Talk:DNA base flipping

Untitled

We are in the process of developing this article. If there are any suggestions out there. Please let us know! Amontei2 (talk) 15:25, 28 March 2014 (UTC)

Comments from Cchandu1

The article seems to be coming along great! The lead section is a good introduction to the topic, concise, clear with inline citations, and a neutral point of view.

The contents for each section do seem to be appropriate. Also, the images placed along-side the text are very useful especially when trying to understand what is happening in these passages. For the “Experimental Approaches” section, it was great to read about techniques that work differently. Adding a few more images here could really help the reader grasp a better picture of the results seen.

One part that you could consider adding more information to would be to the end of the “Discovery” section. It ends with mentioning the hypothesis of this process but it could help to know when this process was definitely proven.

Wiki-linking does seem to be appropriately used throughout the article page. The only part that you may want to consider additional use of this to the end of the “Discovery” section when mentioning the other proteins “helicases, recombination enzymes, etc…”

The references included are appropriately used throughout the page through the use of inline citations. The references used in the lead section and a few throughout the rest of the page do seem to all come from reliable sources.

I look forward to seeing how this page will develop and will continue to add reviews onto this page.

Cchandu1 (talk) 16:05, 28 March 2014 (UTC)

Thank you Cchandu1 for the great feedback, we will definitely consider your suggestions :) Amontei2 (talk) 18:21, 30 March 2014 (UTC)

The page looks to be coming along really great! I saw that you did make changes to the Discovery section and seems to have worked out really well. I look forward to seeing this page once complete.Cchandu1 (talk) 05:19, 16 April 2014 (UTC)

Comments from Klortho

Hi. Outstanding job, so far! I did not have time to read the whole article, but here are some comments on the first half.

• General
  • Some parts are written at too technical a level. Remember that your target audience should be a smart high school student or college freshman, not a biologist.

• Lead
  • I think you could use more wikilinks here. Yes, it's good not to have too many in the lead, but you have none, and some of the terms could definitely benefit.
  • "it has shown" -> should be "it has been shown"?
  • I think, here in the lead, you could also add a sentence or two summarizing the mechanism, and naming the major players in the process. For instance, is there a generic name for the enzyme that performs this? If not, is C5-methyltransferase one such enzyme? Are there others? Even after reading the "Mechanism" section, I am still not sure.

• Discovery
  • The first sentence is at too technical a level. For example, what is a "C5-cytosine DNA methyltransferase", as opposed to an ordinary methyltransferase? I should probably know, but I don't. If the "C5-cytosine" part is important, then you need to explain it. If not, then drop it: simplify the language.
  • Taxon names, e.g. Haemophilus_haemolyticus, should definitely be wikilinked.
  • "When the 2.8Å structure ..." - again, too technical. You mention the "2.8Å structure" without first introducing it, and without ever explaining what it is.
  • Copy-edit for grammar: "These observations led to the hypothesis of this feature be employed "

• Mechanism
  • I think this could be edited for clarity.

• Experimental approaches
  • Maybe you could make the title of this section more specific. "Experimental approaches" to what?

Klortho (talk) 22:15, 30 March 2014 (UTC)

Thank you Klortho for the great feedback! We will definitely work on the simple wording aspect of the article! Amontei2 (talk) 14:32, 31 March 2014 (UTC)

Comments from DHayes14

The article is looking to be in great shape so far! I have reviewed your article and have some comments/suggestions that I hope you will find helpful. Please feel free to let me know if any of this information would benefit from further clarification.

I appreciate that you have clearly presented each category and that the categories are logically sequenced. The lead is presented early in the text and it uses words that are familiar to the reader. Words and terminology are consistent throughout the document and the sentences used are short, simple, direct, and neutral. The titles, subtitles, and other headers help to clarify organization of the text; however, I agree with Klortho that you may want to consider tweaking the “Experimental Approaches” title so that it is more specific to the prose that follows.

The graphics you have chosen to use so far are helpful in explaining the text, easy to understand, and seem as though they would be meaningful to the audience. The text and graphics go well together and they are simple and uncluttered. Each graphic is directly related to one message.

As for the “readability” of this article, I wanted to mention that I ran a “Flesch-Kincaid Grade Level” analysis and it appears that it is written at a 12th grade level. It seems to me that you are doing a good job at writing for your target audience.

I have added your article to my “Watchlist” and I look forward to seeing new and interesting information added as the semester progresses. DHayes14 (talk) 13:29, 1 April 2014 (UTC)

Thanks for your suggestions! I didn't know about “Flesch-Kincaid Grade Level” analysis. Thanks for running it and letting us know the results. I know we can make it a little better and a little less technical, but I like knowing what level we are currently! Magladem96 (talk) 00:17, 2 April 2014 (UTC)

I checked out your updated article page and it is looking great! I noticed that you updated the lead section with wiki-links and additional prose and I think that the section benefited from those changes. The information within the "Discovery" and "Mechanism" sections is clearly presented and easy-to-read. DHayes14 (talk) 16:54, 15 April 2014 (UTC)

I took a look at your article page and I am impressed by the number of quality references that you have added. Looks great! DHayes14 (talk) 16:44, 22 April 2014 (UTC)

Thanks! we are definitely working hard on it :) Amontei2 (talk) 17:50, 22 April 2014 (UTC)

I had a chance to review your "Experimental approaches for detection" section and I wanted to say that you did a great job of capturing the essence of each diagnostic tool while adding new information that is not already included on each tool's wiki page. Great job! DHayes14 (talk) 14:08, 6 May 2014 (UTC)

Comments from Amanaresi

Hi Ana and Jen! I haven’t read others’ comments as to not be biased so I hope this isn’t too repetitive! I’m not sure what state the article was in before you started working on it, but overall it looks pretty good! Some comments/suggestions (note that I compiled these thoughts based on the state of the article yesterday afternoon...I noticed that you've made some changes since then so feel free to ignore some comments!):

In the first general paragraph, it is mentioned that “a base in the DNA structure is rotated out…so that the enzyme can perform work on it.” May want to clarify what is meant by work?

For about the first half of the article, there seem to be no references cited. I think the addition of sources here would be a major improvement, especially for the factual information in the Discovery section, and where phrases such as ‘recent research has demonstrated…’ are used.

I think the addition of some wikilinks for certain mentioned things could be helpful, e.g. RNA polymerase, DNA polymerase, DNA methylation, and the experimental approaches listed such as x-ray crystallography.

I think Experimental Approaches as a section header could be clarified. Maybe something like Detection (or Visualization?) Techniques/Methods.

Finally, I’m not sure the last sentence in the NMR spectroscopy section is needed (Therefore…base flipping.), or it could be combined with the first sentence.

I think you are in great shape at this point, and I think the images are well placed and clear. Good job!-Amanaresi (talk) 01:40, 2 April 2014 (UTC)

Thank you Amy for the great suggestions, we just changed the section heading for the experimental approach as suggested by you and Klortho!Amontei2 (talk) 23:11, 3 April 2014 (UTC)

Hi Ana and Jen! Just wanted to comment that your article is very well formatted, not cluttered at all and has great information and images! I find it very clear and informative, great job!-Amanaresi (talk) 04:43, 30 April 2014 (UTC)

Article updates in progress

Hello everyone and thank you for all the great comments! We are updating the article following your suggestions above and we would love some follow-up comments that you might have. Please post these comments here so we can easily find them and address the issues as needed. Once again, thank you for all the help! Amontei2 (talk) 00:07, 4 April 2014 (UTC)

HI Ana! I just found out that we don't need to source the same reference twice in a row. For example, in our discovery section. We just need to cite it once. I'll make the correction during our third contribution. Magladem96 (talk) 21:31, 13 April 2014 (UTC)

Discovery Section Edits

Hi! I was thinking about re-wording the discovery section, but wanted to use this space to test it out before I did on on the article space. Please let me know what you think! Magladem96 (talk) 02:35, 4 April 2014 (UTC)

• Discovery Section:

Base flipping was first observed in 1994 when researchers Klimasauskas, Kumar, Roberts, and Cheng used X-ray crystallography to view an intermediate step in the chemical reaction of a methyltransferase bound to DNA. The methyltransferase they used was the C5-cytosine methyltransferase from Haemophilus haemolyticus (M. Hhal). This enzyme recognizes a specific sequence of the DNA (5'-GCGC-3') and methylates the first cytosine base of the sequence at its C5 location. Upon crystallization of the M. Hhal-DNA complex, they saw the target cytosine base was rotated completely out of the double helix and was positioned in the active site of the M. Hhal. It was held in place by numerous interactions between the M. Hhal and DNA.

The authors theorized that base flipping was a mechanism used by many other enzymes, such as helicases, recombination enzymes, RNA polymerases, DNA polymerases, and Type II topoisomerases. Much research has been done in the preceding years and it has been found that base flipping is a mechanism used in many of the biological processes the authors suggest.

Thanks for any input! Magladem96 (talk) 02:40, 4 April 2014 (UTC)

Looks good to me, the language is easier to understand and you explained M. Hhal nicely! Amontei2 (talk) 13:43, 4 April 2014 (UTC)

I particularly like this section! I think that it is a great addition and others interested in this topic will benefit from having this information available. As you work on this section you may want to consider adding more wikilinks to the text. Some of the possible wikilinks could include: enzyme, double helix, and DNA. Regarding the last sentence "Much research has been done in the preceding years and it has been found that base flipping is a mechanism used in many of the biological processes the authors suggest" you may want to think about adding references to published research studies to beef it up a little. DHayes14 (talk) 17:34, 8 April 2014 (UTC)

Thanks! I appreciate your review and suggestions! Do you know how much wikilinking is too much? Most of the terms I have wikilinked somewhere else in the article. I didn't want to over-do it, but I also want to make sure it's easy to get the info the reader needs. I also like your idea of adding some citations to the last sentence. Thanks! Magladem96 (talk) 23:02, 8 April 2014 (UTC)

That is a great question! I really don't know how much wikilinking is too much and I am considering looking at other class B or GA articles to see what is "normal". I have been given this feedback on our own article page from the AO so I am may be trying to be uber-careful about under-wikilinking. You should definitely wikilink at a level at which you feel comfortable :) DHayes14 (talk) 23:22, 8 April 2014 (UTC)

I don't think there is such a thing as too much wiki-links, with that said I think we should just make sure we don't wiki-link the same work twice! Good progress so far :) Amontei2 (talk) 00:56, 9 April 2014 (UTC)

I also think the updates to the Discovery section are helpful and clear. I like that you discuss x-ray crystallography, and then make that the main experimental detection technique later in the article, and remind the reader that this was how base flipping was first observed. As for too much wikilinking, I personally think it is possible--but you also have definitely not reached that point! I think you have a good amount of linking right now-and thanks Ana for the reminder not to wikilink the same topic more than once. I will need to check our article for that!`Amanaresi (talk) 02:50, 9 April 2014 (UTC)

Comments from Mnemcek (peer review 2)

First of all, this is a great topic for a wiki page. I could be mistaken, but if I remember correctly there was no base flipping page on Wikipedia a few months ago, so thank you for working on this page! This is definitely an important topic to discuss and you've done a great job so far adding information to this article. I especially like the organization of the article. Each section adds important information in a logical order. I also like the use of wikilinks in the article to direct less-informed users to pages regarding the related genetic/molecular biology topics that are associated with DNA base-flipping. You have included plenty of references to credible sources that support the information in your article.

One addition I might add to your article is a section discussing the implications of DNA base-flipping on human disease. I'm not sure if there is a lot of information on this, but if there is, it might be beneficial to include. I'm not sure if you came across anything on human diseases related to base-flipping in your research on this topic. The disease implications may be too indirectly related to include, but it might be good to briefly discuss these implications regardless.

Another thing to consider adding is a figure, image, or possibly even an animation for the "Mechanism" section of your article. This would be a great way to display the mechanism visually, since it is such a specific biological process.

I also have a question about the abbreviation M. Hhal. Should this be italicized in any way, since it refers to a specific species?

Finally, I would recommend adding a "See Also" section at the end of the article. This list could include some of your wikilinks (DNA repair, methylation, etc.) and also some general related topics like protein structure, epigenetics, epigenomics, DNA structure, etc., just to give readers some more context and resources. Mnemcek (talk) 20:08, 14 April 2014 (UTC)

Thanks for your suggestions! I'll look for a mechanism picture - there are several good ones, but we don't have permission to use them. We'll keep looking though. And the "See Also" section was a section we were going to add in the next contribution - so great timing! Thanks! Magladem96 (talk) 22:38, 14 April 2014 (UTC)

Thanks again for taking the time to review our article!Amontei2 (talk) 20:21, 16 April 2014 (UTC)

I've been looking into whether we should italicize M.HhaI or not. In some journals it is italicized, in some it isn't, and in others only part of it is italicized. I think Ana and I will just have to decide which we prefer and then be consistent. Thanks for the suggestion though! Magladem96 (talk) 00:36, 23 April 2014 (UTC)

Review 2 from Graeme

ON the topic of Wikilinking, there is no need to repeat the links too much. But once you are in another section it is OK to repeat a link. Some kind of technical terms still have no explanation or link. For example: link DNA once in the lead paragraph (otherwise I think the amount of linking in the lead is fine), M. Hhal, C5-cytosine, free-energy barrier, UV radiation could link to an article on UV radiation to DNA, dNTP, -10 element, strand invasion, homologous recombination, Cancer epigenetics talks about DNA methylation in cancer, S-Adenosyl methionine, S-Adenosyl-L-homocysteine, HinP1I endonuclease, high salt back-extraction, hanging-drop vapor diffusion, FAST detector, refined apo structure, X-PLOR, MERLOT, TRNSUM, 4‑amino‑6‑methyl‑7(8H)‑pteridone or 6MAP but there looks to be no article yet, Pyrrolo‑C (or is this Pyrrolo‑dC?).

• Using a term like "Recent research" causes the writing to be out of date in the future, so it is much better to be more specific about when that research was 1990s, 2000s or what?
• In "Tn10 Transposition" should the second T be a t?
• "Studies have shown that " sounds like a space filling clause to me.
• "In this 2006 published work by Horton and colleagues" another piece of fluff, instead just make the statement and reference it clearly to that paper.
• The big quote from Cheng is not needed as it is not some controversial opinion or famous statement, better to rewrite this in your own words.
• "to study important the dynamic aspects" something is wrong here.
• The NMR spectroscopy paragraph should tell us more about what has been revealed about base flipping, currently it just teases us without giving us any information.

Graeme Bartlett (talk) 21:15, 15 April 2014 (UTC)

Great suggestions! Thank you for reviewing and providing feedback! We'll definitely add additional wiki-links. What if the page doesn't exist? For example high salt back-extraction or hanging-drop vapor diffusion. Should we still add a wiki-link to show that there is nothing yet? or just leave it not wiki-linked? I really appreciate your feedback on our choice of words. We'll look into each of your suggestions. Magladem96 (talk) 01:55, 16 April 2014 (UTC)

Thank you for all the suggestions, we will definitely consider these changes. Amontei2 (talk) 20:23, 16 April 2014 (UTC)

Where the article does not exist, that will make what is called a Red link. These are OK to create, even if red looks scary. But you can do a bit of a search to see if there is an article with another name on the topic (then create a redirect). Alternately you can click the red link and then create a stub with one or two sentences, to say what it is. Anyway this is also being nominated for WP:DYK, and if it succeeds it will get a listing on the Wikipedia main page, and be read by hundreds of people. This is probably the last chance (last couple of hours) to have a really cool picture. Graeme Bartlett (talk) 21:29, 16 April 2014 (UTC)

Ok. I have looked and looked for a cool base flipping picture. I can't find any that has permissions so that I can use it. I created the top picture in our lead by modifying another picture. I can't even find a picture that I can modify. I'd love to find one that shows an enzyme around the DNA with the base flipped out into the active site. I'll keep looking or see if I can come up with something. What is the saying - "It's an honor just being nominated."  :) Ana and I will continue to improve it, even if we don't win theWP:DYK. Magladem96 (talk) 22:54, 16 April 2014 (UTC)

I looked for some images too and videos with no success :( Thank you for all the feedback, and I will make sure to improve the NMR section! Amontei2 (talk) 01:06, 18 April 2014 (UTC)

I have a question that I'm hoping you can answer: I found an article that has a picture that I was thinking about using: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3380923/#__ffn_sectitle. Under copyright it says "This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." Can I just upload the picture to Wiki Commons? If so, how do I determine what type of Creative Commons license it is: Creative Commons Attribution 3.0, 2.5 or CC0 Waiver? I'm nervous about plagiarism and don't want to do anything wrong. Thanks! Jen Magladem96 (talk) 23:15, 22 April 2014 (UTC)

Over here http://www.plosone.org/static/terms it links to http://creativecommons.org/licenses/by/2.5/ so it's CC-BY-2.5. Images with this license are OK for Wikipedia or commons. Graeme Bartlett (talk) 10:23, 29 April 2014 (UTC)

Comments from Tatabox8

You article looks practically complete. Great job! Your lead section is clear, concise and well written. The article is organize and flows nicely. I see that you have appropriately added wiki links to the article. All the images that you have are great and have proper citations. You guys went through a great deal of research with an impressive amount of references used in this article. Even though, we discussed this topic in class I feel like I learned even more information reading through your article so, I know the audience looking up this topic will be thankful you created a wiki page. I know the wikipedian above mentioned red links are ok, but I feel that they are useless if they dont lead to another article giving more detail on the subject matter. I guess society has engrained in my head that red means error I wish wiki made those green instead it would be less alarming, but still not so useful. I agree with Graeme that if you can link it to another article that would be more useful for the reader or not have it at all. (Just my opinion though) I know images are hard to come by checking whether they can be used commercially, but if you could add one to the mechanism section that would be good or even NMR spectroscopy. Overall, you guys have done a great job! Congrats on being nominated for the WP:DYK!Tatabox8 (talk) 03:50, 24 April 2014 (UTC)

Thank you Linda for your input :) We are still working hard to get that image, but it seems like other students are having the same issues. Good luck on your final edits to your article. Amontei2 (talk) 13:23, 24 April 2014 (UTC)

I'm glad you guys were able to find some new images to add to your article. They are spaced out nicely. I just added some spacing between the hybridization probing section and see also, there was some word wrapping around the image and now they are separate sections.Tatabox8 (talk) 04:00, 4 May 2014 (UTC)

Thanks for adding the space! I've tried playing around with adding spaces, but Wikipedia always takes them out later. I hope this one sticks!  :) Jen Magladem96 (talk) 10:50, 4 May 2014 (UTC)

I see what you mean by wiki taking out the spacing again. I looked at it just now and it went back to wrapping. :( Tatabox8 (talk) 16:15, 4 May 2014 (UTC)

So I moved the picture to the other side. I think that will fix the See Also section spacing.  :) Magladem96 (talk) 19:10, 4 May 2014 (UTC)

Nice, I'm not sure why I didn't think of that in the first place. :)Tatabox8 (talk) 20:12, 4 May 2014 (UTC)

New Image?

Model of Entamoeba histolytica DNMT2, Demonstrates DNA base flipping

I uploaded an image to Wikimedia Commons. Do you think it would be beneficial to include it?

https://upload.wikimedia.org/wikipedia/commons/4/48/Model_of_the_EhMeth-DNA_complex.jpg

Magladem96 (talk) 19:44, 27 April 2014 (UTC)

This image can be benefical to your article. Is Hhal the same/similar to Mhal? This could be a picture added to your discovery section if it is. I'm sure you will add a description of what the picture is showing as well.Tatabox8 (talk) 21:28, 27 April 2014 (UTC)

I think that image looks great!! Good job working on that :)I just added a chemical shift image on the NMR spectroscopy section.Let me know what you think! Amontei2 (talk) 15:29, 28 April 2014 (UTC)

The NMR image looks great! I like that you put it on the left side.Tatabox8 (talk) 03:03, 29 April 2014 (UTC)

Comments from Neelix

I am impressed with the work you have been doing on this article. Here are some recommendations for further improvement:

1. There should be no need to include any citations in the lead as the lead should only be a summary of the body.
2. All information should be sourced; much of the first paragraph of the "Discovery" section is currently unsourced, as are other portions of the article.
3. DNA base currently redirects to the Nucleobase article, but there is no mention of the term "nucleobase" on this article, nor is there any mention of the terms "DNA base" or "DNA base flipping" on the Nucleobase article. Can the connection between these concepts be clarified somehow? Are "nucleobase" and "DNA base" synonyms?
4. This article currently has only two incoming links from other Wikipedia articles. I would recommend linking to this article from other articles, either manually or by adding a relevant navbox. You may wish to consider whether or not this navbox would be suitable.
5. In order to be considerate of users with visual impairment, it would be beneficial to add alternative text to the images.
6. Any other Wikipedia article linked in the body of this one should only be linked once, but some are currently linked more than once, such as DNA, Haemophilus haemolyticus, RNA polymerase, etc.
7. The article would look better if the lead image was moved to the top of the article so that the image and text of the lead were side-by-side.

Thank you for doing such great work with this article. Please let me know if you have any questions about the above. Neelix (talk) 20:54, 27 April 2014 (UTC)

Thanks for you suggestions!

• We'll remove the citations from the lead. Thanks!
• We were told that you only cite the same source one time per paragraph. For example, all of the discovery section is sourced from the journal article where it was first described. How should we handle this situation where most sentences in the section come from the same source?
• Thanks for letting us know about the nuceobase link - we'll check it out and fix it if it's wrong.
• I manually added the incoming links because since this is a new page, it was orphaned. I did some searching around, but I couldn't find other articles that used the phrase base flipping so that I could link it.
• Great suggestion about the visual impairment consideration. We'll definitely add that to our to-do list.
• Another question - we were told to link as much as we could and that we should not link the same article twice in the same section, but we could link the same article in different sections. What is the appropriate Wikipedia practice?
• I'll take a look at moving the image up - we're also interested in improving the overall look and feel of the page!

Great Suggestions! Thanks again! Jen Magladem96 (talk) 21:29, 27 April 2014 (UTC)

Thank you for reviewing our article! As mentioned by Jen, we will make sure to address it all soon. Amontei2 (talk) 15:35, 28 April 2014 (UTC)

After receiving conflicting suggestions regarding red wiki-links, multiple wiki-links to the same article, and citing the same source in back-to-back sentences, we decided to do the following (per Wikipedia:Be_bold):

• remove red wiki-links
• cite the same source in back-to-back sentences for clarity - we want it to be obvious that where we got the information from
• use one wiki-link to a different article per section, but can use the wiki-link to the same article in a different section

Magladem96 (talk) 16:32, 3 May 2014 (UTC)

Comments from Wpeissner

This already a very, very good article. Congratulations for the terrific progress you have made so far! I can only try to suggest some minor additions or corrections:

• There are many cases of broken wikilinks (appearing in red), for example: C5-cytosine methyltransferase, HinP1, Crystallographers, M.HhaI, hanging-drop vapor diffusion, FAST detector, TRNSUM, chemical shift analysis, (4‑amino‑6‑methyl‑7(8H)‑pteridone). Consider removing the wililink or modifying the term for proper linking.
• Passive base flipping: It is mentioned twice in the text (in the lead and in section "Mechanisms") that base flipping can also occur by a passive process, unfortunately without further explanation. I'm wondering if maybe a given base has a high probability of forming hydrogen bonds with its paired partner, but still a small property of flipping out. So, is this a purely stochastic process? Is the frequency of spontaneous base flipping temperature dependent? Can you cite any literature reference on the frequency of passive / spontaneous base flipping?
• In the last sentence of the "Discovery" section, you write: "Much research has been done in the preceding years and it has been found...", maybe this should read following years? (referring to the research that has been done after the initial discovery?)
• In section "Mechanism", it is unclear to me if the free-energy barrier can be lowered by 17kcal/mol or to that amount.
• In section "DNA methylation", the fragment "therefore, resulting in gene regulation in eukaryotic cells." is lost between the sentences. Consider rewording this part, maybe by intergrating it into the preceding sentence.
• The next sentence in section "DNA methylation" starts with "in dramatic cases". I think that phrase is somewhat misleading: DNA methylation is a very general and widely used mechanism of gene expression regulation, so it is supposedly involved in many, if not most, forms and instances of cancer.
• In section "X-ray crystallograph" the abbreviation "M.HhaI" is quite far away from its initial explanation in the lead. You may consider adding the full name of the enzyme for improved readability.
• Section "Hybridization probing" is too short and somewhat confusing to me: "... This technique uses molecule that has a complementary sequence..." What kind of molecule is meant here? DNA oligos? How do potassium permanganate and chloroacetaldehyde relate to the sequence complementarity mentioned in the preceding sentences? Do these two only recognize single nucleotides, while the oligos recognize short sequences?
• Finally, a more general suggestion: After reading all those examples of enzymes that use base flipping for moving the base of interest into their catalytic site, are there any examples of enzymes involved in DNA repair, replication, transcription, or whatever, that do not rely on base flipping? It may be possible that the size of the catalytic center usually is so large that base flipping is actually required for all those protein-catalyzed reactions. Are you aware of any counter-examples that do not involve base flipping?

Keep on with the good work. Best wishes, Wpeissner (talk) 15:42, 29 April 2014 (UTC)

Thank you for the suggestions! I will definitely address them soon!Amontei2 (talk) 19:46, 29 April 2014 (UTC)

Thanks for your feedback! We definitely used many of your suggestions, like removing the red wiki-links and updating some of the text to make it more clear. I really like your suggestion about adding more information about the mechanism in which it works (relating to cellular environmental conditions). We're not planning on doing that right now, but base flipping is a very active area of research. I hope that, in the future, more is discovered about this process and we (or anyone else!) can update this page. Also, thanks for your final suggestion about adding information about adding counterexamples to base flipping. We decided not to include anything about this. We really want to focus on the known base flipping processes and not cloudy the waters, so to speak, about adding converse information. We appreciate your critique! Thanks again! Jen Magladem96 (talk) 16:22, 3 May 2014 (UTC)

Thanks for the response. Maybe there was some misunderstanding regarding my last comment. I just wanted to underline that base flipping is an extremely important mechanism, applied by almost all DNA modifying enzymes. When I asked about counterexamples, I was just wondering if you had encountered any during your research. The fact that you did not find those examples seems to further highlight the central importance of base flipping. Congratulations to your great article, Wpeissner (talk) 01:06, 7 May 2014 (UTC)