The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.

The article was promoted by Ian Rose 02:51, 13 July 2012 [1].

DNA nanotechnology[edit]

DNA nanotechnology (edit | talk | history | protect | delete | links | watch | logs | views)

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Nominator(s): Antony–22 (talk⁄contribs) 22:37, 25 May 2012 (UTC)[reply]

This article, my first attempt at promoting an article to featured status, was up for FAC back in January. The nomination got lots of helpful comments but no support !votes, and I was encouraged to resubmit it after the two-week waiting period had expired. I opted to take a little more time to do some extra rewriting, and the article has also gotten a copyedit from WP:GOCE.

Don't be intimidated by the technical nature of this article! I have tried my best to make the concepts understandable to a general audience by explaining things simply and including background information, while including enough details to make the article useful to more technically-minded readers who are looking for an introduction to the field. This kind of comprehensive, understandable treatment of a field of current research is something which would not usually be available to the general public, since most scientific literature tends to be behind a paywall, making it especially important for Wikipedia to have these kinds of articles.

Of course, any feedback is welcome and appreciated, and I am happy to make revisions which further improve the article as part of the FAC process. Thanks in advance for your reviews. Antony–22 (talk⁄contribs) 22:37, 25 May 2012 (UTC)[reply]

All fixed. Antony–22 (talk⁄contribs) 20:16, 29 May 2012 (UTC)[reply]

Sources. Reference numbers based on this version.

A quick search for DNA nanotech articles from 2012 yields 4000+ results. The following look promising:

I see only one source in the article from 2012. For an article like this, which relies heavily on giving specific examples of experiments and research results, I would think that the most recent examples would be the most relevant, yes? The History section of the article should summarize old progress, and the rest of the body should summarize the current state of information on the subject. --Cryptic C62 · Talk 14:52, 1 June 2012 (UTC)[reply]

  • Regarding Ref. 2, I have added an extra reference that supports this explicitly.
  • Regarding Ref. 8, I believe it is not OR to describe something with an appropriate word that doesn't happen to appear in the cited text.
  • Actually, my interpretation of the guidelines is that recentism is to be avoided. Wikipedia's goal is to cover all notable aspects of a field regardless of age, based on what secondary sources such as reviews say about them. The notability of any specific advance is usually unclear until a year or two after it has been first published, and I generally try to avoid using my own "expert opinion" to decide which of the many very recent results is worth covering. Antony–22 (talk⁄contribs) 21:55, 1 June 2012 (UTC)[reply]
    • Agreed, especially for articles on nanotech. - Dank (push to talk) 15:31, 11 June 2012 (UTC)[reply]

Update from nominator This FAC seems to be going much more slowly than the first one. I've contacted all the participants in the first FAC, as well as a couple of other Wikipedians with a background relevant to this area, for their additional input. Antony–22 (talk⁄contribs) 03:41, 8 June 2012 (UTC)[reply]

Comment - In the prior review, there were a couple of editors that remarked negatively on the bold-face notations within the footnotes. I see that has not been rectified. It still looks off-putting to me. --Noleander (talk) 11:48, 8 June 2012 (UTC)[reply]

Okay, I can change them into a more standard annotation format. Antony–22 (talk⁄contribs) 01:51, 9 June 2012 (UTC)[reply]
I quite like the subject headings in the refs, altho maybe boldface is too strong for all the repetition. Could they be put into sections?Dcrjsr (talk) 17:10, 9 June 2012 (UTC)[reply]
I was just going to move the annotations from the beginning to the end of the references, but using shortened footnotes might be another viable option. It would be a lot of work though, so I'd like to hear what others think. Antony–22 (talk⁄contribs) 20:29, 13 June 2012 (UTC)[reply]

Good Work - This is a quite complete, objective, well written and illustrated article. I've contacted an RNA nanotech expert who I hope might contribute some images & info of that end. The black-background picture of the 4-way tile could really use upping the brightness & contrast, to make it clear that the short-loop ends are separate strands. - Dcrjsr (talk) 17:18, 9 June 2012 (UTC)[reply]

Comments. As always, feel free to revert my copyediting. Please check the edit summaries. - Dank (push to talk)

Support Comments by Emw: I'm not an expert in DNA nanotechnology, but I am knowledgeable about biochemistry and molecular biology and find this subject interesting. Some notes:

Lead

  • "This use is enabled by the strict base pairing rules of nucleic acids, which cause only those portions of nucleic acid strands with complementary base sequences to bind together to form strong, rigid nucleic acid double helix structures."
Can "nucleic acid" be excised from the phrase "rigid nucleic acid double helix structures" without significantly damaging this sentence? The fact that "nucleic acid" is mentioned two times previously in the sentence makes me think so. Using five adjectives to describe "structures" borders on verbose, especially in the lead. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
Good catch, I reworded the sentence to only mention nucleic acids once. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
  • "...but structures incorporating other nucleic acids such as RNA and peptide nucleic acid (PNA) have also been constructed..."
Although mentioned here in the lead, the body doesn't seem to reference any RNA- or PNA-containing structures that have been constructed. The last sentence of the 'Applications' section mentions that there has "additionally been interest" in RNA structures, but seems to indicate that they haven't yet been constructed. WP:MOSINTRO#Relative_emphasis notes that "Significant information should not appear in the lead if it is not covered in the remainder of the article...", so it would probably make sense to mention specific instances of RNA- and PNA-containing structures in the body. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
It's in the lead because it's a direct comment on the field's name. I suppose it could go in in the background section instead but that would make mentioning the "nucleic acid nanotechnology" alternate name a bit more awkward. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
I've added two refs to the RNA nanotech comment in the lead, an early specific example and a recent review. They make it followable, and could be a start for developing a child article. This satisfies my concern about needing at least a nod to the RNA nanotech subfield, which has some enormous advantages on the 3D-structure aspect. - Dcrjsr (talk) 16:09, 23 June 2012 (UTC)[reply]
Antony-22, I agree that a specific note about RNA and peptide nucleic acid structures is appropriate context when mentioning "nucleic acid nanotechnology". (And I agree that the lead is an appropriate place to make that comment about the field's name.) My concern is just that the sentence mentions such structures have been constructed, but the body seems to indicate that RNA nanostructures have not yet been constructed, and makes no specific mention of peptide nucleic acid/PNA nanostructures. The review The Emerging Field of RNA Nanotechnology provided by Dcrjsr mentions some such structures (though not PNA structures) -- perhaps these could be mentioned in the body of the article? Emw (talk) 21:04, 24 June 2012 (UTC)[reply]
I see. Yes, I can add a few sentences in the Fundamental concepts section. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]
  • I believe "mid 2000s" should be "mid-2000s" per MOS:HYPHEN #2. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
    • "Mid" is now being listed as a word in most dictionaries, and consistent use with or without the hyphen is fine. - Dank (push to talk) 12:02, 19 June 2012 (UTC)[reply]
  • Ah, good point. Unfortunately Google includes the unhyphenated phrase "mid 2000s" when searching for the hyphenated phrase "mid-2000s" specifically (i.e. with quotes), so there's no way to easily determine the two styles' relative prominence via search result count. Emw (talk) 16:44, 19 June 2012 (UTC)[reply]
Very neat, thank you. Emw (talk) 21:04, 24 June 2012 (UTC)[reply]
  • "Researchers in the field have created both static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and arbitrary shapes made by the DNA origami method; and functional structures such as molecular machines and DNA computers."
The parallelism in the sentence above is set up nicely, but its delivery seems off to me. The sentence is on the long side, too. My suggestion: "Researchers in the field have created both static structures such as two- and three-dimensional crystal lattices, nanotubes, polyhedra, and functional structures such as molecular machines and DNA computers. With the DNA origami method, arbitrary shapes have also been made." I think the "static" vs. "functional" parallelism works better than what had been there. I'm less confident about the second sentence, though I think it's an improvement overall. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
I separated out the DNA orgami mention into an extended second sentence that talks about the different types of assembly mechanisms used in the field. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
The rewording looks good to me. Emw (talk) 21:04, 24 June 2012 (UTC)[reply]
  • The File:DNA_tetrahedron_white.png image would likely look better with a transparent background rather than its current white background. If it's possible for Nanoengineer-1 to export a PDB file then I might be able to put together a nice ray-traced, transparent-background, auto-cropped image for the DNA tetrahedron, like the PDBbot images (and I'd customize it to maintain the current coloring scheme). Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
Yes, Nanoengineer can export as PDB files, and also QuteMol and POV-Ray. I'll get you a copy. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]

Properties of nucleic acids

  • "Nucleic acids such as DNA are well-suited to nanoscale construction, as a nucleic acid double helix has a diameter of 2 nm and a helical repeat length of 3.5 nm"
I'm having trouble sourcing the 3.5 nm figure for the helical repeat length of B-DNA mentioned above. I've got a copy of Lehninger's Principles of Biochemistry, 4th edition handy, and in Figure 8-15 on page 282 it says "The original model proposed by Watson and Crick had 10 base pairs, or 34 Å (3.4 nm), per turn of the helix; subsequent measurements revealed 10.5 base pairs, or 36 Å (3.6 nm), per turn." Both the 3.5 nm figure in this article and the 3.6 nm figure in Lehninger are inconsistent with the figure of 3.32 nm pitch/turn for B-DNA in the table in Nucleic acid double helix#Helix geometries. Which figure is correct? Given the apparent lack of consensus in these figures, it would probably be reasonable to cite the source of the 3.5 nm figure (or whichever value is eventually determined to best reflect reliable sources). Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
It's from Seeman, 2010 which is the reference for most of that paragraph. The pitch of DNA is one of those things where you get slightly different numbers based on the method, and few people actually care about getting a precise answer anyway, so the literature tends to be inconsistent. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
  • "to assemble in the desired conformation.[5][3]"
I haven't participated in an FA nomination in a while, but if I recall correctly, the numeric order of a group of references should be ascending. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
Fixed. This tends to happen when a pre-existing ref is added or removed somewhere else in the article, causing all the numbers to change. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
  • The File:Mao-4armjunction-schematic.png illustration has some distracting visual artifacts that could be cleaned up. The blue, red and teal arrowheads overlap with nucleotide letters. The right-angle corners in the middle of the the pink and teal arrows are misaligned. This is more minor, but the numbering starting in the upper-left quadrant seems possibly unnecessary, and at least unconventional. Are the numbers worth including? If so, I'd suggest re-labeling the numbers to match conventional quadrant numbering, i.e. as used here. (Again, this latter point about numbering is mostly nit-picky.) Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
Clearly, our standards are higher than PLoS's.  :-) I'll make these changes. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
I've made the changes to the image, although it may take a while for the thumbnails to be refreshed. Antony–22 (talk⁄contribs) 23:18, 26 June 2012 (UTC)[reply]

Subfields

  • (Non-issue) This is more of a general comment on our coverage of DNA-centric mechanisms, but it be a boon to the encyclopedia and upper-level biochemistry students everywhere if our coverage of these had accompanying animations. I find animations of molecular mechanisms to be a great learning tool, and think an animation would greatly help convey, for example, the gist of something like toehold-mediated strand displacement covered in the last paragraph of 'Subfields'. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]
The strand displacement figure is in the Dynamic DNA nanotechnology section; I put it there because that part of the article had no images while the Fundamental Concepts section already has two. Animations would be great, but designing and making them takes a lot of thought and time. See, for example, this video. Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]

Design
Structural design

  • I think I understand the gist of 'Tile-based structures' and 'Folding structures' based on this article's coverage. However, I'm having trouble piecing together the individual sentences about 'Dynamic assembly' into a basic high-level understanding. Some specific points that might help clarify things for me, and hopefully other readers:
  • This approach directly controls the kinetics of DNA self-assembly, specifying all of the intermediate steps in the reaction mechanism in addition to the final product. This is done using a nucleic acid hairpin structure as the starting material, which assembles in a cascade reaction in a specific order.
My trouble here is with the second sentence. It seems slightly ambiguous, and possibly inconsistent. Does "assembles" describe individual hairpins, or collections of them? If it describes individual hairpins, then it seems inconsistent to describe hairpins as the "starting material" and then go on to describe the assembly of that starting material -- I think most people consider starting materials to be something that doesn't require assembly, but what one assembles with. If it describes collections of hairpins, then I think it would be worth stating that more explicitly -- that "dynamic assembly" means using collections of nucleic acid hairpins as building blocks to assemble a target structure. Emw (talk) 20:42, 24 June 2012 (UTC)[reply]
  • This class of methods has the advantage of proceeding isothermally, and thus does not involve the thermal annealing step that is required by solely thermodynamic approaches.
Can the reason that dynamic assembly methods are isothermal be explained very succinctly? I think that would help. Emw (talk) 20:42, 24 June 2012 (UTC)[reply]
A second point about this sentence: 'isothermal' and 'thermal annealing' are both technical terms, and it would likely benefit readers to better define/describe those terms in context. Do the methods not involve annealing because the hairpins are already self-complemented? Emw (talk) 20:42, 24 June 2012 (UTC)[reply]
I've reworded this paragraph to be clearer and give a bit more exposition. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]

Structural DNA nanotechnology
Extended lattices

  • Have you ever considered using figure numbers in the thumbnails for this article? Especially in technically heavy areas of articles, I think it greatly help readers to label the images with 'Figure 1. (caption)', 'Figure 2. (caption)' etc. and referring to those figure numbers within the coverage of the corresponding topic. This practice is somewhat rare, but the Mechanical filter article uses it to good effect. I think it would be particularly helpful with this section, where a more explicit link between the text and the image would help users visualize what's being talked about. Emw (talk) 20:42, 24 June 2012 (UTC)[reply]
Hm, my impression (which may be incorrect) was that figure numbers were discouraged. I've added sentences to the text pointing out the appropriate images. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]
That works too. Emw (talk) 21:45, 30 June 2012 (UTC)[reply]

Dynamic DNA nanotechnology
Strand displacement cascades

Done. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]

Materials and methods

The two instances of 'using' here seems redundant in style, but a fix doesn't immediately come to mind. Can you think of a way to neatly eliminate at least one of the instances? Emw (talk) 20:42, 24 June 2012 (UTC)[reply]
Fixed. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]

From what I've combed through so far, this seems to be a high-quality article. I'll continue my review some time within the next few days. Emw (talk) 04:50, 19 June 2012 (UTC)[reply]

Thanks so much! Antony–22 (talk⁄contribs) 17:25, 22 June 2012 (UTC)[reply]
This article is among the encyclopedia's finest. It is well-researched, comprehensive, and engaging. More notably, in my opinion, the article takes an advanced subject of active research and makes it nearly as understandable as possible to the average reader, while also making the content relevant to those with background in the subject area. I think this article is a exemplar of how to successfully execute that difficult balancing act. I support promoting 'DNA nanotechnology' to featured article status. Emw (talk) 00:37, 13 July 2012 (UTC)[reply]

Comments – It's a bit of a dense read so I'm not sure how approachable this article will prove to the subject matter. But I'm not sure what to suggest as an alternative. Here are a few concerns that caught my eye:

Regards, RJH (talk) 19:22, 13 June 2012 (UTC)[reply]

Thanks for the comments. I've dealt with most of the issues raised above. The image does refer to the Properties of nucleic acids subsection in addition to the Subfields subsection, because it demonstrates maximizing the number of base pairs. I think you're right that the use of thermal annealing and lack of enzymes deserves more prominent mention; I'll have to sit down and write a few extra sentences about that. Antony–22 (talk⁄contribs) 00:08, 17 June 2012 (UTC)[reply]
Okay. The caption for the File:Mao-4armjunction-schematic.png image points to a second image that is actually a Holliday junction, rather than a four-arm junction. Regards, RJH (talk) 03:57, 19 June 2012 (UTC)[reply]
The Holliday and immobile four-arm junctions have the same structure, just the strand sequences are different. The linked image doesn't contain sequence information, and thus accurately represents both junctions. Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]

Comments.

Comment from ~SME I'm expert in the related area of protein and RNA 3D structure, am acquainted with a number of DNA/RNA nanotech researchers (Ned Seeman, Eric Schultes, Luc Jaeger, etc), and one of my former postdocs (Thom LaBean) works in this area. He reviewed the article and made a number of comments informally, which have been addressed by the editor. The mention of RNA nanotech I requested has been provided, and I added 2 refs for it; in future it should probably be expanded as a separate section or article, but I don't feel that's necessary for now. I'm not the right person to address the readability for a more general audience (which is being done by others), but I judge that the completeness, neutrality, and technical correctness are excellent. Some of the illustrations could still be improved, but their coverage and what they add to the text (esp the combination of diagrammatic structures with EM photos) is up there with the best of the scientific articles.

Therefore, I would like to vote in support, for FA status when most of the readability issues have been dealt with as well as feasible. - Dcrjsr (talk) 20:48, 24 June 2012 (UTC)[reply]

Yay! Antony–22 (talk⁄contribs) 04:35, 27 June 2012 (UTC)[reply]

Comment from William Avery

Use of "and/or" is a style breach that needs to be fixed. See WP:ANDOR. William Avery (talk) 19:51, 3 July 2012 (UTC)[reply]

Fixed. Antony–22 (talk⁄contribs) 04:29, 4 July 2012 (UTC)[reply]

Support - This is a well written, comprehensive introduction to a complex subject.[2] There are no glaring omissions, and although I realise that some readers might find some terms challenging, I cannot see how they can be rendered more simply without a loss of meaning and precision. I think the nominator has done a superb job here, particularly in explaining how the properties of DNA are exploited. IMHO, RNA nanotechnolgy [3] is a more exciting field of research, given that RNA is a more dynamic molecule; but perhaps this is a subject for another article. I still do not like the bolded headers in the references, but I can live with them. Also, I would trim the polyacrylamide gel figure to remove the wells at the top and the empty gel area at the bottom. Graham Colm (talk) 19:37, 7 July 2012 (UTC)[reply]

Support - I like the suggestion of cropping the gel image, which should be simple. With that done, would we have a consensus? And I'll try to help get an RNA nanotech article going in the future. - Dcrjsr (talk) 15:27, 9 July 2012 (UTC)[reply]

Delegate note -- didn't see a dedicated image check above but, going through each of them myself, the licensing appears satisfactory, either editors' work, PLoS/Commons, or in one case a valid FUR. Cheers, Ian Rose (talk) 02:49, 13 July 2012 (UTC)[reply]


The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.
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