Talk:DNA

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The section on "non-helical forms" desperately needs to be cleaned up.

To-do list for DNA:

 edit - history - watch - refresh

Restructure according to guidelines suggested in WikiProject Science, with the following main sections :

  • Introduction :
  • DNA in practice (avoid description on how it works here)
    • Types of DNA: by species: one DNA instance belongs to only one living organism; all organism in one species have very similar DNA; ... by topology: plasmid, ...; by place where it is found: chromosome, mitochondria, ...
    • Properties of DNA: self-replication; sequence defines proteins, ..
    • DNA in nature: found in all life forms: cells, virus, mitochondria, ...; in dead cells too; mystery of origin of DNA and life
    • DNA in everyday life: DNA used in crime investigation
    • DNA in medicine: treatments based on DNA
    • DNA in industry: genetic engineering, potential use in nanotechnology; project to create man-made life from synthetic DNA
    • DNA in science: methods of sequencing DNA
  • Structure of DNA (and how it explains the properties of DNA)
    • Overview of molecular structure
    • DNA replication
    • DNA sequencing methods
  • History :
    • Discovery of the double helix
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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] FA for DNA

Hi there. I'm hoping to move this page through the peer-review and FA processes over the next month or so. There is a great deal of excellent content here, so most of my edits will be concentrating on formatting and adding references. Any help in this process will be greatly appreciated. TimVickers 23:14, 10 December 2006 (UTC)

Hi Tim, just seen your work here. It looks great. One issue is with the figure Image:Nucleosome with spacefill DNA.jpg. I wonder if it would look better with the histones as space-fill and the DNA as ribbon? At present it is hard to make out the structure even for someone who knows what they are looking at, for those unfamiliar with histones it will be very hard to interpret. David D. (Talk) 17:17, 11 December 2006 (UTC)
As an aside the title of the current figure should read ball-and-stick DNA, or similar, not spacefill DNA. David D. (Talk) 17:24, 11 December 2006 (UTC)
Is the new version an improvement? TimVickers 19:32, 11 December 2006 (UTC)
Defintiely an improvement. I added another picture I took from commons, see what you think. i think having this top view might help a bit more as well as introducing the concept of the interactions that glue the histones and DNA together. Possibly a theme that can be introduced into the text too? David D. (Talk) 21:47, 11 December 2006 (UTC)
Looks good, thank you. As you can see, I'm working my way down through the sections from the top. Much of the history section will need to be moved to a daughter article, but I haven't reached there yet. TimVickers 21:54, 11 December 2006 (UTC)

[edit] Yeay! and random suggestions

Hey Tim and David,

I'm so happy that you're tackling this article! It's already looking good. :)

A few thoughts:

  • The pictures of the nitrogenous bases and the base-pair pictures (thanks, guys! :) don't quite agree. The former don't have the connection to the sugar-phosphate backbone that is represented by the crazy wavy line in the base-pairs. Should we amend that — maybe show the sugar or even the sugar/phosphate backbone explicitly in both? Maybe that's not needed; it's probably clear enough from the context of the wonderful colored picture above them.
Yes, I suppose we could, or I could tweak the text to make it clearer what the images show.
  • Are the lines in the base-pair picture thick enough? I think I still have the ChemDraw file somewhere.
Yes, they could be a bit thicker, but that's a minor issue.
  • Should we show the methyl group in thymine explicitly, rather than as an unlabeled line? Some lay-readers might not know the conventions.
Several of the images use that convention, we'd have to change them all. Groan.
  • Personally, I'd enjoy seeing more on the biophysical/electrostatic properties of DNA, such as its extreme charge density, Manning condensation and its superficially paradoxical ability to condense (e.g., into toroidal forms) in the presence of trivalent cations. But maybe that's too technical? :(
If you can put that in non-technical language making a clear link to biology then that would be great. I wouldn't know where to start!
  • It'd be nice to reference that young fellow who did the pH titrations suggesting a two-stranded DNA back in the 1940's, the one who was killed in a train wreck?
The history section is getting smaller and will get smaller still. Maybe a daughter article?
  • I suppose that the IUPAC definitions of the backbone dihedral angles and the numerical descriptions of the inter-base geometry are also too technical, right? Drat. Probably ditto for concept of the "phosphate backbone". :(
We could put that in the mechanical properties of DNA article?
  • What about mentioning helicases, primases, etc. by name? It would give us a chance to link to that fine article, enzyme. ;) I suppose this article does have links to articles with more details, e.g., DNA replication.
This section is under development, thanks for the suggestion.
  • Perhaps include more about the connection between genes and DNA, possibly with some discussion of SNP's? Please don't laugh — OK, I'll laugh ;) — but the January 2007 issue of Marie Claire has an article about the applications of DNA technology to cosmetics — umm, "cosmeceuticals". It says something like "Thanks to the Human Genome Project and other skin-science advances,...SNPs for genes involved in the repair of DNA damage caused by chemical pollutants and UV radiation...for a mere $270, a scientific DNA analysis by dermagenetics.com will allow us to formulate the optimal skin-care cream for you..." You see how it goes. Despite its silliness, this example does suggest that we should also consider common misconceptions and how we might allay them in our science articles. It's charming to think of Craig Venter and James D. Watson as skin scientists, don't you agree? ;)
Charming! That could go in the last section, which is still entirely unedited in this new revision.

Merrily, Willow 15:53, 12 December 2006 (UTC)

Thankfully, TimVickers 19:27, 12 December 2006 (UTC)

[edit] Suggestions for the lead section

The lead section seems a little short, as I'm sure you're aware. I also noted the "Here be dragons;)" notice at the top, asking for a full discussion before we make any changes. So perhaps this can be a special section for editors to discuss changes/emphases in the lead?

Speaking for myself, I think it might be helpful for lay-readers if we discussed the qualitative function of DNA before delving into the molecular structure. I'm worried that many casual readers won't even know what a polymer is. Could we perhaps add a short paragraph after the first paragraph, something like this:

The main role of DNA in the cell is the long-term storage of information. It is often compared to a blueprint, since it contains the information to construct other components of the cell, such as proteins and RNA molecules. The DNA segments that encode for proteins and RNA are called genes. However, not all DNA belongs to a gene; some DNA serves a structural purpose or is involved in regulating the expression of genes. Unlike proteins and RNA molecules, DNA is inert and does not act on other molecules; rather, various proteins and RNA molecules act on DNA, causing it to be unwound, copied (replicated), edited, rearranged, repaired or transcribed into RNA.

What do you think? It's only a rough sketch, but such a paragraph might allow us to touch on some important themes of the article. Willow 20:00, 12 December 2006 (UTC)

I'm ignoring the dragons at the moment, go right ahead and edit. TimVickers 20:08, 12 December 2006 (UTC)
Hi Willow, you need to be careful how you define gene here. "However, not all DNA belongs to a gene; some DNA serves a structural purpose or is involved in regulating the expression of genes." I would consider sequences involved in regulating expression to be part of a gene. It sounds like you would consider a gene to be restricted to the transcribed region. This is definitely a debatable definition as well as a moving target depending on which genes are being discussed. Here is one definition i found "a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology." David D. (Talk) 00:44, 14 December 2006 (UTC)

Hi, David, thanks very much for clarifying that for me! :) I think I'm supposed to know that (blush) but I didn't. :( If I understand correctly, open reading frame is the correct term for proteins; is it the same for RNA, too? I mainly wanted to introduce "gene" in the lead, so that we could use it to debunk common misconceptions (umm, like mine?) in the main text.

The article is looking excellent. At the risk of losing its sleekness, though, maybe we could mention a few more activities on DNA? I was thinking of recombination and viral tricks such as reverse transcriptases and integrases. Maybe a little more about the wonderful specificity of restriction enzymes; I don't recall hearing of similarly specific enzymes for RNA (I suppose there's RNase H, but that's cheating; strange omission from the RNA world, no?) or for proteases (maybe TEV? not thrombin). Perhaps mention the function of restriction enzymes in vivo, too?

I agree that the History section could be shrunk considerably. However, I wouldn't mind a verifiable statement like

Neither Watson nor Crick mentioned Franklin in their Nobel Prize lectures, despite the key role of her experimental data in developing their model.

at the end of the next-to-last paragraph. But that might provoke an edit-war, which I wouldn't wish on you for the world, especially before an FAC. It's perhaps best to stick to the science and leave such historical details for another article.

Under technological applications, I remember hearing about DNA being used in nanotechnology as a means for making regular structures reliably. I might be able to dig up a reference or two if I look hard, but I'm leaving tomorrow for the holidays and might not have the time. I probably won't have access to a computer for a few weeks, so — happy holidays! Warm and happy wishes to all, Willow 11:19, 14 December 2006 (UTC)

P.S. Would it be useful if I made a Figure of positively/negatively supercoiled DNA for the article? I've never done it, but it might be fun and instructive for me. You do have the histone picture already, though, so perhaps it's superfluous.

[edit] Section plan for functions of DNA

I've been struggling with this. I don't want to write a bloated overview of molecular biology and detail transcription, translation, recombination etc which are already covered elsewhere. Such an article would swell uncontrollably and lack focus. Instead, I thought it would be more effective to take a strictly DNA-based view of these processes and divide the sections thus.

  • Overview of biological functions - Tell the reader what is going to be discussed and provide links to explain the basic processes in more detail.
  • DNA/DNA interactions - Recombination, telomere structures
  • DNA/RNA interactions - RNA primer in DNA replication, siRNA control of transcription
  • DNA/protein interactions
  • DNA binding proteins - Histones, transcription factors
  • DNA modifying enzymes - Nucleases and ligases, topioisomerases, polymerases and DNA repair enzymes.

What do people think? I'm working on the draft Here if anybody wants to contribute. TimVickers 16:13, 14 December 2006 (UTC)

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