Talk:DNA

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Featured article star DNA is a featured article; it (or a previous version of it) has been identified as one of the best articles produced by the Wikipedia community. Even so, if you can update or improve it, please do.
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Contents

[edit] Archives

  • archive 1
  • archive 2 <= If you want to know why this page was intially protected, read this.
  • archive 3
  • archive 4 <= If you want to know why this page is still protected, read this.
  • archive 5 <= More about protection unprotection and co. If you want to know about the unprotection of early march
  • archive 6 <= About DNA as a disambiguation page
  • archive 7 <= Last discussions on the article itself.
  • archive 8 <= Personal attacks not relevant to the issue at stake
  • archive 9 <= Earlier proposals for intro and discussion
  • archive 10 <= Discussion about how to manage the conflict
  • Archive 11
  • Archive 12

[edit] Thalidomide a mutagen?

In DNA Damage thalidomide is listed as a mutagen. Not to my knowledge it isn't! Does anyone have a source for this statement or shall I remove it? Fantastic article, by the way! Ewen 06:55, 13 February 2007 (UTC)

Additional ref added. TimVickers 14:43, 13 February 2007 (UTC)
If you mean [1], there is nothing noted about thalidomide as a mutagen. The thalidomide article states that it is not a mutagen and references [2]. So, we have two articles with conflicting statements. --Gadget850 ( Ed) 23:25, 13 February 2007 (UTC)
Thalidomide by my reading is tetragenic - which means it interferes with normal embryo development; it does not necessarily mean that it is a DNA mutagen.--Peta 23:30, 13 February 2007 (UTC)
However these guy showed it intercolates with DNA (T. D. Stephens, C. J. Bunde and B. J. Fillmore, Biochem. Pharmacol., 2000, 59, 1489. PMID 10799645)--Peta 23:36, 13 February 2007 (UTC)
Reword to make clear that thalidomide is mentioned as an intercalator, but not necessarily a mutagen. TimVickers 00:00, 14 February 2007 (UTC)
I'd cut it from the section all together, it's just one of several examples.--Peta 00:04, 14 February 2007 (UTC)
I put it in as it is a drug many people have heard of, while most people are unlikely to have come across the other examples in the newspapers. This drug does intercalate with DNA, what is the problem? TimVickers 04:55, 14 February 2007 (UTC)

[edit] The audio version

I have a problem with the audio vesion of this article seems to imply that viruses are alive. and it does this in the very paragraph! the written article does a better job. —The preceding unsigned comment was added by Adenosine (talk • contribs) 09:37, 13 February 2007 (UTC).

  • The spoken article was narrated word-for-word from a previous written article. This is stated in the Spoken Article box. From there, you will be able to access the old version of the written article in the state it was in when narrated. If you would like to replace the audio with a newer version, please feel free! All you need is a microphone, clear pronunciation, and 5-6 hours of spare time ;-) 82.45.61.117 15:11, 13 February 2007 (UTC)
  • Virues are considered to be alive by many biologists. It all depends how you define alive so it's quite subjective. David D. (Talk) 16:42, 13 February 2007 (UTC)

[edit] jehovah's witness link?

the last external link is to a jehovah's witness website, which starts off sounding scientific, and then begins to explain how the Creator made the genetic code.. is that appropriate? 131.111.8.99 18:39, 13 February 2007 (UTC)

Spam addition, I've removed it. TimVickers 18:46, 13 February 2007 (UTC)

[edit] All living things DO NOT contain DNA.

Namely, retroviruses only contain RNA, which they use to produce DNA inside the host cell. --132.69.234.73 18:59, 13 February 2007 (UTC)

Viruses are typically not considered to be alive. Raul654 19:02, 13 February 2007 (UTC)
Actually, sometimes they are. · AndonicO Talk · Sign Here 19:04, 13 February 2007 (UTC)

This possible exception is noted and discussed in the first paragraph, just keep reading. TimVickers 19:04, 13 February 2007 (UTC)

Sorry. As you can see, I didn't do my homework. --132.69.234.73 19:29, 13 February 2007 (UTC)

Not a problem, it is a grey area, as you can see from the discussion above. :) TimVickers 19:42, 13 February 2007 (UTC)

Virus are not alive because they are simply carriers of RNA/DNA to create copies of themselves. however, once the D/RNA is inserted into the host cell the Virus is simply a protein shell. Also it doesn't need nutrients to do anything. Therefore viruses should not be concidered alive.

To sum up viruses are generally classified as not "living organisms" but "quasi-living organisms" ie. half-living organisms.-ArazZeynilitalkcontrib19:31, 3 January 2008 (UTC)

[edit] Article has been defaced

In the Physical and Chemical Properties section, there is some egregious text: "The common knowledge is that gays love dna and cause dna to swirl." It probably doesn't add anything to the article, and can be removed.  :) 72.164.10.151 19:43, 13 February 2007 (UTC)

I can find no such text in the current version, try clearing your cache. TimVickers 19:51, 13 February 2007 (UTC)

[edit] Random Suggestion

In the introduction DNA is said to never act directly on molecules (unlike enzymes). Unfortunately this is not always true. It is believed that DNA may act on molecules in some situations (e.g. siDNA, although in that case it is DNA acting on DNA). Perhaps this section could be edited to read "in most cases..." or "coding DNA..." 69.255.38.193 19:54, 13 February 2007 (UTC)Byron Smith

Possibly you mean siRNA, which is not DNA. There are several examples of RNA acting on molecules. David D. (Talk) 19:58, 13 February 2007 (UTC)

[edit] Sense and antisense

The second sentence of this section is incorrect. The sense strand is not the one copied by RNA polymerase (template strand). I edited the section in Sense (molecular biology). Maybe you can look there and see how you want to change this. Telliott 21:30, 13 February 2007 (UTC)

Thank you, good catch. TimVickers 22:13, 13 February 2007 (UTC)

It says "overlapping genes increase the amount of information that can be encoded within the small viral genome". But does the amount of information actually increase, or is it just the usefullness of the gene? 131.111.8.102 00:17, 14 February 2007 (UTC)

More compact storage of information, therefore more information per unit size. TimVickers 04:49, 14 February 2007 (UTC)
fair enough; upon reading some of the information article, i see what you mean.. the data is the same but the information is different. 131.111.8.102 10:33, 14 February 2007 (UTC)

[edit] Brief congratulations

Well, the stuff of life made the Main Page :) (my, that sounded cheesy) Congrats to Tim who made the push for FA and all the editors who valiantly fought vandalism to this article today, and, in spite of and due to 260 edits, here we have in my humble opinion a rare instance of an FA which came out of its Maindate even better. Fvasconcellos 00:26, 14 February 2007 (UTC)

[edit] The AGE OF DNA

reproduction, a process in biological DNA that dates back 3.5 - 4.6 billion years.[1]

I have removed this as it is inaccurate, early life may not have used DNA as its genome, RNA is a possibility but we have no evidence. Similarly, we have no evidence when sexual reproduction evolved. Most of the history of life on earth is bacterial and archaeal, and these organisms reproduce asexually. TimVickers 17:07, 14 February 2007 (UTC)

I have added some material on the evolutionary history of DNA to the "Overview of biological functions" introduction. TimVickers 17:54, 14 February 2007 (UTC)

Hi Tim this is interesting that time frames of 3 billion years plus or minus a billion are not able to be included. DNA needs a structure of time to place life, sexual life, and asexual life into. I would suggest at this point that the time line of atomic formulation is important to discuss. All heavy elements like Gold and Uranium are formed in exploding stars or supernova and then recollected together to from solar systems. The atoms that form molecules that then form DNA have time lines that take place after atom formulation and conglomeration. As we look back into time we can say that DNA formed between the formation of Atoms/Molecules and say up to the formation of the Wikipedia page on DNA. This is a large time period and we know something happened in there. I give you your point that it is hard to prove but I still suggest that a time frame is important at the beginning of this page for new readers to DNA to have some perspective on when DNA started the formation of life. First the solar system formed, then DNA formed and then Wikipedia formed. Please puts some dates on this to inform the reader.RoddyYoung 09:23, 24 February 2007 (UTC)

The formation of atoms is indeed a very interesting area. However, a problem I see in adding information to this article on the formation of matter is that this material would have to be repeated in every article that deals with mater-based objects. It might be better to simply add this once to the specific article on matter. TimVickers 17:10, 24 February 2007 (UTC)
The same agument you put forward on matter could be used for adding a time frame as to when DNA and RNA started replicating. I agree with you that Matter formation does not have to be included in the DNA page due to its generally accepted understanding. However to not include a date for the formation for DNA in the DNA page is missing an important element in the wiki. RoddyYoung 13:16, 6 March 2007 (UTC)
If you can find a reliable high-quality source that deals with this, then please by all means add it to the section on "Evolution of DNA-based metabolism". However, I have not been able to find this information, since, as I explain in this section, I don't think anybody really knows. TimVickers 17:18, 6 March 2007 (UTC)

The development of DNA by Stephen Hawking is outlined here and covers the points I made as well as your points. This will give the reader a background. However after you read it could you put a date on when you understand DNA to have formed 12 billion years as an outside (when no carbon atoms existed in the universe) to 2001 when wikipedia was invented and DNA could be edited in this form. If you can narrow this down form my inadequate attempt then that would be good. Other wise I am happy for my numbers to stand and go into the main document.RoddyYoung 04:48, 11 March 2007 (UTC)

In that document it states "We do not know how DNA molecules first appeared." It also does not state when this might have occurred. I don't see how I can use that document to write about how and when DNA originated. TimVickers 15:14, 10 March 2007 (UTC)

"We do not know how DNA molecules first appeared" does not imply that they did not appear. (Truism). Dating when DNA appeared is independant as to how DNA molecules first appeared. We see today how DNA works and we know also that the complimentary stand process was the start of the process back then and that complimentary stand replication links all the way through time to today. I am making these points as I was happy with the time frame 4 billion to 3 billion years ago DNA formed and replicated. By deleting this you become the gate keeper of the timing and by providing no date you perport that is better than a date plus or minus a billion years. You should not be able to have it both ways. RoddyYoung 04:48, 11 March 2007 (UTC)

As I pointed out above, 3-4 billion years ago life may have been based on RNA. To say that it was DNA-based is supposition. If we have no references to support a statement, then it has to be removed as it is not attributed to a reliable source. If you can find a reference that says when DNA evolved, then I will be happy to add that date. I have been unable to find any such references. TimVickers 05:15, 11 March 2007 (UTC)

The point is made well in the wiki. The presence of a hydroxyl group at the 2'-position of the ribose sugar is what separates our positions. Because of the weaker information transmission vector of RNA it seems that DNA was a stong contender from the start. Lumping them together and dating them that way holds the best path forward. I think the wiki reads well as it has evolved. The time line link is very good and more than covers the point I was making. Thank you for your time. RoddyYoung 13:45, 12 March 2007 (UTC)

[edit] Suggested edits

Overall the article is excellent, congratulations. I noted some issues in a few places. See what you think:

DNA
p. 2 What is meant by "act directly"? Distinguish binding from catalysis.
Reworded.
p. 3 Implies that a given RNA can be used either as message or structural RNA.
Reworded.
Physical and chemical properties
p. 1 The width is 3.3 angstroms.

From the reference "Combined measurement of the rotational and translational frictional coefficients of rod-like DNA molecules in dilute aqueous solution yields 22 to 26 Å for the hydrodynamic diameter and 3·34(± 0·1) Å for the length per base-pair."

p. 3 third and fifth carbon atoms in adjacent sugar rings.
Reworded.
p. 4 When does uracil not replace thymine in RNA? I have to check my references, but when the 5 position of uracil is modified, it is typically more elaborate than simple methylation, e.g., 5-methyl-amino-methyl-2-thio-uridine.
Ribosylthymine is found in some RNAs such as tRNAs, added ref.
p. 5 These grooves result from the relative position of the glycosidic bonds for a base pair, as seen in the figure.
Indeed, feel free to add this if you think this would make the section clearer.
Sense and antisense
p. 1 The 5' to 3' copying is irrelevant to sense and antisense. It results from the nature of the substrates.
Good point, removed.
Supercoiling
The basic explanation is inaccurate. Although there may be some distortion at the level of the double helix, the main effect is to cause intertwining of different parts of the double helix, hence, super-coiling.
I disagree, the main effect in biology is to alter the ease with which the strands can be separated.
DNA damage
Double strand breaks are dangerous because there is no easy way to fix them in non-replicating cells. Telliott 21:18, 15 February 2007 (UTC)
Expanded.
Thank you for a most though review. TimVickers 23:06, 15 February 2007 (UTC)

[edit] Base Stacking

This article erroneously states that the two strands of DNA are held together by H-bonds between bases on the antiparallel strands, when in fact it is more base stacking that contributes to the stability of DNA. H-bonds certainly play a part, but certainly not as much as the stacking does. I would be glad to add the edit, but unfortunately the article is still semi-protected. [3] --Redsquareblack 18:26, 24 February 2007 (UTC)

Reworded the sentence to The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. Base stacking is discussed further in the base pairing section.. This arrangement of two nucleotides joined together across the double helix is called a base pair. In a double helix, the two strands are also held together by forces generated by the hydrophobic effect and pi stacking, but these forces are not affected by the sequence of the DNA.[14]
As you are logged in, Redsquareblack, you can edit semi-protected pages. This only blocks anonymous IP editing. TimVickers 19:15, 24 February 2007 (UTC)

[edit] DNA Structures

Just looking for confirmation of the number of DNA structures known so far - this article states A,B,C,D,E,H,L & Z DNA. However, the article on Mechanical properties of DNA is missing H & L, as well as adding P-DNA. Is P-DNA a structure or a description of the DNA's function (as I'm guessing rDNA (ribosomal) DNA is). This page seems to indicate P-DNA as a new structure: [DNA Structure: Yet another avatar?] I also found this page: [Boehringer Ingelheim Biopharmaceuticals - pDNA Production]. Zarius 07:43, 26 February 2007 (UTC)

This one of the refs seems pretty comprehensive. Ghosh A, Bansal M. A glossary of DNA structures from A to Z. Acta Crystallogr D Biol Crystallogr. 2003 Apr;59(Pt 4):620-6. 25. I've not heard of ribosomal DNA, are you sure you don't mean rRNA? TimVickers 16:47, 26 February 2007 (UTC)

[edit] Lead

Since this is probably going to change, I'd best paste the version I'm talking about:

Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Unlike proteins, DNA does not participate directly in most of the biochemical reactions it controls; rather, various proteins act on DNA and copy its information into either more DNA, in DNA replication, or transcribe it into RNA which can then be "translated" into protein. Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins in the cell nucleus, and thus affect what genes are active at any one time.
Chemically, DNA is a nucleic acid, a long polymer of simple units called nucleotides, which are held together by a backbone made of sugars and phosphate groups, to which are attached at regular intervals one of four types of molecules called bases. The sequence of these four bases along the backbone encodes information. The major function of DNA is to encode the sequence of the amino acid residues that make up the basic building blocks of proteins, which are interpreted through the genetic code. To read the genetic code, cells make a copy of a stretch of DNA as the similar nucleic acid RNA. Some RNA copies are used to make proteins, but others are used directly as functional components in their own right.

That done, Is this really the best way to arrange the information between these two paragraphs? Also, should we cut the sentence "Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm." - this seems the sort of thing that would be far more understandable with an illustration, and it'd be hard to include one in the lead. Adam Cuerden talk 18:26, 25 April 2007 (UTC)

Sorry to just stick my nose in, but do you really feel the lead is not lay-accessible? I get where you're coming from with regard to an illustration improving intelligibility, but don't you think that wikilinks are sufficient for a lay reader to form a "mental image"? (I don't have a formal background in biology, in case you're wondering.)Fvasconcellos (t·c) 18:35, 25 April 2007 (UTC)
It had problems earlier today that, thanks to active contributors have mostly gone away. However, that particular statement seems unduly difficult without either a pre-existing understanding of basic cell biology, or an illustration, and isn't really all that important to understanding of DNA. In other words, it seems more difficult than its importance really calls for. Adam Cuerden talk 20:53, 25 April 2007 (UTC)

I've replaced the "blueprint" analogy and the statement that DNA functions to store information, since these are very useful for explaining in a non-technical way what DNA does. I think cutting these from the lead makes it less intelligible to the layperson, rather than more. TimVickers 18:40, 25 April 2007 (UTC)

Other things I've fixed
  • Proteins are not "interpreted through the genetic code.", mRNA is - this was not what you meant.
  • Why is translated in quotes, but transcribed is not? Removed quotes and reworded.
  • DNA is not a complex molecule, it has a very simple structure. TimVickers 18:50, 25 April 2007 (UTC)

Tim, i removed the following sentence:

"Unlike proteins, DNA is not directly involved in most of the chemical reactions it controls; rather, various proteins act on DNA and either duplicate the DNA, in DNA replication, or copy its information into the related nucleic acid RNA."

To me this seems to be fully redundant with a previous and simpler sentence.

"DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules"

The key in the second sentence is the word instructions that immediately rules out any direct role in the function. Clearly we lose some links but how much are they worth. I think it is a little confusing to imply that DNA controls chemical reactions. I can also live without DNA replication unless we tie it with inheritance. David D. (Talk) 20:34, 25 April 2007 (UTC)

I'd put that in to introduce the critical importance of DNA-protein interactions, which are a theme that run through the text and forms the topic of section 5. Maybe there is another way we could introduce this? TimVickers 20:44, 25 April 2007 (UTC)
I think your final sentence in the lead covers that pretty well:
"Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and control which genes are transcribed."
If you want more I'd add it to that third paragraph which seem to be more on topic. David D. (Talk) 21:12, 25 April 2007 (UTC)

[edit] Reorginisation

(Some discussion copied from the FAR) What about (using the current numberings, and X. for new headers.)


  • 1 Physical and chemical properties
    • 1.1 Base pairing
    • 1.2 Sense and antisense
  • First Paragraph of 4. Genes and Genomes, 3 Overview of biological functions
    • 3.1 Transcription and translation + Paragraph 2 of 4. Genes and Genomes
    • 3.2 Replication
    • X. New section briefly describing mitosis and meiosis, though not in much detail. (Knowledge of this is presumed in section 6) Just a paragraph saying what they are, no real detail.
    • 6. Genetic recombination.
  • X. [New header to collect some moved subsections] Structure (with, somewhere in this section or its subsections, Paragraph 3 of 4. Genes and Genomes.)
    • 1.3 Supercoiling
    • 1.4 Alternative double-helical structures
    • 1.5 Quadruplex structures
  • 2. Chemical Modifications
    • 2.1 Regulatory base modifications
    • 2.2 DNA damage
  • 5 Interactions with proteins
    • 5.1 DNA-binding proteins
    • 5.2 DNA-modifying enzymes
      • 5.2.1 Nucleases and ligases
      • 5.2.2 Topoisomerases and helicases
      • 5.2.3 Polymerases
  • 7 Evolution of DNA-based metabolism
  • 9 History
  • 8 Uses in technology
    • 8.1 Forensics
    • 8.2 Bioinformatics
    • 8.3 DNA and computation
    • 8.4 History and anthropology

What do you think? Adam Cuerden talk 20:44, 25 April 2007 (UTC)

I disagree very strongly, you can't discuss biological functions without first describing the structure of DNA. The structure of this molecule is absolutely central to its functions. This is also the most logical direction to discuss the topics, moving from the basics of what this molecule is, onto the more complex areas of its interactions with other molecules. This proposed change also runs the risk of converting the DNA article back to an over-broad discussion of the processes DNA is involved in, rather than concentrating on the subject of the article itself, the DNA molecule. TimVickers 20:51, 25 April 2007 (UTC)

Um, perhaps that's not the best title for the new section, but Supercoiling, A B and Z DNA, and Quadruplex structures aren't, as far as I can see, mentioned in the Overview of biological functions anyway, so it made sense to me to delay them to after the biological introduction. Would it help if I made up the new arrangement on a temporary page? Adam Cuerden talk 21:01, 25 April 2007 (UTC)
Also, it'd probably help if I actually crossed out text I changed my mind about. Have another look at what I actually proposed for the new layout, instead of what I stupidly said about it. Adam Cuerden talk 21:06, 25 April 2007 (UTC)
You could try that and see what it looked like but I still feel it is deeply unwise. Including mitosis and meiosis also seems a random inclusion to me, this is moving very far away from DNA. I think it would be best to only include the processes where DNA plays an active role. Throughout the article I've tried to focus on the DNA molecule, its structure and interactions - with DNA structure, DNA-protein interactions and DNA-DNA interactions forming the heart of the article. We have articles on the processes that DNA controls, so this article shouldn't repeat their content but should take an almost myopic "DNA eye's view" of the cell. TimVickers 21:10, 25 April 2007 (UTC)
The inclusion of mitosis and meiosis is based solely on section 6's lengthy discussion of crossing over, which presumes knowledge of them. The alternative is to expand the description of them in section 6. Adam Cuerden talk 21:30, 25 April 2007 (UTC)
Removed ref to meiosis in section 6. TimVickers 21:34, 25 April 2007 (UTC)

Talk:DNA/Test This incorporates your removal of meiosis, so doesn't need the new section. Thoughts? I'm not that fixed on the actual details of the order, but think a reorginisation something like this would be useful. Adam Cuerden talk 21:46, 25 April 2007 (UTC)

Surely super coiling is required reading to understand function? Helicases, for example, makes no sense if one does not know about supercoiling. David D. (Talk) 21:54, 25 April 2007 (UTC)
My major problem with this propose rearrangement is that it is moving focus from "DNA" to "processes in which DNA is involved". The article is about DNA, the functions of this molecule are a secondary area included for completeness, not the primary focus of the article. TimVickers 22:07, 25 April 2007 (UTC)
Helicases are described in the new section 5, supercoiling in the new section 3. It's only "Basic functions" that are described in the new section 2.
I think the best reason for this new arrangement is the last sentence of the Supercoiling section. "These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.[38]" By putting the biological processes before that, we're now referring back to processes already described. As it stands, we're mentioning, without explanation, processes that haven't been mentioned yet. Adam Cuerden talk 22:48, 25 April 2007 (UTC)
I was not clear, I was referring to their mention, along with topisomerase, in the DNA replication figure. If you understand that DNA is supercoiled then that makes a little more sense. David D. (Talk) 01:29, 26 April 2007 (UTC)
These processes were described in the lead until they were removed today. I could solve this problem by replacing them in the lead. TimVickers 22:53, 25 April 2007 (UTC)
Well, there are other reasons for the rearrangement: I suspect that the information on the basic structure (e.g. sections 1, 1.1 and 1.2) and the basic biological processes are the most important to the layman, as well as being the information generally taught first about DNA in educational texts I've seen. The sections on quadruplex structures and regulatory base modifications are actually fairly difficult, and the section on DNA damage would probably benefit if the results of changes to the DNA were made clear beforehand by explaining its biological function; particularly the bit about point mutations. Regulatory base modifications would also benefit, as it's not actually explained why the regulatory base modifications are done, and doing so would probably need an understanding of biological functions. Adam Cuerden talk 23:29, 25 April 2007 (UTC)
As laymen, by definition know little about a subject, their opinions on what is important are not a reliable guide to follow. The section on modifications of bases and alternative conformations follows easily and naturally from describing the normal chemistry of the bases and normal conformation of the molecule, placing this later separates two closely-related areas for no clear benefit. I have replaced transcription and DNA replication in the lead. TimVickers 23:46, 25 April 2007 (UTC)
That's fair enough. However, could we make an effort to simplify the sections on quadruplex structures, regulatory base modifications, and DNA damage (and try to make it clearer what the regulatory base modifications do)? The difficulty of those sections is my major reason for the rearrangement, and if we can fix that, it probably wouldn't be necessary to rearrange it anyway.
Also, would you object to me dividing up the "Genes and Genomes" section? It's a bit of a mish-mash of concepts that would work better under pre-existing categories. Adam Cuerden talk 00:18, 26 April 2007 (UTC)
Great! I'm sorry if I come across as over-protective, but I put a lot of thought into the current structure. Please, go ahead and edit or highlight pieces here that need improving. TimVickers 00:36, 26 April 2007 (UTC)
Don't worry. A bit of caution is a good thing, and, well, there's other ways to get the same good result. I'll make a new section for the discussion. Adam Cuerden talk 01:27, 26 April 2007 (UTC)

[edit] Simplifications and other problems

  • Section about chromosomes, etc, in the lead: I'm not sure this is strictly true. I mean, it is for Eukaryotes, but the circular DNA and plasmids of prokaryotes don't follow quite the same rules.
What's the problem? Bacteria have chromosomes, just like eukaryotes link some of them are even linear link.
  • Alternative double-helical structures - I'm not quite sure what to do about this section, because it needs an explanation of methylisation to explain Z-DNA (and if we're going to talk about the alternative structures at all, we have to talk about Z-DNA. It also doesn't do a very good job at describing why the differences between B and Z DNA are important, or why A-DNA was important (largely historical, as it's the form used in the X-ray crystallography that helped elucidate DNA's structure. I.... don't know what to do. Maybe if we merged the section on methylisation or something?
The reaction is called "methylation", some more material added on Z-DNA function, but I don't think a lot is known here to be honest.
  • Quadruplex structures: This has worse problems. The description of replication in the lead just isn't enough for this, an explanation of structures involved in fixing a problem with DNA transcriptase. I... honestly don't know how to fix this short of a rearrangement. We could move the section about the biological functions back up, and merge methylisation with the Alternative double-helical structures or something... suggestions?
This isn't related to transcription, it is a replication problem. I've tried simplifying it a bit more, is it understandable now?

Other problems include the section "These guanine-rich sequences may stabilize chromosome ends by forming very unusual quadruplex structures. Here, four guanine bases form a flat plate, through hydrogen bonding, and these flat four-base units then stack on top of each other, to form a stable quadruplex.[41] These structures are often stabilized by chelation of a metal ion in the centre of each four-base unit." which requires feats of visualisation not sufficiently helped by the model, and doesn't explain chelation very well. (Also, "quadruplex" is not an easy word, so perhaps something like "These guanine-rich sequences may (may?) stabilize chromosome ends when four guanine bases form a flat plane through hydrogen bonding, and these flat four-base units then stack on top of each other, forming stable quadruplex structures." Unfortunately, "Here, the single-stranded DNA curls around in a circle stabilized by telomere-binding proteins.[43] The very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.[41]" is also difficult to visualise.

I've reworded this to split the concepts up a little and give a clearer description of the structures involved.
  • Methylisation: "cytosine methylation to produce 5-methylcytosine" - this doesn't really say much to the non-chemist. We need another illustration here. Adam Cuerden talk 02:02, 26 April 2007 (UTC)
You've used this term methylisation a few times now. Originally i thought it was a typo, but is this a term you have heard used for methylation? I have made some changes to that section but not ones that really address your issue here. I don't understand why the wikilinks are not sufficent here. Can you give an example of what you think should be done to clarify this more? David D. (Talk) 03:42, 26 April 2007 (UTC)
"Methylisation" is probably just me being stupid. It's not a term I've had to use much, to be honest - most of my classes are botany and zoology. Anyway, we don't really explain why methylation is important, nor do we really explain what it is. An illustration will explain what it is to a non-chemist in plenty of detail, so that's easily fixed, and explaining what it does is easy as it basically turns off genes by blocking transcription factors and causing histone binding which... we don't actually explain, do we? This article's very deficient in describing higher-level DNA structures. Adam Cuerden talk 03:55, 26 April 2007 (UTC)
Image added. part of response from TimVickers on 03:58, 26 April 2007 (UTC)
I added a bit more to the figure. With respect to Adams comments one of the problems with the role of methylation is that is still a black box. Is it the primary cause of heterochromatin or a secondary modification for maintenance? Histone methylation also correlates with chromatin structure. Do methyl DNA binding proteins recruit histone acetylases or do methylated histones recruit DNA methyltrasnsferase. Maybe we are seeing both occuring together, belt and braces type thing. Basically it is hard to discuss this accurately without getting into a debate about the primary literature at a level that is inappropriate for this article. It is better to be vague than wrong, in my opinion. David D. (Talk) 04:51, 26 April 2007 (UTC)
"It is better to be vague than wrong" Thank you, that is SO stolen! TimVickers 15:53, 26 April 2007 (UTC)
It is? Where from? David D. (Talk) 16:49, 26 April 2007 (UTC)
I was saying that I intend to steal that phrase and use it myself in the future, when exactly I can't say - as it is better to be vague than wrong. TimVickers 17:16, 26 April 2007 (UTC)
I'm flattered, thanks :) David D. (Talk) 17:52, 26 April 2007 (UTC)
  • DNA damage: The paragraph "Many mutagens intercalate into the space between two adjacent base pairs. Intercalators are mostly polycyclic, aromatic, and planar molecules, and include ethidium, proflavin, daunomycin, doxorubicin and thalidomide. DNA intercalators are used in chemotherapy to inhibit DNA replication in rapidly-growing cancer cells.[55] In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations. As a result, DNA intercalators are often carcinogens, with benzopyrene diol epoxide, acridines, aflatoxin and ethidium bromide being well-known examples.[56][57][58]" should probably be cut pretty heavily to trim all the lists. They don't really help understanding much. Adam Cuerden talk 02:02, 26 April 2007 (UTC)
The lists include several common drugs and poisons, which many people will have heard of - thalidomide and aflatoxin being prominent examples. I've removed a few less-prominent examples and tried to simplify the text a little.
  • Genes and genomes: This section isn't really very coherent, consisting of three paragraphs that should really be redistributed into the sections they relate to: The first into Overview of biological functions, second into transcription and translation, third... The first half would make a good introduction to quadruplex structures, the second half on pseudoggenes somewhere iin the biological function section.
This section deals with the structure of genomes and the functions of the various parts of the genome. I have renamed it and reworded it a little, to try to make the subject clearer.

However, we have a major problem here. What on earth are we going to do about Quadruplex structures needing a DNA replicase explanation first? We can't very well just break off that section, so I'm going to have to presume we do it as a group. Here's the possibilities I see:

I think that problem has now been solved, see text. TimVickers 03:58, 26 April 2007 (UTC)

A

  • 1 Physical and chemical properties
    • 1.1 Base pairing
    • 1.2 Sense and antisense
  • 3 Overview of biological functions
    • 3.1 Transcription and translation
    • 3.2 Replication
  • X. Structure
    • 1.3 Supercoiling
    • 1.4 Alternative double-helical structures
    • 1.5 Quadruplex structures
  • 2 Chemical modifications
    • 2.1 Regulatory base modifications
    • 2.2 DNA damage

(This doesn't fix 1.4's problems, though a little rearrangement might.)


B.

  • 1 Physical and chemical properties
    • 1.1 Base pairing
    • 1.2 Sense and antisense
  • 3 Overview of biological functions
    • 3.1 Transcription and translation
    • 3.2 Replication
  • 2 Chemical modifications
    • 2.1 Regulatory base modifications
    • 2.2 DNA damage
  • X. Structure
    • 1.3 Supercoiling
    • 1.4 Alternative double-helical structures
    • 1.5 Quadruplex structures

(This has the advantage of putting methylisation before Alternative double helical stuctures, and an explanation of the genetic code before the DNA damage section on mutations.(

C.

  • 1 Physical and chemical properties
    • 1.1 Base pairing
    • 1.2 Sense and antisense
  • 2 Chemical modifications
    • 2.1 Regulatory base modifications
    • 2.2 DNA damage
  • 3 Overview of biological functions
    • 3.1 Transcription and translation
    • 3.2 Replication
  • X. Structure
    • 1.3 Supercoiling
    • 1.4 Alternative double-helical structures
    • 1.5 Quadruplex structures

(This puts biological functions as late as is reasonable, but I'm not sure it's as good as B) I'm not sure what else to do. You have any ideas? Adam Cuerden talk 02:02, 26 April 2007 (UTC)

[edit] Thymine or thymidine

I just realised that I used thymidine in the base modification section to replace thymine. I have always used thymidine and have rarely heard thymine. Is this a chemist vs biologist nomenclature difference? Or is it a historical difference and, if so, which is the current standard for publications? David D. (Talk) 03:50, 26 April 2007 (UTC)

Thymidine is the base-sugar unit, thymine is the base alone. TimVickers 04:00, 26 April 2007 (UTC)
Duh, thanks for breaking it gently :) David D. (Talk) 04:08, 26 April 2007 (UTC)
I got it wrong once when I was giving a seminar, my boss wasn't gentle! TimVickers 04:12, 26 April 2007 (UTC)

[edit] "Nucleotide repeats"

Is the article meant to say "nucleotide repeats"? - "The nucleotide repeats contain both the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix." If so, what does it mean? --Seans Potato Business 18:11, 28 April 2007 (UTC)

Perhaps this would be clearer: "The repeating units are called nucleotides and these contain both a segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix." Better? TimVickers 18:24, 28 April 2007 (UTC)

Edit conflict: I think, taking a step back, I see that it just means a bunch of nucleotides... I don't know if anyone else would get confused the way that I did, but maybe "each nucleotide contains" would avoid such a thing. --Seans Potato Business 18:27, 28 April 2007 (UTC)
I like your adjustment better. :) --Seans Potato Business 18:27, 28 April 2007 (UTC)

[edit] Genes In Telomeres?

This sentence implies that telomeres contain genes; Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes. Is this true? --Seans Potato Business 08:51, 3 May 2007 (UTC)

It depends on how you define them, authors differ on if they only designate the telomeric repeat sequences as telomeres, or if they include the larger region of sequence involved in telomeric structures such as loops. In the larger definition, "sub-telomeric" genes such as the VAR genes in Plasmodium fall within the telomere region. I decided that in David's excellent terminology that it was "better to be vague than wrong" and skim over the top of this controversy. TimVickers 15:53, 3 May 2007 (UTC)
Okay, thanks. :) --Seans Potato Business 04:10, 8 May 2007 (UTC)
Agree here, of course ;). Centromeres certainly have functional genes and they are required to maintain the heterochromatin structure of the centromere in a negative feed back type interaction involving RNAi. Telomeres, as Tim mentioned above are less clear since it depends on the definition. David D. (Talk) 04:21, 8 May 2007 (UTC)

[edit] Chromatin and prokaryotes

I recently changed the opening section's mention of chromatin to specifically only apply to eukaryotes, but this was reverted by TimVickers. According to the Wiki article, "Chromatin is the complex of DNA and protein found inside the nuclei of eukaryotic cells." Personally I can't remember seeing the term chromatin ever being used about prokaryotic DNA-protein complexes, although I can't rule it out (it would be logical to use the term in prokaryotes since the term chromosome is also used there). My trusty old textbooks didn't have any final word on it but only mentioned eukaryotic chromatin (for example, Stryer 5th Ed. page 875). I then checked my dictionary of biological terms (Henderson, 12th Ed.), which defined chromatin as "the complex of DNA and histone proteins that makes up the basic material of eukaryotic chromosomes." But that's just a dictionary of course. In any case, either this article should be changed to say that chromatin is in eukaryotes only, or the chromatin article should be changed to say that chromatin is both eukaryotes and prokaryotes. Right now they contradict each other. Sakkura 20:13, 3 May 2007 (UTC)

Bacterial chromosomes are not free DNA but are found in association with chromatin proteins homologous to the proteins found in eukaryotes. link 1 link 2 This isn't covered much in textbooks, but I added some references to this in the protein-DNA interactions section. Thanks for pointing out the inaccuracy in the chromatin page, I've changed that lead a little and added a reference. TimVickers 20:35, 3 May 2007 (UTC)
I know the DNA doesn't just float about freely in prokaryotes, but never heard of the DNA-protein complexes in bacteria or archaea described as chromatin. I guess the literature tends to gloss over it since the importance of chromatin and histones is more established in eukaryotes than in prokaryotes. Thanks for clearing this up Sakkura 21:00, 3 May 2007 (UTC)

[edit] small change

After the last sentence of the third paragraph of the "Physical and Chemical Properties" section:

"One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.[6]"

Can you put "(hence the nomenclature Deoxyrido(in italics)nucleic Acid and Ribonucleic Acid)" or something to this effect which gives further clarity to the names DNA and RNA.

Thanks

Anna —The preceding unsigned comment was added by 82.32.25.174 (talk) 19:01, 13 May 2007 (UTC).

[edit] Genetic mutation : Is it possible?

Is it possible that to geneticaly mutate humans using animal DNA e.g Spider Man put comments on this page. —The preceding unsigned comment was added by 196.209.61.246 (talk) 12:34, 14 May 2007 (UTC).

See genetically modified organism. TimVickers 14:51, 14 May 2007 (UTC)
Thanks Tim!!! 15:26, 02 June 2007 (UTC)

[edit] Scientists isolate the gene for political party votes!

This isn't psychobabble, I read it on Yahoo so it must be true - remember, you're spos'ta trust everything you read!

http://news.yahoo.com/s/livescience/politicalpreferenceishalfgenetic;_ylt=AsbP0KuvHdTuU3YFsO9d446s0NUE

You have grossly misrepresented the actual study. There was no gene sequencing involved; the study was done by a psychologist. Genetics was brought in by looking at families and identical twins. This really doesn't belong in the DNA article.—WAvegetarian (talk) 23:48, 29 May 2007 (UTC)

[edit] Triple helix DNA

This is a very comprehensive page on DNA, but I did miss a part on triple helix formation, using Hoogsteen and reverse Hoogsteen base-pairing. I've been in the field in the '90 (elucidating their crystal structure, see this and this scientific article), and from then I remember their biological role was unclear, but that triple helix formation might have some important applications, since it allows for the base-specific blocking of the major groove. --D-rex 08:55, 9 June 2007 (UTC)

Thanks for the comment, I'll try to add this to the article somewhere. TimVickers 13:15, 9 June 2007 (UTC)
Thx, I didn't want to imply that you have to use the references to my articles though, it was just to prove my credibility. Anyway, there is a article on Triple-stranded DNA that deserves a link to from here. --D-rex 20:15, 15 June 2007 (UTC)

[edit] Uracil query

Hi! I would like to comment to this DNA page only, that I found a mistake! By the bases, you wrote, that the uracil is only in the DNA, but in small mass in bacterial DNA too... So this not right, you should write, that in oly RNA, and in small mass in bacterial DNA too!:) Only this! This page is very good, thank you for it!

Christian from Hungary

I can't see that statement, where in the article do you mean? TimVickers 14:34, 17 June 2007 (UTC)
It is under the "Physical and chemical properties" section in the sentence, "Uracil is normally only found in DNA as a breakdown product of cytosine, but a very rare exception to this rule is a bacterial virus called PBS1 that contains uracil in its DNA". Christian is correct. --Thorwald 23:55, 17 June 2007 (UTC)
I see that sentence could be read in that manner, I've reworded it to try to make its meaning unambiguous. "Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine,..." TimVickers 01:15, 18 June 2007 (UTC)

hello, could anyone tell me why doesnt DNA usually have uracil? —Preceding unsigned comment added by 220.224.83.186 (talk) 16:58, 19 January 2008 (UTC)

Bases have to pain with one another, A with T and G with C, so there an only be an even number of types of bases in DNA. Tim Vickers (talk) 19:22, 19 January 2008 (UTC)

[edit] Citizendium version of this article

Hi there, I've been reading the Citizendium version of our article and notice it is based on an old copy that contained several errors. Most seriously, it retains the incorrect definition of the sense and antisense strands that we fixed in February. If anybody with access to this page can correct this error that would be great. Tim Vickers 16:31, 16 August 2007 (UTC)

[edit] DNA: Biological Binary?

I apologize if I am posting this in the wrong location or something but I am working on a bit of fiction and would like a bit of clearification in regards to base pairs. I was reading the base pair section and, I think I am right but to be safe: In a nutshell, can DNA be viewed as a biological form of Binary or did I miss read? I mean I know DNA is so much more but I'm looking for this particular aspect. Any info would be great to help me. —Preceding unsigned comment added by DigitalSaber (talk • contribs) 00:02, 29 October 2007 (UTC)

I don't know anything about binary numbers, but DNA has 4 states C,G,A or T. These are coded in triplets to read one of twenty amino acids, eg ATG = methionine. Hope this helps. Tim Vickers 02:39, 29 October 2007 (UTC)
You could imagine that it is like binary machine code, but that the machine it runs on is a cell. and as Tim says DNA is quaternary. Graeme Bartlett 03:01, 29 October 2007 (UTC)

[edit] Title: DNA or deoxyribonucleic acid?

IMO the article should be moved to deoxyribonucleic acid. I find it very strange to use acronym here while at the same time we have LSD under Lysergic acid diethylamide. The word deoxyribonucleic acid explains the structure of the molecule and the people who don't know what DNA stands for will be redirected to deoxyribonucleic acid. --Eleassar my talk 11:19, 19 November 2007 (UTC)

99.95% of our readers will search for DNA, so that's the title we should use - see the Wikipedia:Naming conventions which states:
"Generally, article naming should prefer what the majority of English speakers would most easily recognize, with a reasonable minimum of ambiguity, while at the same time making linking to those articles easy and second nature." see also Talk:DNA/Archive 6 for last time this was discussed. Tim Vickers (talk) 16:47, 19 November 2007 (UTC)

From the same page: "Avoid the use of abbreviations, including acronyms, in page naming unless the term you are naming is almost exclusively known only by its abbreviation and is widely known and used in that form.". I don't think this is the case here. --Eleassar my talk 19:29, 19 November 2007 (UTC)

I disagree, DNA is almost exclusively known by its abbreviation and is certainly most widely known and used in this form. Ask 100 people on the street what DNA stands for, how many do you think will be able to give you the correct answer? Tim Vickers (talk) 19:33, 19 November 2007 (UTC)
I agree with Tim, I'm betting most people don't even know its an acronym. David D. (Talk) 19:53, 19 November 2007 (UTC)
And only 0.0001% of people will know if "deoxyribo" or "deoxyribose" is correct. I know I had to check! :) Tim Vickers (talk) 20:05, 19 November 2007 (UTC)

This surprises me very much. I was sure the majority of people know "DNA" means "deoxyribonucleic acid". I'll really do the test you have proposed. :) --Eleassar my talk 20:15, 19 November 2007 (UTC)

Be sure to ask if it is "ribo" or "ribose"! Tim Vickers (talk) 20:49, 19 November 2007 (UTC)

Ok, according to this pool two thirds of Americans know what does DNA stand for. This clearly refutes your claim that DNA is almost exclusively known only by its initials. Can you prove otherwise? --Eleassar my talk 21:40, 19 November 2007 (UTC)

Untrue, in a multiple choice format 2/3 of people could select the correct answer, we don't know what the alternatives were or how many alternatives were given. Most obviously, choosing something from a list isn't the same as using the term in common discourse or even being able to recall it by oneself. That news article itself uses the term DNA throughout, even in its headline - it doesn't say "The deoxyribonucleic acid IQ of americans! Tim Vickers (talk) 21:45, 19 November 2007 (UTC)
Looking at other news sources, a search for DNA in Google news gives 24,488 articles, while "deoxyribonucleic acid" gives just 51. Tim Vickers (talk) 22:02, 19 November 2007 (UTC)
I gotta go with the status quo here. I work in a large research institute on projects that emphasize cell and molecular biology (I'm being vague to protect my privacy), and I can't remember the last time that I or any of my colleagues used the term deoxyribonucleic acid. Yes, DNA stands for deoxyribonucleic acid, but even among experts in the field nobody uses the full form. Is there any harm in having DNA under the name DNA? TenOfAllTrades(talk) 22:39, 19 November 2007 (UTC)

There are several benefits in having DNA under its full name: technical accuracy, clarity of information, consistency in style, etc. The guideline is very clear: "Acronyms can be used in page naming if the term you are naming is almost exclusively known only by its acronyms and is widely known and used in that form." I have done my duty; I've expressed my doubt whether this is true and have even supported it with a poll. Now it's up to you to a) prove otherwise, b) explain why this guideline does not apply here (while at the same time it obviously does for LSD, THC, GABA, ISDN, ISBN etc), or c) gain consensus and change its wording. We're writing an encyclopedia, which means we should not use jargon like it is used in news and elsewhere unless DNA is indeed almost exclusively known by its acronym. --Eleassar my talk 09:20, 20 November 2007 (UTC)

It is exclusively known by its acronym. David D. (Talk) 14:08, 20 November 2007 (UTC)

This suggestion has been brought up before, what would people think about a straw poll to try to get a better idea of the balance of views on this issue? Tim Vickers (talk) 19:11, 20 November 2007 (UTC)

I think it is a waste of time. The basis of this argument is that LSD is at its full name but a reading of the wikipedia guidelines is clear that:
"Acronyms can be used in page naming if the term you are naming is almost exclusively known only by its acronyms and is widely known and used in that form."
If DNA is not an example of this exception then what is? Far better would be a discussion of why Lysergic acid diethylamide is not at LSD rather than using that as a precedent to move this article to deoxyribonucleic acid. David D. (Talk) 19:39, 20 November 2007 (UTC)
My straw vote would go to “DNA”. Although it’s possible to use the full name in the article title, it seems silly if during the rest of the article it will be referred to only as DNA (not just because it’s shorter, but because it’s less confusing). And as a scientist, “deoxyribonucleic acid” falls under the category of “trivia question” rather than “practical term”, at least for me.
Dihydrogen monoxide anyone? (sorry, couldn’t resist...) Forluvoft (talk) 20:14, 20 November 2007 (UTC)
Even searching in the scientific database PubMed gives you 938,211 results for DNA, and only 10,567 for "deoxyribonucleic acid" - almost a 100:1 ratio. Tim Vickers (talk) 20:35, 20 November 2007 (UTC)
I've proposed Lysergic acid diethylamide to be moved to LSD. You may comment this at Talk:Lysergic acid diethylamide. --Eleassar my talk 12:30, 4 December 2007 (UTC)


[edit] Transformation : Discovery

This is in reference to the history section of the main article. O. Avery did not find transforming principle . It was Fedrick Griffith who discovered that a transforming principle ( as coined by him)transforms rough strains of pneumococcus into smooth strains. Avery and his co-workers found out that the transforming principle was DNA. pp Pahini —Preceding unsigned comment added by 117.98.8.84 (talk) 06:37, 7 December 2007 (UTC)

Thank you, that was a major error. It has been corrected. Tim Vickers (talk) 17:24, 7 December 2007 (UTC)

[edit] Pi stacking and base pairing

Quote:

In a double helix, the two strands are also held together via forces generated by the hydrophobic effect and pi stacking, which are not influenced by the sequence of the DNA. (DNA#Base pairing)

This sentence suggests that pi stacking contributes to basepairing. I doubt whether this is correct. As far as I know, pi stacking stabilizes the overall structure of the double helix, but does not contribute significantly to base pairing. Josq (talk) 10:53, 18 December 2007 (UTC)

[edit] long

Isn't this article a bit too long.Skele (talk) 21:54, 5 January 2008 (UTC)

I agree. The article should be more concise. I will remove some details that are too specialistic. Josq (talk) 15:02, 7 January 2008 (UTC)
Don't expect that we can reduce the article 50% in size, there are so much important things to tell about DNA ;) But I think the article still contains too much details. For example, the section about alternative helix structures/ G-quadruplex should be much shorter. Josq (talk) 15:19, 7 January 2008 (UTC)
yeap Skele (talk) 01:47, 12 January 2008 (UTC)

I'm interested to know why removing the three words that refer to RAD51 would help this problem of length? Certainly it makes it less clear where a reader should go for more information. When connfronted with the recombinases disambiguation page which one would a reader choose? David D. (Talk) 03:09, 12 January 2008 (UTC)

Honestly, I was a bit too ambitious when I said that I would remove too specialistic details. To make the article less specialistic requires a restructuring of many sections. But an enzyme name of 3 letters and 2 digits really says nothing to non-experts. The recombinase disambiguation page should explain that some recombinases are eukaryotic and other prokaryotic etc, or it should even be an article with an overview of research on recombinases. To send the reader to a page about a specific recombination enzyme is kind of POV, as there are many kinds of such enzymes. Josq (talk) 13:09, 15 January 2008 (UTC)
If there is an article on recombinases your edit makes sense but a disambiguation page does not help. For example, Cre has nothing to do with recombination as described in the article. I don't agree that linking to RAD51 is POV, it just happens to be one of the relevant recombinases that has an article in wikipedia. Non-experts don't have to look at the RAD51 article, but I see no harm in pointing out it exists. Why not raise the bar high, I see no reason to dumb down all articles in wikipeda. As an aside there are two different articles for Evolution, the second being Introduction to evolution, a similar partner article here would be a better approach than make massive changes to this one, IMO. David D. (Talk) 17:40, 15 January 2008 (UTC)
Kind of ironic that some people are complaining that the article contains too many details, while others complain that we have missed out triple helix DNA and say we need more details. Tim Vickers (talk) 18:06, 15 January 2008 (UTC)
Well, I see a kind of snowball-effect. Once you describe some specialistic aspect in detail, users will ask for detailistic descriptions of all other aspects to keep the article in balance. Indeed, now that the quadruplex is described in detail, people wonder why there is not a detailed description of the triple helix. But I think that this should really be an article which gives an overview, specialistic information can be found in many other articles. So don't talk about dumbing down articles, it's just about making a good separation between topics of general interest and details for experts.
You can say that you shouldn't care about RAD51 when you are a non-expert, but I believe that the reader really will become tired, when they have to wrestle through a piece of text which is full of details you shouldn't bother about. Indeed, I don't really care about a reference to RAD51, but I care about a habit of adding yet another detail... until the article becomes uncomprehendable.
Making an "introduction to DNA" might seem a solution, but this article will become redundant as soon as the "introduction" contains good references to all articles that explain the several aspects in detail. Josq (talk) 21:09, 15 January 2008 (UTC)
It's not just another detail, it links to a place to get more information on a recombinase, something the disambiguation page for recombinases does not achieve without confusion. Why don't you create a subpage of what you are aiming towards. It sounds to me that removing much of the information you are planning to will leave the article hollow. Minor details now, then whole sections later. What size of article are you aiming for? David D. (Talk) 21:30, 15 January 2008 (UTC)
The introduction gives an overview, the rest of the article gives details. The contents are actually a pretty broad picture of the structure and importance of DNA, with much of the specialised detail omitted. Have a look at the sub-pages to see how simplified this article really is - compare the "Supercoiling" section with the sub-page DNA supercoil. Tim Vickers (talk) 21:15, 15 January 2008 (UTC)
Example to give an idea of what I mean: would it really be a loss if we substitute the sections DNA#Alternative double-helical structures and DNA#Quadruplex structures by the following text:
The double helix can exist in many conformations, like A-DNA, B-DNA and Z-DNA. B-DNA is the most common conformation. The other conformations can arise under experimental conditions, or through phenonemons like supercoiling and methylation of DNA. There are also forms of DNA with three or four strands: the triple helix and the G-quadruplex. In these structures, alternative forms of base pairs named Hoogsteen base pairs occur.
(The part about telomeres should be moved to DNA#Genome structure)
I think this would be clear and concise, without omitting information that is really essential. And sorry about possible language errors, I'm not a native speaker. Josq (talk) 21:35, 15 January 2008 (UTC)
(Actually, I made this edit before I read your messages). Josq (talk) 21:38, 15 January 2008 (UTC)
That would remove a lot of useful information and replace it with a rather confusing and abrupt summary. It is a common error to think that B-DNA is the only biologically-important form of this molecule, and removing these sections would only reinforce this confusion in our readers. Tim Vickers (talk) 21:39, 15 January 2008 (UTC)
Why confusing? And why do you think I reinforce that "error" - I explicitly have mentioned some biological circumstances under which alternative conformations can arise! And well, I'm afraid we will not agree if you think that all other details have to be mentioned in this article. Josq (talk) 21:45, 15 January 2008 (UTC)
The idea of summary style is to introduce the sub-articles and summarise the important points in these more detailed pages. Your proposed version fails to do this adequately and glosses over the structures and roles of other forms of DNA. I just don't think that is adequate. Tim Vickers (talk) 21:50, 15 January 2008 (UTC)
I'm not amazed that you reject my fast-typed proposal, but that's not the question. It's about the principle, the extend of using what you call "summary style". Do you think this article is now a good example of such a summary style?
Another very important question: what readers do we target? I think many high school students that have learned their first lessons about DNA will return with horror from this page. Possibly the same for a law student that wants to learn more about DNA because of its growing role as evidence material. Even a second-year biochemistry student will find many things that appear (too) detailistic.
@David D.: thank you for making the subpage. But I will spare my efforts as long I'm not sure whether they will stand a chance. Josq (talk) 22:03, 15 January 2008 (UTC)
I've been grappling with the same problem. I couldn't agree more that we need to recruit more scientists to write about their fields of expertise. Great scholarly reviews result. But not all scientists want to "bend over" far enough to make an article accessible to a lay audience. Theoretically it should be possible to "shade" an article from general to technical and appeal to a wide range of audiences, but I think in practice it is difficult, not only to craft such an article but then to maintain it in that state.
I love Wikipedia because I can know almost nothing about the French revolution, read up on it, and then not only feel like I understand the event but also understand a little bit of the fascination that historians feel for their subject. I want my brother to feel the same way when he reads a molecular biology article to understand what I do in the lab. But I know that this is far from the case.
At one point Tim had mentioned that less technical scientific articles might go on Simple English Wikipedia. At first I recoiled at the idea. The name "Simple English" is a bit condescending. My friends also think it is bad to write there, beings Google searches are less likely to pick up those articles. But the more I think about it, the more I think it's worth a try, especially if prominent links could be made from the more technical Wikipedia articles. The language restriction is a pain there (they are catering to English as a second language speakers) and most of the biology articles are poor, but I want to see what I can come up with. It is really hard to write an article for someone with only high school biology (and whatever they pick up in the media) without insulting their intelligence (which makes scientists seem very arrogant).
I have been working on some pictures for the DNA article on Simple English. I haven't done much with the page yet, but you're welcome to help if you want! Forluvoft (talk) 22:27, 15 January 2008 (UTC)
I agree with the first part of your contribution. However, the decline of the Wikipedian Empire has begun when messages appear: if you want to understand this topic, please visit the Simple English version of this article
I really wonder: is there anyone that would find this article interesting? For laymen it's way too detailistic. Academics have already a lot of knowledge about DNA, so they would be interested in more specialistic articles - so an academic level for this article is not an important requirement. Maybe a biochemistry student will be interested - but somebody who wants to review how DNA is organised in higher-level structures, probably will get lost in the wealth of information.
I'm aware that, although it is easy to say what the problem is, it's very difficult to solve. The article should be simple but scientific, concise but complete. One needs a combination of academic, editorial and education skills. Josq (talk) 23:27, 15 January 2008 (UTC)
The article is written for a broad audience, in particular it tries to avoid jargon and explain any technical terms. I think the best way to make it more accessible is not to remove useful material, which only makes the article less comprehensive and might result in it failing FA criteria 1b, but to find any parts of the text that are unclear and make them more understandable. Tim Vickers (talk) 23:45, 15 January 2008 (UTC)
FA criteria 1b speaks about major details. As there are so much major details for DNA, any details of minor importance or relevance should be omitted. Remember the snowball-effect, every detail asks for more details. This is strengthened by the fact that you have to explain all difficult concepts. I should make lists of details that might be superfluous or unclear. Josq (talk) 23:59, 15 January 2008 (UTC)
Have a go at editing the subpage, that would be much simpler. Tim Vickers (talk) 00:05, 16 January 2008 (UTC)
I have made a start. Josq (talk) 00:44, 16 January 2008 (UTC)
I don't agree about gutting the alternative structures section, we need to tell the reader how these differ from B-DNA and why they are important. I condensed the quadruplex section a bit. The organisation of the article flows from chemistry to structure to function, this puts all the biology together. Tim Vickers (talk) 01:46, 16 January 2008 (UTC)
Although we don't agree on some aspects, I want to thank you for taking some of my comments serious. That's encouraging - I feel still a beginner here ;) Josq (talk) 01:49, 16 January 2008 (UTC)
I'm probably a bit attached to the present text, its mostly my work. I cut the non-biological conformations, since these are covered in the sub-article. Please continue, with your comments on the sub-page, but could you use bold, and bold italics, makes the comments easier to pick out of the rest of the text. Tim Vickers (talk) 02:04, 16 January 2008 (UTC)
Oh, I hope my comments weren't too offending. I think I will continue tomorrow, its 3-4 hours past bedtime here ;) Josq (talk) 02:07, 16 January 2008 (UTC)

[edit] adding a "simple" section?

I've been thinking a while on the suggestion to make an introduction to DNA-article for laymen. But I don't think that is a good idea, it would be an indication that we have missed the goal to write this article for a broad audience.

After reviewing this article and the modifications Tim made, I acknowledge that this article is not too detailed and specialistic. Most things are well explained now.

However, the amount of new concepts will be overwhelming for people with little or no background in biology and chemistry. I think that is a serious problem.

My proposal is to make a "simple" section which explains the most important concepts. One should be able to get an idea what a nucleotide is, without worrying what 3' and 5' means, or roughly understand how replication works, without getting confused by the details of the replication machinery.

I made a list of the concepts that should be understandable for every reader. Maybe I missed something, or the order has to be adjusted.

  • Structure:
    • Nucleotides, bases, base pairs
    • strands, sequences
    • double helix, complementary strands
    • chromatine, chromosome
  • Function:
    • genes, transcription, genetic code, translation
    • replication, heredity
    • mutation
  • Context:
    • Location of DNA in cell
    • Differences between DNA and RNA

Off course, most of these concepts are now already mentioned in the introduction. However, with a very brief explaining and without pictures, these concepts will remain unclear to the unprepared reader. When a "simple" section is added at the beginning of the article, the introduction can be shortened. Also, this main concepts don't have to be explained anymore in the rest of the article.

I hope this idea will help making this article more accessible for a broader audience. Josq (talk) 18:53, 17 January 2008 (UTC)

This is similar to what I did for enzyme kinetics, it seems a very good idea to me. Go ahead, but try to keep it to a few paragraphs so we can keep repetition to a minimum - this article is already quite large, as noted above. We could work on it at Talk:DNA/More_simple#General_principles - I copied across the most recent version of the article. Tim Vickers (talk) 20:31, 17 January 2008 (UTC)
This simpler introduction is now part of Introduction to genetics. Tim Vickers (talk) 18:48, 7 June 2008 (UTC)

[edit] semi-protection

Hi people! I am blitox, from spannish wikipedia. I am writing this message in order to ask the administrators to take out the semi-protection advertisement. The problem is that I am working with a translation of this article and I can not copy the last edits with the references included. For this reason, I am really looking forward to hearing from someone here!!!

Waiting for an answear, click here as the link here does not work: http://es.wikipedia.org/wiki/Usuario_Discusi%C3%B3n:Blitox; this is my talk ok.

See you!

Done. David D. (Talk) 15:58, 26 March 2008 (UTC)
Note - I had already copied the article into a subpage of this user's account on the Spanish Wikipedia, so if vandalism appears again we can reinstate semi-protection without worrying about it. Tim Vickers (talk) 16:35, 26 March 2008 (UTC)
Good job, I didn't notice that. David D. (Talk) 16:59, 26 March 2008 (UTC)

[edit] How many nucleotides are in human DNA?

It would be great to see quantitative information about nucleotides amount. Couldn't find it in article, also googling can hardly help. Seems like it should be manually estimated to get the value. —Preceding unsigned comment added by 91.76.138.160 (talk) 19:19, 29 March 2008 (UTC)

okay. found it as '3 billion base pairs' => like 6 billion nucleotides? —Preceding unsigned comment added by 91.76.138.160 (talk) 19:21, 29 March 2008 (UTC)
Yes, that's right, see genome or this website for more details. Tim Vickers (talk) 18:51, 30 March 2008 (UTC)

[edit] DNA: more like a "recipe" than a "blueprint".

I think that the analogy with a recipe is much more adequate than the analogy with a blueprint. A blueprint is an schematic drawing which is far more close to the real thing in every detail, they're somewhat like "photos" of the real thing, whereas the genome hasn't such degree of specifity, therefore we can have things like a banana and a human sharing about 30-40% of the genome, if my memory doesn't fails. Recipes, in the other hand, are not like "photos" of the end result, but an initial set variables of a process in which more variables will emerge from complex interactions along the way to the final result, and such thing makes possible to have more different results from slighter changes in the recipe; the whole pastry, things like bread, pizza, panettone, croissant and even some sorts of biscuits start with similar ingredients. Unlike a blueprint of something, we can not look at the genome of an organism and actually know how it would look like; at most, we can know that it would have certain proteins, if we know its genetic code; we only know that the genome of a certain species belongs to it because we extracted from the species beforehand, it's not like we can see "ah, here's the genetic schematic for the head of a lizard... let me see the size specification... wow, it's too big, it must be a komodo dragon". I believe that Richard Dawkins makes a short case for the "recipe" analogy versus the "blueprint" in the "Blind Watchmaker". I think he makes some example that some chocolate droplets in a cake are not necessarely dictated precisely in the recipe, but they rather tend to repeat a certain pattern because the recipe and the cooking procedures are similar; and likewise, the bodily features of the organisms result from a similar process in which nowhere there's the level of specificity that a blueprint implies (I may have almost made this up; I read that book a long time ago). --Extremophile (talk) 17:07, 23 April 2008 (UTC)

See Talk:DNA/archive_12#The_.22blueprint.22_fallacy for the last time we discussed this. (I didn't mean that to sound snappy, but posted the link so people can read the previous opinions on the topic) Tim Vickers (talk) 17:32, 23 April 2008 (UTC)
Most of the points have already been made then. I second the opinion that the "recipe" anaolgy is somewhat better to pass the idea to the lay people; I think that much more than "blueprint" it avoids the concept of exaggerated genetic determinsm, and yet is far from giving an exaggerated importance to the environment. I disagree that it's insignificant, anyway. Both are essential; neither the environment nor the genome alone turns the microbe into an elephant or vice-versa. There can not be "environmentless" organisms, but of course there aren't also genomeless organisms, with the possible exception of a fuzzy situation in the preambles of the origin of life where the division/"sustained disequilibrium" between organism and enviroment hadn't quite clearly arised, and maybe some eventual simple microbe could survive somewhat "inertially" for some time after its genome is removed and still have some functioning with what is left. Much of the autonomy attributed to genome is actually due to the fact that the cell is somewhat like an encapsulated micro-environment with most of which the genome needs to reproduce. But that's really a nerdy bio-philosophycal semi-pedantic and probably arguable digression, anyway.
About your point that DNA is just information whereas a recipe implies a set of instructions, I think that in a certain way, the genome also has recipe-like instructions, such as TATA boxes, roughly the equivalent of "add this to the mixture". The thing I don't like myself about the recipe analogy is that implies somewhat that "someone else" than the cell is doing the "cooking", but again this is not in a better situation with the blueprint analogy. In this sense, the genome is somewhat more like a computer program (alternative splicing also fits somewhat better with the program analogy than with the other two).
But I do agree that that a blueprint-like analogy has a point, but I think that it's only if we're referring more specifically to the gene/codon level than to the whole genome or an indefinite part of the DNA (which is more or less the same rationale behind the change to "set of blueprints").
I think that perhaps all the points of each analogy could be satisfied by a more complete set of analogies: the genetic code is like a computer or human language (perhaps "cell language" does the job better), the genomes are like recipes or programs written in that language, and the genes are something roughly like words on the recipe (perhaps chromosomes could be "paragraphs"). I think that it explains both the higher blueprint-like specificity of the individual genes (perhaps with the advantage that the same "word" can be interpreted differently depending on the context, which is somewhat like alternative splicing, even though I think that the analogy does not really need to go that far) and obviously the whole advantages of the recipe and program analogies for the genome are retained as well. --Extremophile (talk) 15:50, 24 April 2008 (UTC)
I suppose we don't have to choose between these two options, what do you think of the new version with both? Tim Vickers (talk) 16:42, 24 April 2008 (UTC)

Quite good and simple way to solve the issue. --Extremophile (talk) 22:53, 25 April 2008 (UTC)

[edit] hydrogen bond between the lowest O and H

Isn't there a Hydrogenbond between the lowest O and the H which is attachet to the C and therefore not marked? --Saippuakauppias ⇄ 09:35, 27 April 2008 (UTC)

No, C-H bonds are not polar, since these atoms do not differ enough in electronegativity, so the C and H will not differ significantly in charge and no hydrogen bond will be formed. Tim Vickers (talk) 17:02, 27 April 2008 (UTC)

[edit] History of DNA research

The last line of the third paragraph of this section: "However, debate continues on who should receive credit for the discovery, as the Watson and Crick article in Nature was based on Franklin's data without either acknowledgment or her knowledge.[129]" is a little strong, and slightly gossipy in tone. In fact, the part concerning Franklin's acknowledgment is factually wrong.

Franklin was in fact acknowledged in the original Watson-Crick article, in the penultimate paragraph: "We are much indebted to Dr. Jerry Donohue for constant advice and criticism, especially on inter-atomic distances.We have also been stimulated by a knowledge of the general nature of the unpublished experimental results and ideas of Dr M.H.F Wilkins, Dr R.E Franklin and their workers at King's College, London."

It would probably be better just to make note of the debate, and leave any reasons out. Something like: "However, debate continues on who should receive credit for the discovery.[129]".

87.102.65.129 (talk) 21:34, 30 April 2008 (UTC) Magsmanston

Excellent point, thank you. Yes, I see they were in the acknowledgments, so I have rearranged the sentence as you suggested. Tim Vickers (talk) 21:45, 30 April 2008 (UTC)


Watson and Crick stole the credit from Rosalind Franklin. The article should definitely be changed, although I can't do it myself since I can't remember exactly what she did (Huey45 (talk) 11:37, 5 June 2008 (UTC))


[edit] 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)