Talk:DNA

Firefox Crash

Article page is crashing Firefox 3.6. Something to with the images? —Preceding unsigned comment added by 183.83.183.121 (talk) 14:59, 19 October 2010 (UTC)

ARCHIVING

• I have moved 36 discussion sections to Talk:DNA/Archive 12. Anthony Appleyard (talk) 15:04, 30 April 2009 (UTC)

Two images have errors!?

Image:Benzopyrene DNA adduct 1JDG.png and Image:A-DNA, B-DNA and Z-DNA.png from DNA:

• 
  Benzopyrene DNA adduct 1JDG.png
• 
  A-DNA, B-DNA and Z-DNA.png

I removed them, but Ben (talk) reinserted them and suggested to start discussion. Maybe there is no need discussion. I just ask people who know this subject well to look into the largest version of images carefully and post findings here. I see few errors:
1) I do not see Major and minor grooves in them.
2) Second image (Benzopyrene DNA adduct ) shows hand drown and rare conformation. It may be just one person fantasy!
3) deoxyriboze is in somehow strange position in both. Compare 1B with main image they should be same.
--GODhack (talk) 15:46, 6 June 2008 (UTC)
Also here I see super-nice B form images but not GPLed:
http://www.lmb.uni-muenchen.de/groups/Biostruc/chap-08/B_dna.gif
http://www.hgs-model.com/gallery/img/4DNA-B.jpg
--GODhack (talk) 15:52, 6 June 2008 (UTC)

Those aren't as good looking - low resolution, lack a white background. Ben (talk) 16:10, 6 June 2008 (UTC)

Do you really think that good looking images with mistakes in them are better than good ones no matter how looking? --GODhack (talk) 20:30, 6 June 2008 (UTC)

No, of course not. But I don't see any mistakes. The first image is based on PDB 1JDG. Have a look at that and decide if it is accurately represented in the image here. Ben (talk) 20:48, 6 June 2008 (UTC)

The B DNA image (middle of the three) seems to be very clear with regard to the distinction between the major and minor groove. So why would you say "I do not see Major and minor grooves in them."? David D. (Talk) 21:22, 6 June 2008 (UTC)

Per David, I clearly see minor and major grooves in the second figure, though they aren't labelled and may not be as conspicuous because only a short segment of DNA is shown.

The benzopyrene adduct structure is from an NMR study of real adducts in solution (Pradhan et al. (2001) "Solution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully complementary DNA duplex: evidence for a major syn conformation." Biochemistry 40:5870-81); it is neither 'hand-drawn' nor 'fantasy'. TenOfAllTrades(talk) 22:28, 6 June 2008 (UTC)

All these images are direct representations of data published in a peer reviewed process, the references are available and may be checked if you wish. I really don't see how they may be regarded as inaccurate. As per the specific "errors":

You can easily see the major and minor grooves, look at the spacing of the phosphate backbone as you go up one side of each image.

It is a rare conformation, but it is the only published structure for that particular DNA aberration (AFAIK).

I think you are getting distracted by the different ribbon cartoon representations in the images. - Zephyris _Talk 19:55, 7 June 2008 (UTC)

As to the author of the original image, http://en.wikipedia.org/wiki/Image:A-DNA%2C_B-DNA_and_Z-DNA.png, I can assure you that it is accurate. Not only did I create the image using the "ideal" parameters for each type of DNA, I previously studied Z-DNA and have published papers on it. The image should stay. (Note that the original image I uploaded had a black background and User:Zephyris modified it to have a transparent one.) --Thorwald (talk) 03:24, 7 July 2008 (UTC)

Outsiders often make good points the wrong way, and this was an example. The article was structured to introduce the major and minor grooves without explaining these only look that way in B-DNA, then showed people a picture that contradicted this teaching. I just altered the first section on the grooves to make this clearer - hope I didn't muddy things further instead... Wnt (talk) 20:31, 23 January 2009 (UTC)

Do you know someone is selling this article on Amazon for $9.99/£6.99?

See the text of the book here [1] and read the new Wikipedia article at Filiquarian Publishing LLC--Doug Weller (talk) 11:35, 26 June 2008 (UTC) Should have added a link to a discussion on this at the help desk. [2] Doug Weller (talk) 18:50, 26 June 2008 (UTC)

Cool, glad somebody found it useful! Tim Vickers (talk) 19:44, 26 June 2008 (UTC)

thats why i no longer contribute to wikipedia; it is bad enough having amateurs trash your stuff, and having to go back and undo mistakes that are at the level of 2+2=3, but that someone takes my hardwork and makes a profit is repulsive.

Untill wiki put out some sort of no charging money rule, i won't be doing muchCinnamon colbert (talk) 01:53, 27 October 2010 (UTC)

The whole point of wikipedia is to collect and share information for re-use any way that people want, without the restrictions of "non-commercial" and such. Note that the "book" in question is also available as a free download. I wouldn't assume they're making a profit; but a sucker is born every minute, so I guess it's possible. Dicklyon (talk) 03:57, 27 October 2010 (UTC)

Appearance

Might it be a good idea to add a paragraph to the Physical and Chemical Properties section about the macroscopic physical appearance of DNA? This would help clarify the lay conception of DNA as little twisted ladders floating and interacting in empty, environmentless space as it is usually illustrated, and present it as something more concrete. I am suggesting this here because I have almost zero expertise on the subject and would feel irresponsible adding it myself. --Joseph 75.4.60.216 (talk) 03:04, 6 August 2008 (UTC)

Interesting suggestion, thank you. FYI, DNA is a white fluffy and fibrous solid (a bit like cotton wool) and a clear solution (that gets a bit gloopy at high concentrations). I'll think about how that might fit in. Tim Vickers (talk) 03:09, 6 August 2008 (UTC)

under physical chem properties, the idea of DNA as a anionic polymer, eg in gel electrophoresis, you can model DNA wiht polystyrene sulfonate.Cinnamon colbert (talk) 01:51, 27 October 2010 (UTC)

_HUGE_ problem with image

The first image gives the measurements of DNA as 3.4nm/bp. In reality it is 3.4 _Angstroms_ per bp (nm=10^-9, A=10^-10). The "width" is correct (2nm = 20A). —Preceding unsigned comment added by 128.104.119.87 (talk) 14:14, 7 August 2008 (UTC)

No, the image is correct since it says that one turn (10 bp) are 3.4 nm. --hroest 14:23, 7 August 2008 (UTC)

Agreed. —Preceding unsigned comment added by 98.26.162.210 (talk) 15:18, 16 September 2009 (UTC)

DNA isolation

This article contains no reference to DNA isolation - how it works, techniques employed etc. An article on such a subject would be appreciated. Perhaps with a paragraph linking to it on this article. The Spith (talk) 10:24, 10 October 2008 (UTC)

Added as a sentence at the start of Genetic engineering. Tim Vickers (talk) 17:31, 10 October 2008 (UTC)

I just deleted that whole section; I thouhgt the whole gen eng thing was poorly written, and since the GE article has a great lead, I just copied it. re phenol - I'm sure people somewhere still use phenol chloroform, but it is pretty rare; most people nowadays buy isolation kits from companies like qiagen, invitrogen, Sigma, etc. (use of toxic reagents like phenol is frowned upon by safety officers, phenol is a pain in the but - you have to store it frozen or it oxidizes and turns all sorts of colors, it causes severe burns, etc) eg http://www.promega.com/tbs/tm330/tm330.pdf describes a proteinase K protocol , which should take the place of phenol, which is a deproteinization reagent. anyway, isn't there a prohibition against how to do it stuff in wiki ?Cinnamon colbert (talk) 01:46, 27 October 2010 (UTC)

Terminology issue

The second paragraph of the Properties section states that "In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules." Usually (e.g. in the referenced Biochemistry book) such pair is referenced as single double stranded DNA molecule. —Preceding unsigned comment added by Ignatich (talk • contribs) 15:39, 16 October 2008 (UTC)

I know, confusing isn't it. I followed the definition here of a molecule as a set of atoms connected by covalent bonds. By that definition, which is the usual definition of a "molecule", a double helix consists of two associated molecules. I know some people do use the term "DNA molecule" a lot more loosely though. The IUBMB explains the exact terminology here, with the unit being a polynucleotide chain and multiple chains coming together in noncovalent associations. Their guide to base nomenclature (link) refers only to "double-stranded nucleic acids", which I think is the best way of referring to them routinely, since "DNA molecules" is a bit redundant, like saying "pyruvate molecules". Tim Vickers (talk) 15:46, 16 October 2008 (UTC)

I hope I am doing this right! I came across this page because one of my students plagiarized from here. DNA is - as a whole - considered a molecule (for all practical and functional purposes). So, when the article says that "consists of tightly-associated pair of molecules" it is rather misleading. Perhaps the original writer should reconsider the statement. Hroychow (talk) 23:39, 25 November 2008 (UTC)

I would not say it is misleading, rather, it is correcting a common misconception. David D. (Talk) 15:16, 17 April 2009 (UTC)

By the strict definition of a molecule used in many chemistry texts, one might consider each antiparallel chain of DNA to be an individual molecule since the complimentary strands are bound not by covalent bonds but by hydrogen bonds. This is so restrictive as to be unconventional at best and in the realm of biological sciences, unnecessarily confusing. For example, a broader definition of a molecule in the "Dictionary of Chemistry", by McGraw Hill does not restrict a molecule to having only covalent bonds. Although some texts restrict the term "molecule" to atoms covalently bonded some don't...eg., General Chemistry, Zumdah. I just reviewed a variety of cell bio and general bio texts: "The Cell", by Alberts et al, "Biology" by Arms and Camp, "Facts on File Dictionary of Biology", "Biology", Campbell and Reece; all which refer to the DNA MOLECULE being double stranded. By convention, the DNA molecule is considered as two antiparallel strands held together by hydrogen bonds. I am sure you have heard numerous times in labs when fellow scientists refer the the DNA molecule melting...(the basis of PCR). If the WIKI article on DNA wishes to split hairs and break from convention, based on the more restrictive definition of a molecule, it should clearly state the reason... otherwise it is very confusing. Also, the citation of the Watson and Crick seminal paper in this regard is peculiar since it does not address anywhere that the DNA exists in living organisms as separate molecules. The paper proposes "A" structure for the "salt of deoxyribose nucleic acid..." They describe what is now known as the 'B" form.

Medicuspetrus (talk) 19:27, 12 August 2009 (UTC)

Just a note. The article states a that adenine...is a nucleotide. It is NOT...it is a nucleotide base. Medicuspetrus (talk) 13:31, 12 August 2009 (UTC)MedicusPetrus

I think the problem is that the word "molecule" is most useful for things like benzene and water; for things as large as DNA it isn't really precise; eg, almost any real chromosome probably has, at any one time, numerous strand breaks or nicks. Rather then get bogged down in a pedantic discussion of what a molecule is and the role of covalent and noncovalent forces (the conformational changes in prions as an example of semipermanent noncovalent changes) the central idea has to be of two chains that are complementary with base pairing - that is really the important thing; everything else stems from tht (eg sugar pucker - surely something a wiki level article doesn't need to ref, there a good book by bloomfield/carothers/tinocco about this...)

I think what conveys the right idea is to talk about two strands that are nominally a single molecule by the standard of covalent bondsCinnamon colbert (talk) 01:39, 27 October 2010 (UTC)

Sugar pucker

Searching for 'sugar pucker' leads to this article, but then doesn't appear to be covered in the article. Is it possible to get a page or section for this topic? —Preceding unsigned comment added by 134.36.68.234 (talk) 00:12, 20 October 2008 (UTC)

What an odd redirect. As far as I know that is a reference to conformational isomerism in sugars. Cyclohexane conformation seems the only article that comes close to this topic and it isn't really all that relevant to DNA (as far as I know). Tim Vickers (talk) 16:17, 20 October 2008 (UTC)

See [3] - whichever one carbon in the five-membered ring of the backbone sugars is left out of the plane (the "pucker"), controls whether DNA is in the A or B form. Wnt (talk) 20:11, 23 January 2009 (UTC)

I have removed the redirect and have instead written a very short note explaining the change. Aaronstonedd (talk) 16:09, 14 April 2010 (UTC)

I have reinstated the redirect, you can't just put a note that creates a dead-end. If you want to redirect it elsewhere that is fine, but if it isn't a redirect then it needs to be an article. - Ahunt (talk) 16:36, 14 April 2010 (UTC)

I think A-DNA is a better target, so I have redirected it there instead. - Ahunt (talk) 16:39, 14 April 2010 (UTC)

DNA Polymerase

In the section Labeled Polymerases it states, "Consequently, all polymerases work in a 5′ to 3′ direction.[82]" this is an inaccurate quote for the source. Most DNA polymerases work in the 3' - 5' direction. This part should be edited so as not to confuse new biology students

Ezendl1 (talk) 02:43, 11 November 2008 (UTC)ezendl1

• The article is correct. Are you confusing polymerase with nuclease activity? Graham Colm ^Talk 13:35, 11 November 2008 (UTC)

Polymerases add nucleotides onto the free 3' hydroxyl group of a DNA strand, this extends the chain at the 3' end, but in the 5'-3' direction. Tim Vickers (talk) 17:05, 11 November 2008 (UTC)

The problem appears to be that Ezendl1 is referring to the template direction not the new DNA direction. The normal way to describe the direction of the polymerase is with respect to the activity, in this case polymerisation, so 5' to 3' direction is correct. Possibly the quoted sentence above could include the word polymerisation just to ensure the context of "work" is clear? David D. (Talk) 20:49, 26 November 2008 (UTC)

• Many of my text books agree with Ezendl1, they anchor to the template strand and move in the 3’-5’ direction while synthesising new strands in the 5’-3’ direction starting on a primer. This often confuses many biology students, I would recommend new wording instead of “work in 5’-3’”; maybe it should say “synthesise in a 5’-3’ direction”. It should also be noted polymerase III and I can have 3’-5’ exonuclease activity. anon 6:45 Oct 13 2010

This is a problem of long standing; after 20 years I still get confused. The only way to really clear it up is to understand that 5' triphosphates get added to 3' hydroxys, with cleavage of PPi providing a lot of the deltaG

To, Polymerases act by catalyzing the addition of a 5' monophosphate group to the 3' hydroxy group of the primer. This is referred to as 5' to 3' synthesis, since the growing chain grows toward the 3' directionCinnamon colbert (talk) —Preceding undated comment added 01:34, 27 October 2010 (UTC).

Ridiculously pedantic symmetry question

The article on symmetry says that DNA is an example of a non-repeating helical symmetry in which "the angle of rotation θ required to observe the symmetry is an irrational number such as ${\sqrt {2}}$ radians that never repeats exactly no matter how many times the helix is rotated."

Now I understand, of course, that the pitch of real DNA will vary vastly according to the cellular environment, not just binding proteins but just salt concentrations, and at least a little according to the base pair composition, and that it will also vary moment to moment because of thermal fluctuations, so this is an absurd point, but even so...

Is there a physical force that should bring a hypothetical isolated strand of DNA at rest in the vacuum into one or more n-fold helical symmetries, rather than a non-repeating symmetry?

For example, some sort of resonance stabilization that allows transmission of vibrational modes along the helix, or interactions between virtual emissions in the radio spectrum along the axis...? Wnt (talk) 20:06, 23 January 2009 (UTC)

I have absolutely no idea. Even the idea of "non-repeating symmetry" seems self-contradictory to me. We need a crystallographer. Tim Vickers (talk) 20:13, 23 January 2009 (UTC)

I had a look at PMID 10884351, the question of whether or not B-DNA has a symmetry axis running the length of the helix seems much more complicated than you'd reasonably expect. The answer appears to be "sometimes" but perhaps only with palindromic sequences. Tim Vickers (talk) 20:30, 23 January 2009 (UTC)

Thanks for looking - alas, I can't go over that from here. But even if a crystal structure doesn't appear periodic, that may only mean that under the real-world conditions of the crystal there were a range of different periodic forms present. fter all, if you do a poor enough job of crystallizing a compound everything has non-repeating symmetry. ;) Also, they say in the abstract that the crystal packing conditions matter, but my original curiosity was whether a [double helix] of DNA in isolation would be non-repeating, not whether a crystal of it would be. Really, I'm more curious about what long-range forces could impose an n-fold symmetry onto DNA over long distances. Wnt (talk) 20:54, 23 January 2009 (UTC)

Thinking about it, the physiological instance might actually be simpler, since an isolated DNA strand will not be a straight rod, so will not have simple helical symmetry. Tim Vickers (talk) 21:40, 23 January 2009 (UTC)

Oops - I didn't literally mean single stranded DNA, sorry! (Though that's another question...) I meant to say, a single isolated double helix, which stretched in vacuum over a hypothetical infinite distance (and provided with regularly spaced ions to neutralize charge) would seem like the simplest case. Wnt (talk) 19:39, 28 January 2009 (UTC)

RNA

RNA and DNA are similar structures. DNA is a single stranded molecule while RNA is double stranded. They are in no other ways different —Preceding unsigned comment added by 71.120.67.202 (talk) 21:36, 2 February 2009 (UTC)

Not really true. There are chemical differences between the bases and sugars. Both DNA and RNA can exist as single and double-stranded forms. In bacteria, archaea and eukaryotes, the genome is double-stranded DNA, while RNAs such as mRNA is single-stranded. However, viral genomes can be single-stranded DNA, double-stranded DNA, single-stranded RNA or double-stranded RNA, so the answer is not a simple one. Tim Vickers (talk) 22:32, 2 February 2009 (UTC)

Include a section on metaphorical uses?

• Hi there, I removed this section I'm afraid, since in the overall view of DNA noting its use as a metaphor isn't really important enough to be noted in the main article on this molecule. Tim Vickers (talk) 22:31, 16 February 2009 (UTC) (copied from User talk:Anthony Appleyard (Anthony Appleyard (talk) 07:23, 17 February 2009 (UTC)))
• Section restored so people can see it to discuss it here. Anthony Appleyard (talk) 07:24, 17 February 2009 (UTC)

Are there any sources that discuss the metaphorical use of "DNA"? At present this is original synthesis, since all you have cited is an example. To keep this we would need a source that tells us that this usage is both common and important. Tim Vickers (talk) 16:22, 17 February 2009 (UTC)

I ask since if there are no sources that discuss a topic, we can't include it in this article. Tim Vickers (talk) 22:41, 18 February 2009 (UTC)

Without sources this addition compromises the integrity of an FA. The addition of edits that lack a reliable source often results in WP:FAR. It is an essential part of managing an FA that unsourced edits are reverted. Sorry, but IMHO this section, as it stands, spoils the article and should be removed. Graham. Graham Colm ^Talk 23:18, 18 February 2009 (UTC)

• This section is directly verifiable by reading the publication mentioned in the ref in the section. Anthony Appleyard (talk) 23:58, 18 February 2009 (UTC)

Once again. Do you have any sources that discuss this metaphorical use of the term "DNA" as their subject? Tim Vickers (talk) 00:02, 19 February 2009 (UTC)

• OK, OK, leave it out, anything for a quiet life. Anthony Appleyard (talk) 00:05, 19 February 2009 (UTC)

Animation

Could somebody please take out the "Large version" link. It is unnecessarily self-referential annoying since it has been translated into other articles on DNA in other languages (and the reference saying "Created from PDB 1D65" should also be deleted because it is also useless.)98.166.139.216 (talk) 22:57, 20 February 2009 (UTC)

I removed the secondary link, but I think we need the reference, to credit the people who solved the structure. Tim Vickers (talk) 23:18, 20 February 2009 (UTC)

History section

I find the history section is lacking. The story stops around 1960. What happened after? 222.64.113.175 (talk) 03:34, 10 April 2009 (UTC)

Oxidative DNA damage

I just read a minireview from 1997, estimating the number of oxidative lesions in the DNA (per human cell) to about 1,5x 10⁵ and not 500 as it says here. If you want a update the review is by Beckman and Ames; Oxidative decay of DNA, J biol chemistry, 1997. Sniffe35 (talk) 07:55, 26 April 2009 (UTC)

Thank you, a much better citation! Tim Vickers (talk) 15:17, 26 April 2009 (UTC)

DNA lock up ?

RE: ``DNA reference "Hi there, I'm afraid Google searches aren't good references as the results can change over time. If there was something in the DNA article that you think needs more references I'd be happy to try to find something else. All the best" Tim Vickers (talk) 15:47, 3 May 2009 (UTC)

---

Hello, Tim. I 'm also afraid that the current DNA article version has a basic flaw in the over-simplified presentation of A-DNA structure and B-DNA configurations in regards to the interpretation of the corresponding X-ray patterns. This could have been corrected by adding relevant references of published papers that however is being prevented by the over-protection of this entry through locking up the editing. At the very least a new section could be added up that allows the correction of this basic flaw which places in doubt the scientific value of ``comparisons" between A-DNA and what is commonly still called the `B-DNA' configuration set. Furthermore, there are several factual errors also about the conditions under which A-DNA X-ray diffraction patterns have been generated, not to mention the lack of adequate credit to the experimenters involved. For an improved entry such comments with the introduction of the appropriate literature references should help. Cheers. Bci2 (talk) 10:27, 4 May 2009 (UTC).

Not sure what you mean by over-protection? Are you saying there are IP editors you know that want to contribute that cannot? If that is they case then tell them to go ahead as i have unlocked it for now on a trial basis. David D. (Talk) 15:40, 4 May 2009 (UTC)

Yes, that is precisely what I meant, and thank you for the temporary access. Bci2 (talk) 11:27, 4 May 2009 (UTC) WP:PHYS.

The article on Mechanical properties of DNA could also do with some work, and would be a good place to add a detailed discussion of the different forms of the helix. In an article such as this, which tries to give a broad non-technical overview to a general audience, some simplification is necessary. Tim Vickers (talk) 16:28, 4 May 2009 (UTC)

As a comment this edit seems to me to be a little too complex for our intended audience (which is roughly at a high-school level) and uses technical terms without defining or linking them. Tim Vickers (talk) 16:41, 4 May 2009 (UTC)

The facts presented in the edited version contradict the previous statement made above: all the technical terms employed by the editing are referenced by the most appropriate in line cited references; furthermore, incorrect over-simplifications or even omission of key facts are not acceptable alternatives for any form of scientific presentations, whatever its level it may have. One notes also the glaring inconsistency of the above comment "DNA&diff=prev&oldid=287869950" with the previously made, explicit request by the same user (TV) for help (in this DNA entry) by a crystallographer: " have absolutely no idea... We need a crystallographer", that he duly acquired. Moreover, the level and concepts are both related and similar to those further explained in the related and relevant Wikpipedia entry cited at the beginning of this subsection under {{Further information: Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid }}. Not surprisingly this further information was ommitted in previous versions of "DNA" that were locked up and thus could not be suitably edited earlier. Bci2 (talk) 1:37, 4 May 2009 (UTC) WP:PHYS.

You write: "Not surprisingly this further information was ommitted in previous versions of "DNA" that were locked up and thus could not be suitably edited earlier.". I'm a little confused here. Are you saying you could not edit before? And if not, why couldn't other users register an account to edit? It's actually more anonymous than editing with an IP account. David D. (Talk) 19:15, 4 May 2009 (UTC)

Prior to the access you have kindly provided to this "DNA" Wikipedia entry I have attempted to edit this specific subsection on the X-ray structure of DNA forms, and also to provide the much needed/appropriate in line references pertinent to this important discovery, and was unable to do so because the DNA file was locked up, as you already know. Furthermore, my account has been registered for quite awhile, and this was still the case as correctly pointed out above when I attempted for the first time to edit this DNA entry and was blocked from doing it; the DNA entry also had a lock up sign on it at the top of the page that has now disappeared. Bci2 (talk) 1:37, 4 May 2009 (UTC) WP:PHYS.

But you made an edit on May 3rd with no problem? Nothing had changed since that edit. Are you sure you were logged in when you tried to edit? David D. (Talk) 19:46, 4 May 2009 (UTC)

Perhaps he means, when he says "blocked from doing it", that I reverted the addition of a Google search as a reference? Bci2, were you unable to edit the text, or did you make an edit that was later reverted? Tim Vickers (talk) 19:54, 4 May 2009 (UTC)

I described exactly what I saw: having made the editing/ addition of only one reference to this subsection of DNA structure from X-ray studies--when I immediately saved my editing, the text was left completely unchanged. The reference was not inserted either in the text or in the coded page when I checked it. What else would you conclude but that the editing was completely blocked, or locked up? And,Yes, I was logged in because I could see my id at the top of my user page! Thus, the facts/observations do not support at all the idea that the editing was "later" reverted; that is, later when?-- within a fraction of a second?? The records do not support that hypothesis.Bci2 (talk) 1:37, 4 May 2009 (UTC) WP:PHYS.

Tim reverted your addition over ten hours later, so I'm not sure why you would not have seen the addition. Certainly you were not blocked from editing and the article was not locked, except for users editing from IP's addresses or from new accounts. Your addition can still be seen as ref 127 in the history. Can you see that? David D. (Talk) 20:23, 4 May 2009 (UTC)

Actually, in retrospect, it would appear you are describing a different edit since you are explicit that it was in the X-ray section (not the history section). In that case I would suggest you hit preview by mistake, instead of save. I have done that erroneously in the past. David D. (Talk) 20:32, 4 May 2009 (UTC)

The alternative might be that two users attempted to edit at the same time the entry, as it happened just now twice when I was trying to reply to David's message--this is the third attempt to save my reply, as the previous two were unsuccessful because of an "Edit Talk conflict"Bci2(talk) 3:37, 4 May 2009 (UTC) WP:PHYS.

Also possible. David D. (Talk) 20:57, 4 May 2009 (UTC)

"All is well when it ends well" Great Will. Bci2(talk) 5:40, 4 May 2009 (UTC)

How is B DNA form determined?

Currently there is a line that says that the analysis of the x-ray diffraction data "requires a different approach from that of the standard analysis by Fourier transforms of Bessel functions". Even before I started moving things around it was not clear to me what the alternate methodology is. Have i missunderstood or was it never mentioned?

Then of course we have the issue of whether this article should be getting into the mathematical methods of interpreting the x-ray data. Should we be a little more general and just give the gist of what the spots mean i.e. something about determining the pitch, base repeat distance? David D. (Talk) 05:31, 5 May 2009 (UTC)

OK, I've made a whole bunch of changes to try and make it more understandable from my perspective. Is the point about the B-DNA x-ray diffraction data that it is harder to get an accurate structure or that different methodology is required to determine an accurate structure? I now think the former, from reading the references, so please check that what I have written in the text and figure legend makes sense. David D. (Talk) 06:15, 5 May 2009 (UTC)

Appreciate many of the improvements that you've made David D. , but the one about `tractability'--which had an opposite meaning/was inconsistent with the inline relevant references now provided. Have therefore modified the sentence in question so that it clarifies even further the magnitude of the problem: the treatments of the two DNA forms of X-ray diffraction for A-DNA, and respectively, X-ray pattern for B-DNA need to be quite different. Thus, the analysis of the B-DNA X-ray pattern requires a paracrystal model to quantitate the results from the X-ray pattern whereas the A-DNA X-ray diffraction pattern does not require such a paracrystalline lattice model because of the very high degree of crystallinity actually present in the samples of highly oriented/parallel A-DNA fibers produced by Dr. R. Franklin in the early 50's. Neither Wilkins et al (1953) nor Watson and Crick ever produced at any time prior to their Nobel prize (or perhaps even after) such a sample of very high degree of crystallinity of A-DNA as Dr. R. Franklin did --who was a very experienced crystallographer and careful physical chemist-- in spite of her youth at the time when she produced the very high-quality A-DNA x-ray diffraction pattern shown in the visible image that I inserted on this page. Unfortunately, she died before she could be awarded the Nobel prize. With hindsight, the Nobel Committee should have perhaps hurried up the award while she was still with us, if they could have--which we do not yet know. Bci2. (Talk) 09:05, 5 May 2009 (UTC)

I just saw this comment after making a few more changes to try and stream line the text. I don't have time to digest this comment right now but will come back. Bare in mind my last few edits did not take any of this comment into account. David D. (Talk) 14:10, 5 May 2009 (UTC)

Some of this content needs to be moved to the newly-titled article on DNA structure. Tim Vickers (talk) 14:54, 5 May 2009 (UTC)

Bci2, I'm confused, your edit here seems to contradict what you say above. i thought the whole point here is that the A and Z form do not require modeling too? David D. (Talk) 15:06, 5 May 2009 (UTC)

The analysis of high-quality A-DNA X-ray diffraction patterns does not usually require paracrystal models but the analysis still involves the much simpler, single double-helix DNA molecular model as Watson and Crick proposed in 1953.Bci2.(Talk) 12:00, 5 May 2009 (UTC)

Hi, Tim: Sounds like a great idea-- why didn't I think of it (rhetorical quaestion!). Will add the required explanation as my time permits, as it involves a lot more referencing and explanation, but it is obviously of the essence. You are correct--the interests of science are best served by cooperation, as everyone stands to benefit from it. I'm glad that you see the point of the X-ray patterns comparison that I was initially trying to introduce in the DNA entry. Until we have the more complete story I am however suggesting that we should keep the minimal explanation in place so that new readers are not being misled by the 50 year old literature.Bci2 (talk) 12:37, 5 May 2009 (UTC).

Tim: I've run again into the "Edit conflict error" on your website talk as you were writing at the same time a second message before I had a chance to answer your previous one. Have thus lost my reply to you that I am trying to regenerate here. Bci2 (talk) 12:37, 5 May 2009 (UTC).

In cases where you get an edit clash you can save your text by using the back button and then copy it from the edit screen. David D. (Talk) 18:14, 5 May 2009 (UTC)

I've tried that several times and it doesn't work; I've just lost the addition to this message because of your writing at the same time as I am adding to my previous message.Nu 18:17, 5 May 2009 (UTC)Bci2 (talk) 12:37, 5 May 2009 (UTC).

Another useful habit is to press Ctrl+A, Ctrl+C (select all, copy) before clicking any buttons. On most systems, you then have a backup in the clipboard if disaster strikes. Also, when an edit conflict occurs, if you scroll down, you should see your text where you can copy it out. Johnuniq (talk) 01:33, 6 May 2009 (UTC)

one way to avoid this quesion is to cite high quality NMR structures.Cinnamon colbert (talk) 01:48, 27 October 2010 (UTC)

History of DNA research

"In 1953 James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature[6]. Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as "Photo 51")[135] taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases were paired--also obtained through private communications from Erwin Chargaff[136][137][138][139][140][141] in the previous years. According to James Watson, after they had figured out the structure of DNA on February 28, 1953, he and Francis Crick walked into the Eagle pub in Cambridge, England and Crick announced.. "We have found the secret of Life." [142]"

Unfortunately the above paragraph perpetuates the apparent myth of 'We have found the secret of life' and to make matters worse puts the apparent quotation into bold, which needs to be reverted.

There is in fact NO reliable record of Francis Crick having said this; in Francis Crick's 1988 autobiography, he said of this event: "According to Jim, I went into the Eagle, the pub accross the road where we lunched every day, and told everyone that we'd discovered the secret of life. Of that, I've no recollection, but I do recall going home and telling Odile that we seemed to have made a big discovery." (Page 77, "What Mad Pursuit", Chapter 6, "How to live with a Golden Helix".)

However James Watson said (quote) "Francis winged into The Eagle to tell everyone within hearing distance that we had found the secret of life." (Page 111, Chapter 26, "The Double Helix)".

Why does this quotation from James Watson need to be taken with the proverbial 'pinch of salt'? The fact that the person said to have made the statement could not remember having said it! In his "book genes, girls, and gamow", James Watson states (quote): "During my absence, the first newspaper article that reflected an interview with Francis Crick came out. It was in the Sunday Telegraph and reached a large audience." (from page 21, Chapter 4: Cambridge July-August 1953.)

The only problem being that the Sunday Telegraph did NOT exist in 1953, and repeated searches of the newspaper archives have NOT found any trace of such an article, with a Crick interview!

So Watson may not be an entirely reliable source for this quotation, even when repeated by the BBC; I suggest that the text and the BBC reference need to be qualified to reflect the above?

91.110.218.146 (talk) 12:13, 10 May 2009 (UTC) Martin Packer

Thanks for the comments Martin. That sentence is a recent addition to this article, so I've removed it for now. Tim Vickers (talk) 15:35, 10 May 2009 (UTC)

Thanks Tim, I don't doubt that something was 'said' that Saturday afternoon in The Eagle - but I suspect that Watson was referring to Crick's booming voice inadvertently broadcasting the good news of the discovery rather than him making a specific announcement to all and sundry within hearing distance. (Their lunch incidentally was either the shepherd's pie or sausage & beans!) There is some humour in the use of the words "winged into The Eagle" in my opinion.

The first national newspaper coverage was in an article in "The News Chronicle" by Ritchie Calder on Friday, May 15, 1953 - which was followed by "Varsity" newspaper on Saturday, May 30th, 1953. The first American coverage was on Saturday, June 13, 1953 in The New York Times, see: http://www.nytimes.com/packages/pdf/science/dna-article.pdf - for a lot more information.

My request for any assistance at all with the mysterious Sunday newspaper article from June 1953 ("During my absence, the first newspaper article that reflected an interview with Francis Crick came out. It was in the Sunday Telegraph and reached a large audience.") is entirely serious, and hopefully we may get an answer from Jim Watson at Cold Spring Harbor Laboratory!

91.110.183.238 (talk) 16:17, 10 May 2009 (UTC) Martin Packer

It is an interesting question, but since this article tries to provide a broad and general overview of the topic, I'm sceptical as to if this anecdote is really important enough to be mentioned. The article seems no worse off for omitting this factoid! Tim Vickers (talk) 16:30, 10 May 2009 (UTC)

Tim,

http://www.nytimes.com/packages/pdf/science/dna-article.pdf - has been added to External Links; can I leave you to add "The first national newspaper coverage was in an article in "The News Chronicle" by Ritchie Calder on Friday, May 15, 1953 - which was followed by "Varsity" newspaper on Saturday, May 30th, 1953." to the text of the article? Thanks a lot, Martin

Nitramrekcap (talk) 18:26, 10 May 2009 (UTC)

Tim,

I have added the following chronology to the DNA, FRANCIS CRICK, and JAMES WATSON articles:

"The discovery was made on February 28, 1953; the first Watson/Crick paper appeared in Nature on April 25,1953. Sir Lawrence Bragg, the director of the Cavendish Laboratory, where Dr. Watson and Dr. Crick did their work, gave a talk in London on Thursday, May 14, 1953 which occasioned an article in The News Chronicle of London, on Friday, May 15, 1953. The news reached readers of The New York Times the next day; Victor K. McElheny, in researching his biography, "Watson and DNA: Making a Scientific Revolution," found a clipping of a six-paragraph New York Times article written from London and dated May 16, 1953 with the headline "Form of `Life Unit' in Cell Is Scanned." The article ran in an early edition and was then pulled to make space for news deemed more important.(The New York Times subsequently ran a longer article on June 12, 1953.) The Cambridge University undergraduate newspaper also ran its own short article on the discovery on Saturday, May 30th, 1953."

Unfortunately in his "Watson and DNA: Making a Scientific Revolution", Victor K. McElheny quoted Watson's dubious reference the "Sunday Telegraph" (June 1953) rather than mentionning the NYT story of May 16, 1953 - the former did not exist, while the latter definately did!

Nitramrekcap (talk) 19:56, 10 May 2009 (UTC)

Tim,

Unless we do discover the mysterious Sunday newspaper of June 1953, this is the final version of the timeline for newspapers reporting the discovery of the structure of DNA in May 1953!

"The discovery was made on February 28, 1953; the first Watson/Crick paper appeared in Nature on April 25,1953. Sir Lawrence Bragg, the director of the Cavendish Laboratory, where Dr. Watson and Dr. Crick did their work, gave a talk at Guy’s Hospital Medical School in London on Thursday, May 14, 1953 which occasioned an article by Ritchie Calder in The News Chronicle of London, on Friday, May 15, 1953, entitled "Why You Are You. Nearer Secret of Life." The news reached readers of The New York Times the next day; Victor K. McElheny, in researching his biography, "Watson and DNA: Making a Scientific Revolution", found a clipping of a six-paragraph New York Times article written from London and dated May 16, 1953 with the headline "Form of `Life Unit' in Cell Is Scanned." The article ran in an early edition and was then pulled to make space for news deemed more important.(The New York Times subsequently ran a longer article on June 12, 1953). The Cambridge University undergraduate newspaper also ran its own short article on the discovery on Saturday, May 30th, 1953. Bragg's original announcement at a Solvay conference on proteins in Belgium on 8 April 1953 went unreported by the press!"

Martin

ps I find the Wikipedia article on James D. Watson rather poor - are you going to improve it? —Preceding unsigned comment added by 91.110.174.188 (talk) 20:56, 10 May 2009 (UTC)

OK, well thank you for providing those sources. As to the James Watson article, no I don't tend to work on biographies, and I'm still spending most of my time dealing with the tail-end of the swine flu "crisis" on that and related articles. Tim Vickers (talk) 21:16, 10 May 2009 (UTC)

That timeline was a bit too detailed for this general article, so I've moved it to History_of_molecular_biology#Complementary_nucleotides. Tim Vickers (talk) 21:20, 10 May 2009 (UTC)

Tim, you're the scientist and I am not (just an enthusiastic amateur with a son who is an MSci, Cantab. and a daughter who is going onto a PhD later this year) but I could have sworn that a timeline about the newspaper coverage of the discovery of the structure of D.N.A. was relevant to an article 'supposedly' about D.N.A.; as you can gather from my non too subtle attempt at sarcasm, I think this "bit too detailed" information should have stayed in the D.N.A. article! Never mind the fact that this is the first time the timeline has appeared on t'internet!! What about re-instating it in an edited form, without too much detail?

Nitramrekcap (talk) 22:03, 10 May 2009 (UTC)

It all depends on the emphasis of the article. To date this one has not really focused on the history/politics part but rather on the biological perspective. There are quite a few companion articles that would be suitable to such a timeline though. David D. (Talk) 15:14, 15 May 2009 (UTC)

WHY NO MAURICE WILKINS IMAGE IN THIS ARTICLE ON D.N.A.?

File:JamesDWatson.jpg

James Watson

Francis Crick

So why does Maurice Wilkins not get his image in this article? After all, he only shared the 1962 Nobel Prize for Physiology or Medicine with Crick and Watson? His autobiography is not included either! Is the late Professor Wilkins being edited out of 'Wiki' DNA history? RSVP!

|image =maurice_wilkins.jpg |image_width = 200px |caption = Maurice Wilkins

Nitramrekcap (talk) 22:26, 10 May 2009 (UTC)

M. F. Wilkins, Erwin Chargaff and Raymond Gosling's photos added

Not only Professor Wilkins's photo should be present but also

Professor Raymond Gosling's, Erwin Chargaff's, as well as the photos of Herbert Wilson. F.R.S. and Alex Stokes should also be present; however, the latter two were unavailable at this point for Wikipedia use, and if made available it is important that they also should be added because of their very important role played in the X-ray+molecular modeling analysis of DNA saga. Bci2 (talk) 4:26, 15 May 2009 (UTC)

Nobel rules?

The following sentence:

"Unfortunately, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.[141]''"

Implies that the Nobel prize now allows posthumous prizes. Is this actually the case? If not the sentence probably needs to be changed. David D. (Talk) 04:12, 22 May 2009 (UTC)

DNA

I think that the word "easter" in the text about DNA should be replaced with the word "phosphodiester". This is because (as I have learned) "easter bonds" or "easter linkages" are related to lipids and that the nucleotides are polymerized through phosphodiester bonds/linkages

The title is "DNA"

The text I am talking about sais that the back bones of DNA molecule that are made of sugare and phosphate groups are joined by ester bonds. Livinghappy (talk) 17:57, 29 May 2009 (UTC)

Could you copy and paste the sentence you think needs changed? I can't work out which part of the article you are talking about. Tim Vickers (talk) 18:02, 29 May 2009 (UTC)

Sure, here it is:

Title is: "DNA"

"Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds."

I have learned that DNA is polymerisation is done through phosphodiester bonds and not ester bonds. Ester bonds are the one that happen at lipids. --Livinghappy (talk) 18:19, 29 May 2009 (UTC)

They're both examples of ester bonds. David D. (Talk) 18:23, 29 May 2009 (UTC)

DNA

Ok, than sory! ;-) --Livinghappy (talk) 18:31, 29 May 2009 (UTC)

dsDNA and other acronyms

dsDNA is referenced in other articles (Prokaryotic_DNA_replication for example) but not explained here. A section describing the various acronyms used might be useful. dsDNA, sRNA, scDNA, nDNA, ... Cghislai (talk) 14:04, 1 June 2009 (UTC)

Link to Backbone chain

It would be useful if at least the first reference to the backbone of DNA was linked to Backbone chain. Backbone chain needs to be expanded and linking to it may encourage expansion. I cannot edit this semi-protected page. Daniel.dalegowski (talk) 21:36, 13 June 2009 (UTC)

Hmm... Y Done. It does need expansion, though—it's a one-line stub at the moment. Fvasconcellos (t·c) 21:58, 13 June 2009 (UTC)

Inaccuracy in statement about Chromosome shape

The sentence "Within cells, DNA is organized into X-shaped structures called chromosomes." is misleading, as it suggest *all* chromosomes are X-shaped. In the case of telocentric chromosomes, this is not the case.Bowenthebeard (talk) 18:35, 26 June 2009 (UTC)

Bahh even more misleading. Chromosomes are only X-shaped for a brief while right before cells divide. The well known X-shape is actually two copies of the same chromosome stuck together in the center at the centromere. When the cell divides, the X-shaped structure splits into the two individual straight chromosomes, and one goes to each daughter cell. See wikipedia article on mitosis.--66.27.75.3 (talk) 03:58, 7 August 2009 (UTC)

That detail isn't needed in the lead, and anyway does not apply to most organisms, eg bacteria and archaea. Tim Vickers (talk) 16:44, 7 August 2009 (UTC)

Agreed. Maybe something along these lines would be more appropriate in the chromosome article, but I think that level of detail is out of place here. – ClockworkSoul 20:03, 7 August 2009 (UTC)

Permanent protection from IPs

Is it really necessary on this article? The IP activity did not look too bad, and I would like to edit the text some, but not by posting here. Can the semi-protection be removed? --69.226.103.13 (talk) 07:29, 29 June 2009 (UTC)

The article appears to have indefinite protection at the moment, since 8 May 2009. I imagine that this article is very widely referenced in schools all around the world. When a bunch of bored kids are directed to come here, it is quite likely that time-wasting vandalism occurs. I understand and respect how many people (many academics?) resist getting an account, but it's not so bad. Johnuniq (talk) 10:08, 29 June 2009 (UTC)

I see the indefinite protection, Johnuniq, I'm asking for specifics as to is it necessary still.

I'm not resisting getting an account, I won't get one. I've had an account, and I've been the target of how wikipedia treats new editors. I czn edit as an IP and make a positive contribution or I don't edit at all, because as harsh as attacks against IPs are (look at the edit summary in the protection post), they're small compared to attacks against newcomers. --69.226.103.13 (talk) 15:30, 29 June 2009 (UTC)

Correction

MINOR SUGGESTIONS: I would recommend 2 slight changes. In the first, I would suggest inserting "deoxyribose" in front of the word "sugars" in the description of the general structure of DNA (Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds.) In addition, nucleotides consist of more than bases. I would suggest revising the following sentence: " These nucleotides are adenine (A), guanine (G), cytosine (C) and thymine (T)." Instead you need to state that nucleotides consist of 1 to 3 phosphate groups, a deoxyribose sugar, and one of four bases: adenine (A), guanine (G), cytosine (C), or thymine (T).Gudelskj (talk) 00:27, 3 August 2009 (UTC) Gudelskj,8/2/2009

I've cut the redundant parts of that section and reworded it a little. Tim Vickers (talk) 16:40, 12 August 2009 (UTC)

DNA is not like a blueprint

In the introduction section it says, "DNA is often compared to a set of blueprints, or a recipe, or a code..." This is incorrect because DNA is not like a set of blueprints. If it is often compared to that then it must be cited who says it, and it should be from reputable sources (i.e. scientists that work with DNA). Richard Dawkins has stated several times in several different books that DNA is not like a blueprint. For example he states this is in The Ancestor's Tale, The God Delusion, and A Devil's Chaplin. He and others do agree that it is like a recipe, computer code (like binary language), or a toolbox of computer subroutines.

I will give it a little time for someone else to make the change or I'll change it to reflect my previous sentence. I hope that someone might be able to write it a little more eloquently than me.

XXVII (talk) 05:40, 27 August 2009 (UTC)

How about this source: [4] or this one. GoEThe (talk) 13:38, 27 August 2009 (UTC)

Whether or not you agree with the comparison, the comparison is (as the text says) often made. This statement about what people often say is a fact. Tim Vickers (talk) 16:13, 27 August 2009 (UTC)

You really are over reacting to a helpful metaphor. At an advanced level, an instructor can have the kind of discussion with students about A,G,C and T, and how the genetic code is very simple, very lengthy and yet effective. But that does NOT remove the effectiveness of the "blueprint" metaphor. To a newer student, explaining DNA as a blueprint is good enough. It helps him or her understand the basic function, which they may learn in increasing complexity over time. —Preceding unsigned comment added by 69.20.169.7 (talk) 04:19, 8 October 2009 (UTC)

Richard Dawkins doesn't like the term "blueprint" because a "blueprint" implies that there must have been a designer. Richard Dawkins will likely go to his grave shaking his fist at such a "ridiculous" concept. —Preceding unsigned comment added by 24.152.155.87 (talk) 20:07, 29 October 2009 (UTC)

DNA as a blueprint is a misleading metaphor, that should be clarified

DNA is not a program. It is not even know how a protein gets its tertiary or quaternary structure. DNA just code the aminoacid sequence of a protein, and no more.

The problem of the comparison goes in more important conceptual scientific issues that those fanatic ideas in which just some religious fundamentalists are obsessed with intelligent design.

The main problem is that it oversimplifies the notion of life. A living organism is not the realization of blueprints coded in DNA. There is more than that in the development process. Epigenetic issues are often neglected, that factors are as important as the genetic ones. What kind of factors? well, many I should say, like the coordination between proteins and other molecules in the cell. The comunications between cells. The diffusion rates of messages, metabolic molecules and other factors in the physical environment.

When someone talks about blueprints, is adopting a preformationist position, line that sketched in the famous homunculus picture. It puts the discussion of vitalism vs. preformationism in the table.

Researchers in developmental biology, take into account both sources genes and physical factors.

For that reason I do not agree with the person who said that it is an over reaction for a helpful metaphor, because this metaphor just leads to a complete wrong idea of how the thinks work. DNA does not look like a computer program, maybe just as data to build some proteins self organized in metabolic, signaling, ..., pathways machines. Why? because the physical-chemical environment allows and even cast them to interact in such way and they survived to many oddities, being able to be replicated and inherited to descendants or transfered to other organisms (by horizontal transference, for example).

The problem is very complex, in the sense of non-linear systems. Where the behavior of the whole system is not explained just by the isolated behavior of their parts. That is a common place in science, but a not deeply understood issue for many scientists.

As you can see, this issue goes further that just the obsession of Dawkins against pseudoscientific theories from religious fanatics. I would say that that point should at least say it is a "... often wrongly compared ...", because the "often" mentioned by Tim Vickers is not enough.

Please, place more attention to this issue, as it is very common in the tv and written press to hear about things like the gen of madness, the gen of diabetes, the gen of heart attack, the gen of egoism, the gene of ..., which of course is a wrong conception whose source I ignore. Let us extirpate such misconception of general population interested in the subject. Specialized scientist, know that the things work in a more complex way that such metaphor says. There are no magic genes like those in the Hollywood movies. Susan Oyama, has a book on the subject of preformationism vs. vitalism in contemporary scientis, (I do not remember the title at this time). Take a look on it. —Preceding unsigned comment added by Elias (talk • contribs) 22:25, 19 November 2010

Extraterrestrials without DNA

There are people who believe that not all life requires DNA, and that life outside Earth could exist wthout DNA. For instance, in 2001 there were reports about red rains of Kerela being composed of foreign microbes. The question of life without DNA is currently being discussed for the proposed class of nanobacteria. [5] [6] Also, there was a strange report in 2009 in Mexico about a baby alien who didn't have DNA. [7] ADM (talk) 09:32, 27 August 2009 (UTC)

In Bild? How surprising :) Fvasconcellos (t·c) 13:19, 27 August 2009 (UTC)

I'll wait for the Nature paper. Tim Vickers (talk) 16:11, 27 August 2009 (UTC)

Agreed. Not to mention that this article is more on the scope of life on earth than theoretical "baby aliens"Skyintheeye (talk) 22:58, 9 February 2010 (UTC)

Don't butcher whole sentences with sources just because you don't "like" them

I refer to the butchering a of a whole sourced sentence just because someone didn't think it was too short for the introductory passage. If you think you are such a pinnacle of wikipedia at least incorporate it to the rest of the article. Don't destroy the hard work of individuals just because you personal aesthetic view of the article doesn't agree. I'd expect more from people versed into DNA an evolution (a process filled with improvement, not returning to the drawing board). --fs 16:52, 3 November 2009 (UTC)

The word "blueprint" is one word, mentioned in a list of other similes in the lead and nowhere else in the article. Adding an entire paragraph to the lead criticising the fact that some people have used this simile made this section completely unbalanced. Tim Vickers (talk) 21:12, 3 November 2009 (UTC)

DNA double helix stabilized by hydrogen bonds? Inconsistency

Under the "Properties" category, it states that DNA is stabilized by hydrogen bonds. However, under the "Base pairing" subcategory, it says hydrogen bonds only provide specificity for the pairing, and not stability. I think the latter is correct, and it should be edited.24.201.152.230 (talk) 03:04, 12 November 2009 (UTC)

It's mostly stabilised by hydrophobic interaction forces, you are correct. 78.21.38.109 (talk) 20:06, 10 December 2009 (UTC)

Picture of Rosalind Franklin

No matter what Wikipedia policy may be, an article about DNA without a picture of Rosalind Franklin is not acceptable. Also by taking her out of the gallery, you diminish her contribution to the discovery of DNA by only listing the men who took / interpreted her work. Please consider this and show some good faith instead of just blindly removing the picture again due to some Wikipedia policy. I hope we can come to some kind of agreement here. Greetings --hroest 08:30, 15 November 2009 (UTC)

Franklin did not receive the Nobel Prize, because she died before that ...

I do not know what policy was argued to support the removal of Rosalind Franklin from this page, but Franklin's work was substantial to the discovery of DNA structure, she is not mentioned too much, because she did not received the Nobel Prize, because it is not postmortem. But nobody can neglect her important contribution. I agree with Hannes Röst, that Rosalind Franklin picture should appear in this article, more over, linked to the entry about her. —Preceding unsigned comment added by Elias (talk • contribs) 22:25, 19 November 2010

Pronunciation

Can someone add the IPA phonetic pronunciation for deoxyribonucleic to the article.Carlwev (talk) 15:05, 20 January 2010 (UT

Don't know IPA, but it is pronounced DEE-(as in the girl's name)-OXY-RIBO-NUC-(as in nuclear)-LAY-(as in to have lain down)-IC Tim Vickers (talk) 23:55, 9 February 2010 (UTC)

Per dictionary.com, the IPA pronunciation is /diˈɒksɪˈraɪboʊnuˈkliɪk ˈæsɪd/. Considering virtually noone knows IPA, it would be helpful to also have an audio recording (e.g. Media:En-us-England.ogg). Emw (talk) 01:21, 10 February 2010 (UTC)

I've tried my hand at an audio recording of the pronunciation here: File:en-us-Deoxyribonucleic_acid.ogg. Thoughts? Emw (talk) 02:35, 10 February 2010 (UTC)

Thank you for your help and the audio file. I shall add this to the top of the article; matching other articles especially those with difficult words.

()

Carlwev (talk) 15:11, 11 February 2010 (UTC)

DNA as a database?

Can DNA be thought of as a database ?  —Preceding unsigned comment added by 59.103.212.144 (talk) 15:13, 13 February 2010 (UTC) 

No--Adam in MO Talk 20:23, 19 May 2010 (UTC)

You can store DNA and its related data in a database, but as for conceptualizing it, you might be better off thinking of it (together with the cellular 'machinery' that uses it) as a row of factories with variable productivity that is influenced by the other factories and their products. ... if that even helps. ~rezecib ^(talk) 03:25, 21 May 2010 (UTC)

I don't know if this answers your question, but a well known computer guy (adelman, of RSA security) started teh field of DNA computing; there is a ref in the acrydite articleCinnamon colbert (talk) 01:27, 27 October 2010 (UTC)

Lead image

I don't see how an animation of DNA spinning is beneficial to understanding the structure of the molecule; no matter how pretty the image is. The animation catches the eye of the average reader yet explains nothing. Looking through the commons I couldn't find an image that I thought was suitable, but if we can come to consensus on what the lead image should be, I'd be more than interested in attempting to create said image if it doesn't already exist.--Ben Harkness (talk) 00:31, 20 February 2010 (UTC)

The spinning animation seems beneficially because it indicates DNA's 3D structure in a way that's more difficult to convey with a static image. While I wouldn't support removing the animation, I do think it could be improved. For example, although orienting the animation perpendicularly is great for highlighting DNA's major and minor grooves, it makes the nucleotides -- which seem much more important to understanding DNA -- difficult to discern. Maybe a small tilt along the z-axis would help emphasize them. Emw (talk) 00:49, 20 February 2010 (UTC)

I do not find the spinning image to have any benefits. In fact it is annoying, because it demands attention while one is trying to concentrate on the readable material. I would suggest a playable animation, rather than one constantly playing. Lbharti (talk) 18:06, 15 March 2010 (UTC)

Graphic Chromosomal_Recombination.svg misleading?

A graphic in the DNA#Genetic_recombination section shows A-G and C-T pairs throughout, as if recombined chromatids differ as much as antisense strands of DNA. But chromatids M and F should be homologous before recombination, right? I don't believe that fertile parents of the same species might have genetic codes so completely different.
Prari (talk) 03:15, 14 May 2010 (UTC)

I don't think those are paired. I think they're supposed to be representing the corresponding strand of their respective two-strand sequences. So, essentially, it's showing that during recombination, an A-T pair is being swapped for a G-C pair. ~XarBioGeek ^(talk) 04:50, 14 May 2010 (UTC)

I don't think that's quite what the comment above is getting at (although a naive reader might expect two strands of DNA arranged thus to be base paired). What he/she is questioning is why such disparate sequences are coming together in the first place. One would expect at least some homology for strand exchange to succeed, with only sporadic sequence variation, particularly at the site of crossover. The image emphasizes the exchange of alleles at the expense of accuracy, and that's what is misleading.96.54.32.44 (talk) 19:05, 3 December 2010 (UTC)

The word 'Information'

The article uses the word 'information' several times when discussing DNA, yet there is no metric for determining whether DNA has any 'information,' let alone how much. There are several science papers discussing the issue of 'information' in DNA, and most of those are considered controversial due to the lack of such a metric. Attempts by some scientists to show DNA has 'information' have not been convincing, and are often refuted by other scientists. I suggest a different word be used instead of 'information' when discussing DNA. --Desertphile (talk) 22:15, 25 May 2010 (UTC)

Since each base in a single strand is selected from an alphabet of four, there are two bits of information per base pair.96.54.32.44 (talk) 07:39, 3 December 2010 (UTC)

James Watson

I don't know if this issue has been discussed but I noticed that James D. Watson's photo is not present in the history section of this article. I am raising this concern because Watson was the first author (followed by Crick) of the Nature paper. Omitting his photo but including photos of Franklin, Crick, and Gosling (I don't know why there is one of him) in the History section doesn't seem quite right to me. In my humble opinion, I think a picture of both Watson and Crick admiring their DNA model should substitute the photo of Francis Crick. Any thoughts? mezzaninelounge (talk) 21:44, 24 August 2010 (UTC)

I couldn't agree more; to have a DNA 'article' without images of Watson and Wilkins is ridiculous!

I would like to suggest that we either add a picture of both Watson and Crick OR replace Crick's picture with one that includes both Watson and Crick. I found a picture that includes both from the Wikicommons website. As the other reader/editor suggest, perhaps an addition of Wilkins's picture is not a bad idea. Does anyone object or have further thoughts and suggestions? mezzaninelounge (talk) 00:29, 19 September 2010 (UTC)

I agree that the pictures should be there, but even now, at least on my screen (which, granted, is toward the upper end for laptops, 1920x1200), the pictures take up far more vertical space than the text does; perhaps they should be placed in a horizontal arrangement at the bottom of the section, instead. ~rezecib ^(talk) 03:22, 20 September 2010 (UTC)

I don't mean to give you extra work, but would you mind taking the lead and try it? I just don't want to screw it up. mezzaninelounge (talk) 03:31, 20 September 2010 (UTC)

I fiddled with it a bit and replaced the picture of Crick with your suggested picture; due to the different aspect ratios, it seems to work well to have the first two horizontal, with the combined image below that.~rezecib ^(talk) 15:17, 20 September 2010 (UTC)

Thanks a lot, you're the best! mezzaninelounge 15:43, 20 September 2010 (UTC)

DNA Sculpture at Clare College, Cambridge, England

The wording on the DNA sculpture (which was donated by James D. Watson) outside Clare College's Memorial Court, Cambridge, England is:

On the base:

"These strands unravel during cell reproduction. Genes are encoded in the sequence of bases."
 
"The double helix model was supported by the work of Rosalind Franklin and Maurice Wilkins."
 
On the helices:

"The structure of DNA was discovered in 1953 by Francis Crick and James Watson while Watson lived here at Clare."
 
"The molecule of DNA has two helical strands that are linked by base pairs Adenine - Thymine or Guanine - Cytosine."

— Preceding unsigned comment added by 91.110.208.91 (talk) 03:19, 5 September 2010 (UTC)

The problem with this addition is that it really has very little to do with DNA, which is the topic of the article. It's about a sculpture of DNA with some quotes containing information already explained (and better) in the article. If it should be included in the article at all, it would be something to integrate into the history section, but not in the way it's written here; maybe something more like:

Watson donated a sculpture of DNA containing inscriptions of several important facts about DNA to his Clare College in (insert date here), (something about impact or significance of this).

~rezecib ^(talk) 15:40, 6 September 2010 (UTC)

Invitation to editors to vote/discuss definition of science in Talk:Science

There has been an extensive discussion on the Talk:Science of what the lead definition of the science article should be. I suspect this might be an issue that may be of interest to the editors of this page. If so, please come to the voting section of the talk science page to vote and express your views. Thank you. mezzaninelounge (talk) 16:10, 18 September 2010 (UTC)

Edit request from Xforty, 28 September 2010

{{edit semi-protected}} "The two strands run anti-parallel to each other" in the first section should me changed to "The two strands run parallel to each other" as in a double helix, when unraveled such as when a transcription to DNA begins, the two strands are parallel.

Xforty (talk) 08:07, 28 September 2010 (UTC)

 Not done: You are thinking of "parellel" in a geometrical sense. In biochemistry, Antiparallel (biochemistry) is completely different. Thanks, Stickee (talk) 09:09, 28 September 2010 (UTC)

Thanks :) I learnt something too! —Preceding unsigned comment added by Xforty (talk • contribs) 02:00, 24 October 2010 (UTC)

inaccuracy

"The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands" Inter strand H bonds provide part of the energy; more is provided by base stacking, which is seq specific, eg the duplex of GGGCCC is less stable then the duplex of GCGCGC, because stacking energy is most favorable for G,C stepsCinnamon colbert (talk) 01:08, 27 October 2010 (UTC) The inaccuracy is partially repeated here The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). DNA with high GC-content is more stable than DNA with low GC-content, but contrary to popular belief, this is not due to the extra hydrogen bond of a GC base pair but rather the contribution of stacking interactions (hydrogen bonding merely provides specificity of the pairing, not stability).[16] As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA.

It is not just G,C content, but sequence; the GC/CG is much more stable the GG/CC. ref 16 in the article is good, but work by Tinocco or someone like that would be better.Cinnamon colbert (talk) 01:25, 27 October 2010 (UTC)

I made an account today simply to make this point, I am glad you already did. The vast majority of DNA stability is provided by base-stacking interactions from by the hydrophobic nucleotides. They orient at an angle almost perpendicular to the axis of the DNA. I don't know where to find reliable sources but I am looking at a biochemistry textbook right now that says what I just typed. Please someone fix this. I would but I know very little about how to edit wikipedia. Ds2207 (talk) 17:12, 1 November 2010 (UTC)

Update: http://nar.oxfordjournals.org/content/34/2/564.short This journal article supports that base-stacking interactions contribute much more thermodynamic stability at neutral pH vs. hydrogen bonding between base pairs. Ds2207 (talk) 17:16, 1 November 2010 (UTC)

Edit request

{{Edit semi-protected}} Please correct the spelling of the word "axis" in the second sentence of the "Properties" section.

Change from:

....As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same access, ....

to:

....As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same axis, ....

75.40.216.62 (talk) 16:09, 12 November 2010 (UTC)

Oh, wow, what an awful mistake D:

Corrected. ~rezecib ^(talk) 16:33, 12 November 2010 (UTC)

Arsenic based DNA

Suggest entire alternate DNA structure section be rewritten from scratch to include arsenic backbones in light of new research published today. —Preceding unsigned comment added by 64.124.22.9 (talk) 19:00, 2 December 2010 (UTC)

Agreed; this is a HUGE finding. See these references:

Subsisting on Arsenic, a Microbe May Redefine Life, By DENNIS OVERBYE, New York Times, December 2, 2010

http://www.nytimes.com/2010/12/03/science/03arsenic.html?hp

Arsenic-Eating Bacteria Opens New Possibilities for Alien Life

Henry Bortman, Astrobiology Magazine, 02 December 2010, 12:44 pm ET

http://www.space.com/scienceastronomy/arsenic-bacteria-alien-life-101202.html

The discoverer of this bacteria is Doctor Felisa Wolfe-Simon. Her website is this:

http://www.ironlisa.com/ —Preceding unsigned comment added by 208.252.16.225 (talk) 19:22, 2 December 2010 (UTC)

I just created a new sub-section in this article, Alternate DNA chemistry. Much of the exact text I used was borrowed from other material recently contributed to other Wikipedia articles. The problem with all those new (and useful!) contributions) was that they were scattered around several articles. This article, instead, seems the logical place to bring together and summarize the basic information. Details (which will certainly run to several pages) may then develop on other pages linked to this one. RK (talk) 18:02, 3 December 2010 (UTC)

The problem with arsenate in DNA is a much higher rate of spontaneous hydrolysis leading to DNA strand breakage (Why nature chose phosphates. Westheimer FH. Science. 1987 Mar 6;235(4793):1173-8.PMID: 2434996; Formation and properties of sugar arsenate esters. Lagunas R. Rev Esp Fisiol. 1982;38 Suppl:63-72.). Either this organism has enhanced DNA repair systems, or artificially high replication rates under lab conditions of growth manage to keep ahead of accumulation of serious chromosome defects. One consequence would be a higher rate of recombination events and resulting mutation, leading to selection of strains in the lab that tolerate the conditions. It would be interesting to compare the genome of wild-type bacteria from the lake with populations grown in the lab with minimal phosphate.96.54.32.44 (talk) 18:46, 3 December 2010 (UTC)

Good points. It I may throw this idea out there - this may just be a problem with standard DNA molecules incorporating arsenate, as seems to be case. This finding, it is being claimed, opens the door to entirely novel molecules - perhaps with different DNA (or RNA) bases altogether - being used as a genetic code. Such molecules, in their native environment, may be more stable than what we are seeing here in this first example. RK (talk) 20:27, 3 December 2010 (UTC)

Please note it is not proven that arsenic has replaced phosphorus in a working DNA. Write the section in the way that reflects this important fact. There is phosphorus still in the DNA even after being forced-fed arsenic.Hzh (talk) 13:55, 4 December 2010 (UTC)

In addition to that, there's no evidence this occurs in natural environments. It may be worth adding a section dealing with the finding that arsenate can replace phosphate in DNA in some experimental conditions in specific organisms, but it's not yet entirely clear how "mainstream" this theory is and how well-accepted it will be by the scientific community, so focussing too much on this is entirely WP:UNDUE. I'd suggest waiting a while until we actually have something to say about the significance of this discovery; as it stands all we have are greatly-exaggerated releases to the general public about the significance of this research, and little in terms of actual research papers and reviews. GiftigerWunsch [TALK] 14:27, 4 December 2010 (UTC)

"arsenic dna" as well as the currently popular term "arsenic based life" are not accepted scientific terms, and probably wont be. And, its true this is not fully peer reviewed or duplicated yet. I would recommend simply saying "hypothetical partial substitution of arsenates for phosphates within dna" instead of "arsenic dna". There is currently no "name" for this "thing" yet. We are surely not going to give it its name here. I know I dont get into peer reviewed journals, so why should i be allowed to coin a name for it on a group edited encyclopedia?(mercurywoodrose)75.61.136.242 (talk) 08:33, 6 December 2010 (UTC)