

I think that Dr. X is just "used to" using RFLP as shorthand for the test and has forgotten that the initials actually stand for something. I hope you don't think the changes I made sidestepping the issue hurt the article! -- Nunh-huh

I agree that Dr. X was thinking about RFLP only in one context (and presumably this confused the student, who misinterpreted Dr. X's question based on our innocent Wikipedia article). I wouldn't consider myself an expert on this, but with that caveat, I did think that the sense of RFLP as a property of DNA, or something like that is a real usage and worth mentioning. What do you think of my changes to the article? I hope this is a reasonable compromise that wouldn't overly annoy Dr. X or confuse any of his/her students.

Zashaw 02:00, 27 Apr 2004 (UTC)

I think your emendation is very nice. It would be good if Dr. X provides feedback! :) - Nunh-huh 02:05, 27 Apr 2004 (UTC) (Although - sudden thought -- perhaps if we used characteristic rather than property we wouldn't evoke images of chemical property in chemistry professors?) -- Nunh-huh 02:10, 27 Apr 2004 (UTC)

Hmm. Still not quite right I think. How does this sound: "In molecular biology, the term restriction fragment length polymorphism (or RFLP) is used in two related contexts: as a characteristic of DNA molecules (arising from their differing base sequences) by which they may be distinguished, and as the laboratory technique which uses this characteristic to compare DNA molecules. The technique is utilized in genetic fingerprinting and paternity testing." ? -- Nunh-huh 01:17, 29 Apr 2004 (UTC)

I think that's awesome! Much clearer and nicer flowing than what I wrote. I've put it into the article. (I changed "base" to "nucleotide", since I think that's more specific -- change back if you disagree.) I wonder what Dr. X will think... Zashaw 02:30, 29 Apr 2004 (UTC)

Most commonly either RFLP or PCR is performed, not typically both. 165.176.123.2 (talk) 17:20, 23 January 2008 (UTC)

I believe that it may be "RFLP analysis" which many are thinking about. RFLP is just the variation that occurs. It's the analysis of that which is what I think many people are thinking of. I think "analysis" has just been dropped in regard to RFLP due to convienence. See that section below from: Web Database of Molecular Genetic Data From Fish Stocks, J Hered (2003) 94 (3): 265-267.

"The development of DNA amplification using the polymerase chain reaction (PCR) (Saiki et al. 1988) resulted in an increasing number of molecular techniques which are now being applied, such as RFLP analysis. Restriction enzymes are used to digest DNA strands at a specific location (recognition site), resulting in a number of DNA fragments. These fragments can be separated by gel electrophoresis, and differences in the pattern of the fragments between individuals are called RFLPs (Dowling et al. 1990). An RFLP may result from a base substitution that causes the gain or loss of a restriction site, or from an insertion/deletion mutation. " — Preceding unsigned comment added by 137.149.98.24 (talk) 21:26, 9 June 2011 (UTC)

I do believe it is quite common to perform PCR before doing digests. If you only did the digests, you would have very little DNA to see in the agarose gel. For the work I perform, we only perform digests of the the 16S rDNA after PCR. Generally you want more product before you want to destroy what you have for the analysis.137.149.98.24 (talk) 21:32, 9 June 2011 (UTC)

the relation to vntr???

what is the difference between RFLP and VNTR(various number tandem repeat)?

to my understaning RFLP measures the length of the dna segments after treated with restirction enzyem,

and VNTR measures the number of repeating tandemes, so shouldnt they be equal?

i mean,if the tandem repeats are the same i would think that the length of the dna segments is the same.

my only solution to this is maybe that the regions between the tandem repeats are not equal and than the length is different.

if some body could help that would be great. --M siterman 19:38, 30 May 2006 (UTC)

You are right in thinking the two terms are related: in fact, VNTRs were often detected as RFLPs by Southern hybridization, though now more usually a PCR technique is used. The term VNTR refers to the variable sequence rather than to the method used to detect it. - Nunh-huh 19:59, 30 May 2006 (UTC)

Discovery

Botstein, White, Skolnic, Davis (1980) Am. J Hum. Genet. 32(3) 314 defined RFLPs before the 1985 Jeffries citation listed currently —Preceding unsigned comment added by GCdeQR (talk • contribs) 06:46, 15 May 2009 (UTC)

Any idea if that's the first mention of it? Can we attribute its first use as a full assay to Botstein et al. in 1980? Qwerty0 (talk) 15:57, 20 September 2018 (UTC)

Oops, sorry, Botstein et al. didn't invent RFLP; they just referred to it. However, they claim that Grodzicker et al. 1974 did. Qwerty0 (talk) 16:58, 20 September 2018 (UTC)

Restriction Enzyme Site link

couldn't the red link in

... It refers to a difference between samples of homologous DNA molecules that come from differing locations of restriction enzyme sites, and to a related laboratory technique ...

actually link to restriction site?

212.126.224.100 (talk) 17:47, 21 February 2011 (UTC)

Seems like a good place for it to link to, so now it does. Thanks for pointing that out. - Nunh-huh 21:59, 21 February 2011 (UTC)

History largely missing

Like a lot of technical articles on Wikipedia, this one is spectacularly weak on history. Not just who discovered it, but when it became widely used, and when it became obsolescent. The science end of the article is great; the social end is largely absent. If anyone can supply just a few sentences charting its discovery, emergence, expanded use, and then obsolescence, that would be great. Theonemacduff (talk) 00:17, 4 November 2019 (UTC)