User talk:Perescameron/sandbox

Dear Phu, Cameron, and Arjun,

Congrats on finding a new topic to add to Wikipedia. RNA origami is extremely interesting; I think you guys have a lot of opportunity with this choice.

That being said, there were several things I noted that could increase the quality of your article, the first being a set of figures. If RNA origami is anything like DNA origami, I imagine a large part of what makes RNA origami so unique has to do with the visual representations of it. I think adding several figures with representations of what RNA origami looks like is critical to your article. Granted, these would be difficult to illustrate yourself, and I doubt there are any free-licensed pictures of RNA origami out on the web.

There were several grammatical issues in your article that can be easily fixed. For example in the first paragraph your group wrote, "As RNA origami has recently be founded, there is much further research to be done to see the pros and cons..." I think it would make more sense to say something along the lines of: "Due to how recently RNA origami was discovered, there is much further research that needs to be done to fully evaluate the pros and cons..." Later on you wrote, "DNA origami has been studied while approximately a decade now, while the study of RNA origami has only recently begun..." The use of "while" here is out of place. There were several other issues such as this throughout the article; I think going back through to revise and correct these will make your article much easier to comprehend.

I think a good rule of thumb to follow in your article would be to try and utilize a similar page structure as the Wikipedia entry for DNA origami. I'm sure people will come across RNA origami in their search for DNA origami, and vice versa. People will also most certainly compare and contrast the two. When you have parallelism between similar concepts, this makes these concepts easier to grasp for a new reader. With that being said, I think your page should be structured to have an overview section, followed by a bulleted applications section. In addition to this, a detailed figure on the top right side of the page would pull this article together very well.

I think you guys have a good start to an excellent article. I think what you guys should focus on now is adjusting the page structure, adding figures, correcting grammar and word choice, and including applications for RNA origami. I know RNA origami is new, but are there additional sources you can cite? If you do all of these tasks your article will be even better.

Best of luck in your revisions,

Colin Eaton

Colieato (talk) 15:03, 22 October 2017 (UTC)

Hello Phu, Cameron, and Arjun,

To begin, there are a number of grammatical errors that will need to be addressed. For example, in the first paragraph, you say, "...letting the RNA able to create particular shapes to organize these molecules" when it could perhaps be better worded as "...allowing the RNA to create particular shapes to organize these molecules." These are minor grammatical errors and did not prevent me from understanding the draft, but it would certainly help to fix these errors.

In addition, in the second paragraph, you mention, "The first work in RNA origami appeared in Science by Cody Geary, Paul Rothemund, and Ebbe S. Andersen" and cite it afterwards. I think that it is redundant to mention the authors and the journal in the sentence if they can be found in the citation.

Finally, you mention that RNA origami are produced using the cell's naturally-occurring enzymes, but perhaps you could elaborate more on how researchers were able to use these enzymes to "design" RNA molecules. It was confusing for me because you write that RNA folding cannot be predicting by current computer algorithms, yet it appears that the researchers are somehow able to form the molecules that they want.

That is all of the critiques that I have so far. I wish you the best of luck as you continue with your draft!

Justin Yoon — Preceding unsigned comment added by CHEM455 (talk • contribs) 07:22, 24 October 2017 (UTC)

Daniel Harris: Suggestions
Hello all,

I very much enjoyed reading your article! I think that RNA origami was a great topic to choose—it builds off of material we learned about in class and also appears to be an up-and-coming research topic. I only have a few suggestions to improve the article before it is published.

To begin, I think it could be good for you to define “nanoscale folding.” I assume this means forming a particle out of RNA that is on the order of a nanometer, but I think defining this more explicitly may help.

You say a few times that RNA origami is a very new research topic, such as in the first paragraph (“RNA origami has recently been founded”) and in the third paragraph (“ the study of RNA origami has only recently begun”). I think it could be good for you to cite specific dates of when the first papers on RNA origami were published. This would provide the readers with an even better idea of the state of RNA origami research and just how new the topic is.

I also think it could be good for you to talk more about the potential applications of RNA origami. You do mention it at the end of the third paragraph by stating that it can be used to organize cellular enzymes into distinct groups. I think that talking about its potential applications would make the topic seem more worthwhile and valuable, and I am sure there are some cool applications for the topic!

Lastly, I think it could also be helpful to include an image of an RNA origami pattern that has already been made. In the second paragraph, you reference the work of Cody Geary, Paul Rothemund, and Ebbe S. Andersen. Although you do a great job describing the RNA origami pattern they created, I think it would help the reader to include an image of RNA origami alongside the text description.

Overall, I think you do a great job describing what RNA origami is—I left with a clear idea of what it is and how it is made. I think that going beyond this a bit would further strengthen your article, and I am excited to read the final product!

MLibrarian's Topic Review
Excellent topic! Congratulations! Fresh ideas are always welcomed! Couple of comments: 1. This topic definitely overlaps with DNA origami topic on Wiki and in order to publicize your article it would be great if you hyperlink some of the concepts to the DNA origami Wiki page. For example, in your sentence "Although inspired by the DNA origami techniques..." or in the title "Comparison of DNA Origami vs RNA Origami"- hyperlink DNA origami concept. After your article is published on Wiki and lives there, I would recommend to slightly edit DNA origami Wiki page to hyperlink some of the concepts there to your Wiki page.

2. Your section titles shall be in Bold, so that reader can easily focus on specific section. You may want to adopt the structure from DNA oregami Wiki page

3. This article would definitely benefit from Figures

4. Grammar: "letting the RNA able to create .." - please correct to "letting the RNA to create..." or "enabling the RNA to create..."

5 Grammar: "RNA origami is done by being synthesized enzymatically, and fold into their particular shapes while being synthesized" - please correct to "RNA origami is synthesized by enzymes that fold RNA into particular shapes"

6. "DNA gene" - consider hyperlinking to Wiki pages on "DNA" and "gene"

7. Sentence "As RNA origami has recently be founded, there is much further research to be done to see the pros and cons of this new technique." - shall be in the end and changed to "RNA origami is a new concept and research on this topic is ongoing". In fact, you already duplicate it in your sentence "RNA origami is a much newer process than DNA origami; DNA origami has been studied while approximately a decade now, while the study of RNA origami has only recently begun." So definitely avoid duplicating - once said is enough. And it's good to have this statement as sort of conclusion to your article.

8. This sentence "DNA origami involves chemically synthesizing the DNA strands and arranging the strands to form any shape desired with the aid "staple strands." cannot be here in this form. You are not talking about DNA origami here. You shall revise it to something like "In contrast to DNA origami (hyperlinked) RNA origami......" In fact you have a whole section on "Comparison of DNA Origami vs RNA Origami", which shall start with "Although inspired by the DNA origami techniques established by Paul Rothemund[3], the process for RNA origami is vastly different. " and continue with "In contrast to DNA origami (hyperlinked) RNA origami......"

9. Sentence "The first work in RNA origami appeared in Science by Cody Geary, Paul Rothemund, and Ebbe S. Andersen" - please only use PI's name for this and since you give a reference, there is no need to duplicate it in the text. Two sentences, this one and the following one, shall be shortened to "The first work in RNA origami, published by (PI's name)" [Ref], describes RNA molecules that fold cotranscriptionally into rectangles and then further assemble themselves into larger honeycomb patterns " I also suggest this to be the first sentence of your Overview section.

10."adenine (A), cytosine (C), guanine (G) and uracil (U)"- consider hyperlinking to other Wiki pages

11. "non-canonical base pairing." - change to "non-canonical base pairs" and hyperlink "base pairs" to the Wiki page on those.

12. Please hyperlink "RNA polymerase" to its Wiki pageMLibrarian (talk) 14:41, 27 October 2017 (UTC)

Nils' Comments
This is a good start. Keep in mind that this is an article for a broad audience, so start out with a much broader introduction to DNA/RNA nanotechnology and cross-reference whatever articles you can find on the topic. Explain how RNA folds into complex structures naturally, but in this case the designer wants it to fold into a very specific shape as inspired by Rothemund's DNA origami paper. Perhaps also explain in more depth (with figures and references) the topological principles that can be used for RNA origami designs; this then will naturally connect to the role of RNA in the cell that you elude to already.

Gillian's Comments
Great job! As others have mentioned, I would also echo that you should include some ways in which the folding can be controlled starting from computer aided sequence design. Also what type of nucleic acid interactions are important to consider for folding? You may want to discuss more on the variety of designs that have existed.