Talk:DNA

This MedLibrary.org supplementary page on Talk:DNA is provided directly from the open source Wikipedia as a service to our readers. Please see the note below on authorship of this content, as well as the Wikipedia usage guidelines. To search for other content from our encyclopedia supplement, please use the form below:

Related Sponsors

BM Pharmacy Generic pharmaceuticals at unbeatable prices. Insomnia, men's health, hair health, pain control. bmpharmacy.com
Online Pharmacy Carisoprodol, tadalafil, sildenafil, vardenafil and more... xlpharmacy.com
MedBasket.com Discreet. Inexpensive. Fast shipping. Great selection. What more can we say? medbasket.com
Frugalmed 2000 reasons to shop with us first. frugalmed.com
Ads by Tiva

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 so.
Main Page trophy This article appeared on Wikipedia's Main Page as Today's featured article on February 13, 2007.
 
This article is within the scope of the following WikiProjects:
This article has an assessment summary page.
Maintained The following user(s) are actively involved with this article and may be able to help with questions about verification and sources: This in no way implies page "ownership"; all editors are encouraged to contribute.


Contents

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

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)
The problem is that Thalidomide is a well known human teratogen, and possibly not mutagenic at all. Even if it could cause mutations, it confuses the point to use a teratogen as an example of a mutagen. There are a few references in the following link that may be of interest (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1124708) Dr d12 (talk) 00:27, 3 October 2008 (UTC)
True, I can see that argument. You're right. Tim Vickers (talk) 17:58, 3 October 2008 (UTC)

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)

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)

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)

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)

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)

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)


the "code" of DNA and RNA is never the same because DNA has the base thymine and when DNA is transcribed to RNA it is changed to uracil. Blanarae (talk) 00:49, 22 September 2008 (UTC) by the way.

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)

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)

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)

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)

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)

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)

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)

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)

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)

"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)

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)

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)

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).

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)

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)

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)

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)

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)

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)

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)


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)

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 contribu