Talk:Holliday junction

Holliday junction has been listed as one of the Natural sciences good articles under the good article criteria. If you can improve it further, please do so. If it no longer meets these criteria, you can reassess it.
Review: June 2, 2015. (Reviewed version).

A fact from Holliday junction appeared on Wikipedia's Main Page in the Did you know column on 22 June 2015 (check views). The text of the entry was as follows:

Did you know... that the DNA Holliday junction (schematic pictured) was originally studied for its role in genetics, and was later used as a basic structural element in DNA nanotechnology?

A record of the entry may be seen at Wikipedia:Recent additions/2015/June. The nomination discussion and review may be seen at Template:Did you know nominations/Holliday junction.

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Molecular Biology: Genetics

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Arrows on image

What do the arrows on the diagram represent? Cesiumfrog (talk) 05:42, 1 January 2011 (UTC)[reply]

Most probably, the polarity (from the 5' end to 3' end) of affected DNA strands (you could read this and the subsequent section for clarification). 80.240.162.190 (talk) 13:11, 7 January 2013 (UTC)[reply]

Maybe the arrows are in the wrong directions. I think it should be two twisted strands go IN at opposite sides and another two twisted strands go out at the remaining sides. The way the arrows are presently nothing can move. — Preceding unsigned comment added by 58.170.104.35 (talk) 03:34, 11 February 2014 (UTC)[reply]

You know, those arrows are confusing. They represent the 5' to 3' direction of the DNA, but that's not how that is usually shown, and it's easy to confuse it with the direction of branch migration. I'm going it replace it with a different figure. Antony–22 (^talk⁄_contribs) 01:47, 5 August 2014 (UTC)[reply]

GA Review

This review is transcluded from Talk:Holliday junction/GA2. The edit link for this section can be used to add comments to the review.

Reviewer: Chiswick Chap (talk · contribs) 12:57, 22 May 2015 (UTC)[reply]

This seems an interesting and well-written article; I'll take it on. Chiswick Chap (talk) 12:57, 22 May 2015 (UTC)[reply]

Rate	Attribute	Review Comment
1. Well-written:
	1a. the prose is clear, concise, and understandable to an appropriately broad audience; spelling and grammar are correct.	clarity: ok; copyright: passes spot checks; spelling: ok; grammar: ok
	1b. it complies with the Manual of Style guidelines for lead sections, layout, words to watch, fiction, and list incorporation.	lead: ok~~needs to cover whole article~~; layout: ok; weasel: ok; fiction: n/a; lists: n/a
2. Verifiable with no original research:
	2a. it contains a list of all references (sources of information), presented in accordance with the layout style guideline.
	2b. reliable sources are cited inline. All content that could reasonably be challenged, except for plot summaries and that which summarizes cited content elsewhere in the article, must be cited no later than the end of the paragraph (or line if the content is not in prose).	See comments.
	2c. it contains no original research.
3. Broad in its coverage:
	3a. it addresses the main aspects of the topic.
	3b. it stays focused on the topic without going into unnecessary detail (see summary style).
	4. Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.
	5. Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.	stable since February.
6. Illustrated, if possible, by media such as images, video, or audio:
	6a. media are tagged with their copyright statuses, and valid non-free use rationales are provided for non-free content.
	6b. media are relevant to the topic, and have suitable captions.
	7. Overall assessment.

Comments

The lead needs to be extended to reflect the article's contents. For example, the structure's involvement in double-strand breaks is important and certainly deserves a paragraph in the lead. As general guidance, the lead should summarize every section and major theme of an article. This is the main item (now that I've checked through the article); but it shouldn't take too long to draft a suitable lead.

History: ~~"..., with Robin Holliday himself initially doubting the findings." Best to avoid this construction with -ing: try "...; Holliday himself initially doubted the result."~~

~~"copy-choice mechanism" is redlinked: it needs a word of explanation here, whether or not you choose to write a short article on that topic.~~

Use in DNA nanotechnology:

~~tensegrity is linked but needs a brief gloss here.~~

~~Also, the caption of the "Diagram of a tensegrity triangle complex" doesn't really explain what a, b, and c actually are.~~

I can see there's an angstrom scale but even that really needs explaining wrt SI units (nm). Or wikilinking.

Structure: ~~please wikilink mM (milliMole/liter, I presume?).~~

"RNA Holliday junctions are known in some functional biological RNAs": it may be helpful here to explain briefly what these RNAs do, and why having a Holliday junction helps with that function, so readers can connect structure with function. I can see that this might be little more than "This gives the molecule such-and-such a shape, which enables it to present a reaction site ...", but even that would make the article easier to read.

See below, this item remains open.

"RNA Holliday junctions are..." (cont'd): I also think that this paragraph needs to be related to the "Biological function" section, or might actually be a subsection of it, once beefed up with some functional explanation. That would make "Biological function" a section with 2 (named) subsections, not a bad plan probably.

References: ~~Ref 5 is to a whole book (Hartel 2012): a page ref is needed.~~

~~Ref 8 has a Delphic '"43"' - is that a page? chapter?~~

Chiswick Chap (talk) 12:57, 22 May 2015 (UTC)[reply]

I believe I've dealt with all the items above, with the exception of the conceptual description of how the four-arm junction structure contributes to RNA function. I don't think that high-level conceptual questions like that have answers that are well understood at this point. Antony–22 (^talk⁄_contribs) 20:59, 1 June 2015 (UTC)[reply]

Then we need to say something along the lines of while the HJ influences the shape or conformation of the RNA molecules, its precise effect on function is not yet understood. Otherwise people will be reading the article wondering when it's going to get to the point and explain what the structure is actually for. The least we can do is say plainly that scientists don't know. Chiswick Chap (talk) 06:37, 2 June 2015 (UTC)[reply]

That's not quite what I meant. Simple structures like this don't have a "precise effect on function"; the function is the result of the conformation of the molecule as a whole. It's kind of like asking what is the unifying purpose of circles in automobiles. The tires, steering wheel, and buttons on the dashboard may all be circular, but there's no consistent conceptual reason for this. Antony–22 (^talk⁄_contribs) 20:56, 2 June 2015 (UTC)[reply]

No, we're wandering off topic. That isn't what I meant at all, but it's tangential to the article, applying really only to the immobile not-quite-HJs that are mentioned briefly. It'll do as it is. Chiswick Chap (talk) 21:35, 2 June 2015 (UTC)[reply]