Talk:RNA hydrolysis

We are working on this article under the Education program. More content will be added to the article very soon.ChemLibrarian (talk) 02:16, 5 November 2014 (UTC)

Peer review and responses during the educational assignment in Fall 2014

Peer Review 1

I think your page on RNA Hydrolysis is overall really good. I was not sure if there was an original page to this topic, but I could not find it when I looked it up. Nonetheless, I still have a few recommendations in regards to the content of your page, as well as the figure I believe you tried to upload.

Content

First, I think your introduction was good, as it was short and concise. However, if I was reading this introduction as someone who has little science/biochemistry background, I probably wouldn’t know what you are really talking about and why, in comparison to DNA hydrolysis, it is so different. From what I’ve read about RNA hydrolysis, I would include perhaps a few of these facts in your introduction:

--Polynucleotides, such as DNA, are usually stable in aqueous solutions near neutral PH. For DNA specifically, half-life for spontaneous hydrolysis oh phosphodiester linkages are about 200 million year. This makes DNA, in comparison to RNA much more stable and suitable for storage of genetic information, as the structure stays in tact.

--In contrast, RNA is much more prone to hydrolysis and its structure does not usually stay in tact for as long as DNA does.

--Finally, your introduction already mentioned this, but the reason for spontaneous hydrolysis in RNA is due to the presence of 2’ OH group, which provides an internal nucleophile for transesterification of the 3’, 5’ phosphodiester linkage. As a result, there is a scission of the polynucleotide backbone. Therefore, RNA is not very good for storage of genetics information.

Secondly, I think you did an excellent job at discussing each topic of RNA hydrolysis. Since, there is only so much you can say about this topic I think you did an excellent job at summarizing it. For instance, you first described this basic mechanism of RNA hydrolysis in its own paragraph and section. Next, you described auto-hydrolysis in the next section. This part is very important because it makes it different than DNA hydrolysis. For this reason, I think it is very important that you include the differences between RNA and DNA hydrolysis in your introduction, so that your readers know why you are talking about auto-hydrolysis and its spontaneity in the first place. Next, you provide a very important part of RNA hydrolysis when spontaneous hydrolysis is less likely—enzyme cleavage. You did a good job at describing this process step-by-step, which has much more needed detail than the other sections. Finally, to end this Wikipedia page, you wrote about the possible applications RNA hydrolysis, which in my opinion, was not expected. Nonetheless, it was a good conclusion to the page.

Another thing I think you did well was highlighting the important terms/concepts linked to their respective Wikipedia pages. Reading over your page, you highlighted these terms at least once. I also thought they were appropriate. For instance, you highlighted simple words such as phosphodiester bonds, nucleophile, enzymes, and so on, for people who have very little science background. In addition, you highlighted words like hammerhead ribozyme, Ribonuclease A, hairpin ribozyme, and so on, for people who already have a good science background, but do not know about these small details. Also, I think you did not duplicate anything other content on Wikipedia, especially because I could not even find this information on the RNA Wikipedia page.

Figures

As for your figures, I did not see any on your page. There was a link to one of them; however, I could not get access to the image. I cannot talk much about this image for that reason, but you should make sure the image is very specific to the text. The title of your image is RNA Hydrolysis Mechanism, so I’m guessing this should be a problem. I would just make sure the image is original.

References

As for your references, you had six (6) total references. The references ranged from textbooks, to journals, to even articles in print. So I think you did a good job with this. You also referenced things when needed. You referenced things at least 12 times. You also did not reference things that were just simple information that could be found anywhere.

Overall

In conclusion, I think you did an excellent job at summarizing what RNA hydrolysis is. As I said, I think you need to improve your introduction, because I don’t think if a person who had little science background were reading it to get some quick background, would know what the importance of it is. Also, I think it would be nice to have that figure just to illustrate the process for visual learners. Finally, I think your references are all appropriate and their sources vary.

Dialaali (talk) 18:21, 18 October 2014 (UTC)

Topic Peer Review 2

Content

Overall your article seems well written and researched. There are a few things however that may need to be worked on a little more. Your intro is concise and gives a great description about what the main point of the article is. However the wording may be a little too technical. Your first sentence “RNA hydrolysis is a base-catalyzed reaction that breaks a phosphodiester bond in the sugar-phosphate backbone of RNA.” is great. I like that you linked phosphodiester, so people who don’t know what that linkage is can look it up, but when you mention the “sugar-phosphate backbone” I feel like a casual reader would get confused. It’s a little too technical. I would adjust the wording in the opening to be less technical. You can provide a more detailed description in the body of the wiki article.

The mechanism section is nice and concise as well. It provides a solid detailed description of what is occurring during hydrolysis with out being overly technical or using to many extraneous details. The only problem with this section is with the figure, which I talk about below.

The auto-hydrolysis section is a little confusing to me. I have been under the impression that the auto-hydrolysis and the RNA hydrolysis described in the mechanism section are the same process. It seems a little odd to repeat some of the same facts in this section. I think it would make more sense to change the content of this section slightly. I would focus more on the conditions where the autocatalysis is more likely. Focus more on the base catalysis. A figure may be helpful in understanding how basic conditions make the environment more conducive to self-cleavage. However the image of the RNA hydrolysis mechanism is more important.

The enzyme cleavage section is well written but could be expanded on in a few parts. One question that I had after reading the section is why double stranded RNA less likely to self-hydrolyze. Is the double stranded structure more stable? If you could find any articles or readings about that, I think it would be very helpful to explain that in this article. (I tried a little but had some trouble finding anything useful) I think it would also be useful to see a picture of the RNase A mechanism. You describe it really well, but figures are always really helpful when it comes to mechanisms. Again, I know only one figure is required, so I still feel the first figure (showing RNA hydrolysis) is the most important.

The final section on clinical and laboratory applications is really important and gives us a good background on how the concept of RNA hydrolysis can and is being used today. I think it would be really helpful to include an example of RNA specific cleavage with a ribozyme. I know in the Nature Medicine article by Thompson mentions using hammerhead Ribozymes to prevent the expression of a ras oncogene. That would be a great example to show how hydrolysis can be directed and used to treat people.

As for the term linking, I think you did a great job at linking all the more complicated terms to their respective pages. This will be very helpful very helpful for all the non-experts visiting the page. All the terms I was unfamiliar with were linked to and this helped me understand the article better. I could not find any article that had this information. This seems to be unique article. Nith117 (talk)

Figures

I saw that you did link to a figure in the article, however I could no see the image or click on it. There may have been a problem when it was uploaded to the page. Based on your description, I assume it shows the auto-hydrolysis of the RNA in the presence of a base. I think that would be a great image to use. It will help people with less background in biology better understand this hydrolysis process. I think one other image that would be helpful is showing the difference between ribose and deoxyribose. A regular person may not fully understand the difference based on what is said, so that would be really helpful. Nith117 (talk)

References

You have multiple resources and use a wide variety of source types. Textbooks and journal articles are cited. Your journal articles are also from higher tiered journals (Science and Nature), which makes them more trusted articles that have gone through a more strenuous review process. However you introduce a few concepts without citing the idea immediately. You tend to cite at the end of a paragraph, but you should cite after every new idea that is presented. (The RNase A paragraph is a good example. Three sentences are written detailing the mechanism, but only the last sentence is cited. I think you need to cite each sentence)Nith117 (talk)

Conclusion

I believe that you did a great job explaining the more difficult topics in this section and provided the appropriate technical information for this concept. Your page is formatted really well and has a good basic organization. However, I do feel like you can elaborate more on most of the topics. Most of the secondary sections could be extrapolated on a little more and could use a few more examples to better illustrate the topics. Besides this, you need to fix the figure to make it appear in the article and cite your ideas a little more often. Good Job on the article and I look forward to reading the final product on Wikipedia. Nith117 (talk)

GSI Comments

Thank you for your addition to Wikipedia. When finalizing your page, take into consideration the comments from the peer review.

Overall it looks good! I think with a few edits you'll have an excellent page.

Elizabeth — Preceding unsigned comment added by ChemStudent24601 (talk • contribs) 17:25, 27 October 2014 (UTC)

Suggestions from ChemLibrarian

Good work! You are very brave to star a new article. And I did a search of the topic too and didn't find any relevant page. So, hopefully, we can create the new page once you revise the article based on the peer reviews. Your steps of posting the article will be slightly different from others. I might need to create the article for you since your account may not allow you to create a new article yet. When you are ready, please contact me and I can help you to do that.

A few additional suggestions:

1. Please fix the heading level of Mechanism. It's not consistent as other sections.

2. I couldn't see the image you try to upload. Seems like it does not exist in the Wikimedia Commons. If you have difficulties with uploading and post images, please review the video tutorial here. Please let me know if you need additional help.

Editing basics - Uploading and adding images

. A few other useful pages about images are here: Help:picture tutorial and Wikipedia:Graphics tutorials

3. There are a couple of errors to fix in your reference list. The author with the red link, you can just delete the link. For the access date, you can just delete it since you don't need access date for a journal article. Access date is only needed for dynamic content like webpages since it may be different when you access it next time.

Hope it helps. Please let me know if you need additional help. ChemLibrarian (talk) 17:30, 27 October 2014 (UTC)

Peer Review Response

Thank you all so much for the very helpful suggestions. We have done our best to make use of your reviews by making the introduction more understandable, including an original figure (that we drew ourselves, using ChemDraw), and fixing certain citations (both the references themselves, as suggested from ChemLibrarian, and adding more in-text citations, as suggested by the peer reviewers) among other things. We chose not to include additional applications, as the second peer reviewer suggested, in effort to keep our article clean and succinct. Additionally, we felt the application suggested by this reviewer was too specific for the topic of our article, and that we had sufficient applications. Since the new application was not the focus of our article, we chose not to include it. We hope to contribute positively to wikipedia with this article! Cev455 (talk) and srclough (talk)