User talk:Sawagsta/sandbox

Topic Peer Review 1
You've clearly started with a very empty article and made a lot of progress and additions. Make sure all of your citations are *after* the periods at the end of sentences, some of them (such as citations 4, 7, 8, 9, 10 and many more) are floating in the middle of phrases. If you could add something to your introduction about what the definition of "canonical" means explicitly and how base pairs can be canonical or non, that would clarify things greatly. If possible (I know finding images is very difficult) but if you could provide an image in the history section of Hoogsteen himself? Also in the history section you mention different forms of DNA but don't expand on what that means. You should either explain or link to Wiki pages about the different DNA forms. There are some minor grammatical fixes needed throughout (such as the first sentence of the second paragraph under structure; "bases" should be possessive, as should "pairs" in the next sentence). Actually, that entire paragraph is poorly explained and needs expansion for readability. It states the pairs could interact with loops but not why that's a concern, translational arrangements are listed with no explanation of what they mean and how they apply to this situation, crystallography data is mentioned but neither explained in terms of applicability nor related back to structure. The last sentence in the "base pairing" section needs to be matured. Figure 3's caption needs to explain how these 6 models relate back to RNA/DNA. More biological applications would help warrant the section. Perhaps instances where function in eukaryotes is dependent on non-canonical pairing. The entire "detection" section needs to be read over for verb-subject tense agreement, fragmented sentences, and vocabulary choices. The explanation of 3DNA technology is lacking and not understood.

Overall, great additions have been made, I'm anticipating more to come, and this group has some editing to do to help make the article more clear and readable to the uninitiated. But clearly since this article was barely a stub when they started, great strides have been made and it can only get better! HReynolds2324 (talk) 17:07, 11 October 2019 (UTC)Holly Reynolds, from Chem 455

Peer Review 1
Because this “Non-Canonical Base Pairing” section is supposed to provide a summary of the topic before delving into more detail, I think that it would be useful to expand a bit on your information here. For example, maybe allude to some of the possible 3D RNA structures that can be formed. Similarly, I think that a brief explanation as to why this type of non-canonical base pairing is less stable than standard base pairing would be interesting. This can then be elaborated on in subsequent sections such as “Base Pairing”. In general, I think it would be a good idea to add some additional brief background info to this section so that the reader is more informed about the implications of this topic before proceeding to the rest of the article. In the “History” section, the explanation for the alternative-structure regarding the adenine-thymine nucleobase pair is pretty confusing. I think that this needs better phrasing. Additionally, since this is the history section, I think that it would be interesting to briefly include how Karst Hoogsteen discovered these alternative structures.

In the “Structure” section, I think that there should be much more description referring to why bases will take part in canonical vs non-canonical base pairing. For example, it is mentioned that understanding base pair configuration is dependent on the base’s surroundings. What are these surroundings, etc.? Additionally, what is the significance of these different base-pairing conformations? This would be a good place to elaborate on how these base pairings can influence tRNA recognition or any other mechanisms in which they may play an influential role. Similarly, more should be added about how the arrangement of non-canonical base pairs allow for long-range RNA interaction and the recognition of proteins / other molecules. In the “Biological Applications” section, if possible it would be interesting to find more examples of how these non-canonical base pairs influence mRNA splicing, translation, etc. Lastly, the “Detection” section needs to be revised a bit and have some sentences restructured. I also think that more information could be added to the description of you figures - particularly for figures 1 and 3.

Overall, after seeing the original Wikipedia article on this subject I think that you guys have made a lot of great progress. I just think that some of the sections are in need of some expansion to fully explain the significance of non-canonical base pairing. Similarly, I would make sure to go back through and clean up grammar / re-structure any sentences that may not read smoothly. However, I think that the final product will be a huge improvement to the original article. Esirls (talk) 03:25, 22 October 2019 (UTC)

Non-canonical Peer Review 1
The article looks great! There are definitely a lot of details added in and links to other wiki pages that would be helpful to the reader. I think something that could be improved upon is the first section, which ideally would be a general summary of the whole article. I think it would be really good if that first section included a 1-2 sentence summary of the remaining sections, allowing the reader to know what information they will find in this article without having to search through the whole article.

I think diagrams throughout the article would also be extremely helpful to the reader so that they can visualize the base pairing described in the article. Visual representation is always good for the reader to be able to have a clearer grasp of the subject at hand, especially in a molecule in which the repetition of the bonding patterns may become a bit confusing. Diagrams of the canonical base pairing (1st section), as well as non-canonical base pairing whenever they are described (move the diagram from the 3rd section to the 2nd section) would greatly assist in allowing the reader to understand what is written.

Overall, I think there could be a lot more information that could be added to this relatively shorter article. I feel like there is a good amount of history in research in this topic, as it has been around for a while and it is quite a significant discovery. The second section of history could also possibly elaborate more on the other 40 types of non-canonical base pairing, as that would add greater depth of information to the article that I don't think would be provided anywhere else. I think it is also odd how the Hoogsteen base pairing is the only non-canonical base pairing really explained in depth, and it is done so split up in the history and structure section. Maybe having a completely new section just describing the Hoogsteen base pairing would be good, as well as greater elaboration on other non-canonical base pairing structures discovered. That way, the reader would be able to understand more about how significant Hoogsteen base pairing is compared to other types of base pairing, because those aren't even explained at all. The section of biological applications also seems to be missing a lot of potential research; I feel like that section has a lot of potential to be added onto with further research of the applications of the non-canonical base pairing. I also feel like the detection section should be moved to be more near history or structure, because it is with detection of the non-canonical base pairing that we are able to see these structures - the current placement of the section at the very end seems very odd to read.

This was a pretty good article with a lot of potential to grow and add in more information. It seems like in a lot of cases, it is written "this is just one of many examples." I would highly encourage you all to find those examples and write them down! It adds so much more depth to your topic and allows the reader to see the significance of this topic, because I do believe that this topic is more important than it seems like in the article. If there actually aren't any other examples that you all can find, then writing "further research could be conducted" or something along those lines - that would be appropriate as well. Overall, good job and keep working hard! JeffLu98 (talk) 04:20, 22 October 2019 (UTC)JeffLu98

Peer Review MLibrarian
I am glad you are working on this important topic but I would strongly suggest you to revise your language. Here are some highlights:
 * 1) Reading the original Wiki article I find their language easier to understand and I want to know more. They write: "A non-canonical base pairing is an interaction between two bases.." and indeed it is an interaction. You write: "Non-canonical base pairing refers to instances in which nucleobases hydrogen bond, or base pair,..." First, it reads that it is an instance, which is not a definition per se but how often it occurs. Second, in half a sentence you bombard a reader with jargons like non-canonical, hydrogen bond, Watson-Crick base pairs (adenine-thymine in DNA, adenine-uracil in RNA, etc. that makes a reader to lose any interest on the subject. I strongly advice you to either adopt the original definition or to re-write yours. Please, remember that we write for general public and not for Molecular Biologists. Just try to explain this topic to your friend/parent and once they understand, record this final version here.
 * 2) The standard practice with any nomenclature or acronyms is to spell them out on their first occurrence in the text. So please spell out all your acronyms. General public shall not be expected to know what means for example G and U as in "Non-canonical base pairings commonly occur in the secondary structure of RNA (e.g. pairing of G with U), and in tRNA recognition."
 * 3) In the paragraph "Detection" I find first couple of sentences unnecessary and suggest completely deleting: "Watson-Crick canonical base pairing is not the only edge-to-edge confirmation possible for the nucleotide, since non-canonical pairing can take place as well. Sugar-phosphate backbone have an ionic character, which makes the bases sensitive to their environment, leading to conformational changes.[16][1] Changes like non-canonical pairing. " MLibrarian (talk) 16:38, 28 October 2019 (UTC)