Talk:Nick (DNA)

Untitled
I will be adding to this article for the University of Western Ontario's Advanced Genetics 3595 class. Cpozlov (talk) 22:05, 9 October 2015 (UTC)

My team and I will be adding to this article for the University of Michigan's Biochem 505 class, and we look forward to collaborating with your team. Here is a link to our sandbox: https://en.wikipedia.org/wiki/User:A288889000/sandbox

Brenmich (talk) 00:17, 11 November 2015 (UTC)Brenn

Here's a link to my sandbox: https://en.wikipedia.org/wiki/User:Cpozlov/sandbox. Cpozlov (talk) 01:25, 16 November 2015 (UTC)

Wiki Education Foundation-supported course assignment
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Cpozlov.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 05:16, 17 January 2022 (UTC)

Change-log
Introduction

'''Formation of Nicks '''
 * 1) Deleted the header to introduction section
 * 1) Added mechanism and diagram for the formation of the phosphodiester bond per GSI suggestion. The image and mechanism was copied directly from the following page: https://en.wikipedia.org/wiki/LIG1
 * 2) Added additional comments on how physical stress causes nicks anyhow enzymes may induce nicking.
 * 3) Expanded figure 1 captions with descriptions of a/b/c/d. Paraphrased original article and appropriately cited.

'''Repair of Nicks:  Role of mismatch repair:  Biological Implications:  References:'''
 * 1) Due to heavy focus on ligase, it was suggested that we introduce the subject.
 * 2) We felt it more appropriate to link to the ligases wikipedia page to avoid diluting the content on the nick page.
 * 3) Added content on nick idling and nick translation.
 * 1) Further developed the role of mismatch repair. To ground the original author’s contributions, we provided a brief introduction explaining what mismatch repair was and its function in both eukaryotes and bacteria. Further explained the functional role of DNA nicks in mismatch repair.
 * 2) Moved entire section under biological implications as its own subsection.
 * 3) Added content on Okazaki fragments.
 * 4) Added link to textbook definition of DNA mismatch repair.
 * 1) Created new subsection for topoisomerase and DNA nicks.
 * 2) Added content on negative implications of unrepaired nicks.
 * 3) Added citations to role in mismatch repair (second paragraph) and role in transcription (first paragraph)
 * 1) Changed header from “Notes and References” to just “References”
 * 2) Deleted duplicate reference by creating a reference group
 * 3) Fixed links that were U-M only
 * 4) Fixed reference format

DNA Nick Peer Review 1
Hi all, bellow are some general comments on how you might improve your work thus far on your page regarding DNA Nicks. Hope you find them useful!

Accessibility: For the most part, your introduction is accessible to the non-expert. You could perhaps briefly introduce the negative implications of DNA nicks in addition to the positive, biologically mediated mechanisms that your introduction mentions.

Content: In your "Formation of Nicks" section, you could use a deeper investigation into the causes of nicks. How does spontaneous DNA damage occur? Can you introduce sub sections on DNA cleavage by enzymes compared with spontaneous cleavage by physical or chemical stress?

In your "Role in mismatch repair" section, I don't think you address the role of nicks on repair as effectively as you might want to. You discuss the role of nicks in the recognition of newly synthesized regions of DNA, but not their involvement in repair mechanisms. I believe these are separate concepts. DNA mismatch is when two bases do not match each other. Mismatch repair involves removing a mismatch and inserting a correct match. On the other hand, nicks in newly synthesized DNA are found when/where the Okazaki fragment reaches the previously synthesized DNA, and the two unlinked fragments of the daughter strand must be ligated. They are also created in order to remove the RNA primer that begins DNA replication.

In your discussion on the repair of nicks, you are a little roundabout in how you go about telling the reader that DNA ligases are the enzymes that repair nicks. I don’t think you need so much information on the two examples that you give (or perhaps you could reorganize the presentation a bit). You simply need to tell the reader that ligases repair DNA, and perhaps the mechanism by which they recognize breaks and go about repairing them. Also, there’s no need to call the complex of Ligase I “crystalized.” The enzyme has been crystalized in the past for study, but I don’t believe it crystalizes in vivo, and that's what you appear to be suggesting.

In your "Biological implications" section, I believe you could go into more detail on the relevance of nicks in DNA damage and the physiological issues this might engender. I can imagine that failure to repair nicked DNA can cause a whole host of issues for a cell.In addition, you discuss DNA unwinding without really going into depth on why we might want to unwind DNA in a cell, which I believe could be useful information to add. Finally, I think recombination is probably a very relevant implication for nicked DNA, and you could likely spend more time discussing this application of nicked DNA.

Links: All your external links seem to be appropriate and reasonable.

Figures: Your figures look original, but I believe the captions could use work. If you’re going to label the figure with a, b, c, and d, I think it would be valuable to explain what is happening in each section. “The effect of nicks on intersecting DNA forms” is too general, and I'm not sure I understand what you're trying to tell the reader. Are you trying to show how nicks can help unwind DNA? What do you mean by "DNA forms?"

References: These seem reasonable, but I do notice a few potential problems. First, reference 2 and 3 are the same reference. Also, 9 and 10 seem to be U-M only links, or mistakes. You could also perhaps use more references for your general overview information. You cite reference 1 a lot, but the article itself lacks very much discussion of the generalities of DNA damage/nicks and primarily discusses the introduction of ribonucleotides into DNA and how it's repaired. There are likely reviews out there that discuss DNA damage, DNA replication, and DNA repair that discuss DNA nicks in more detail, and it seems a little strange that this is your primary reference. You could also benefit from some non-journal references if you can find them, since your readers likely won't have access to most of the cited research articles.

Overall: This is a very good start to your piece on nicks in DNA. You touch on all the major areas that are important regarding the topic. I think your main sections should focus on the creation, utility (or lack thereof), and repair of these nicks, and you touch on each of these themes. However, I believe that you could definitely approach both the creation and repair of these cuts in DNA with a bit more detail on the mechanisms and the systems involved, and I think that your information on the biological relevance might benefit with a discussion of both the benefits and the drawbacks to a system that allows DNA to be nicked in a living cell. Good work thus far, and I hope my comments prove useful in your coming edits!

D.A.H-M (talk)

DNA Nick Peer Review 2
Content: Overall content has moderate length for each section and informative to the topic. The introductory section is accessible to non-experts and easy to understand what DNA Nick is in the broad field of view. It seems most of the important concepts are linked to the references sources, and some of the important terms are also highlighted and linked to the Wikipedia pages for further references. For a better Wikipedia page, in the Role in Mismatch Repair section, more detailed explanation of how DNA Nick is involved in mismatch repair mechanism could be considered. In Biological Implications section, physiological relevance to DNA Nick could be more explored under the area such as repairing damages, and in particular, single strand breakage and unwinding also could be informative if those are going into more details.

Figures: First, the figure to show the effects of nicks on intersecting DNA forms is well presented for a better understanding of the mechanism of formation of Nicks. The figure is informative and easy to look at following the texts, but detailed explanation toward conformation is insufficient. If the texts under the figure could explain more in details, it would be better. Also, it seems the figure is directly from a specific article, so it might bring copyright issues even if the figure is cited. Second, in the section of Role in Mismatch Repair, if there are visual aids to help readers understand where the nicks exist and how it is recognized by the DNA mismatch repair mechanism, the readers would understand better for the roles of DNA Nick in mismatch repair machinery.

References: A criterion for the number of reference of the Wiki topic is satisfied. There are more than 5 references that are relevant to the topic of Nick DNA, and in particular, half of them are from scientific journals and the rest of them are from direct Internet webpages. Some references are inclusive of non-journals sources. What still needs to be improved for the reference criterion is deleting the overlapped references (2 and 3 are the same reference), and re-naming the unknown article titled with “U-M Weblogin”.

Overal Presentation: Overall, major area of DNA Nick is well focused and relevant information is well organized. However, you could go into depth on more about mismatch mechanisms and how DNA Nick is involved in the mechanisms, then that would be more useful for readers to get information. Also, more of physiological significance could be explored in the Biological Implications section. Minor mistakes on references page could be fixed as well. Again, overall, the formatting of the page looks good, and the informations are pretty accessible for non-experts due to simplification of words. I believe this is a great start to your piece on DNA Nick and could be a great new page in Wikipedia.

yeypark (talk) —Preceding undated comment added 17:29, 22 October 2015 (UTC)

DNA Nick Peer Review 3
Content: First, nicked DNA is a suitable topic for this class project. Being an important concept in molecular biology, it has not been thoroughly developed by any Wikipedia page. And the related enzymes and mechanisms are lack of description as well. The existing page provides a short introduction and then only focuses on DNA mismatch repair mechanism. Your addition to the existing page significantly improves the content qualitatively and quantitatively.

The introduction that you have integrated from the exiting page is informative and also quite accessible for the non-experts. It touches on the definition, formation, and application of nicked DNA in concise language. Along the logic of the introduction, the formation of DNA nicks is illustrated. In my opinion, the second paragraph is very well written, but the first paragraph and the image are not related to the formation of nicks. They describe the function of DNA nicks in releasing DNA torsional stress. My suggestion would be adding a separated part just for this function, perhaps in parallel with DNA nicks’ role in DNA mismatch repair. As to role in DNA mismatch repair, recognition of daughter strand is known to be a critical step in the mismatch repair mechanism. However, for readers without knowledge about the mechanism, reading this part is like looking at a very limited part in a big picture. Therefore, it can be confusing. A good improvement to this section would be describing DNA mismatch repair mechanism in general, and then focusing on the role of DNA nicks. In repair of nicks, the content heavily focuses on ligase instead of the repair process. A brief introduction of ligase as the enzyme to repair DNA nick is enough, and then some description on the mechanism of the repair process would be more suitable for this section. In terms of biological implication, this part seems to be covering nicks’ function in releasing DNA torsional stress as I mentioned above. Switching “repair of nicks” with this section will improve the flow of the writing. Overall, my opinion is adding a “function” section, which includes both roles in DNA mismatch repair, and interaction with topoisomerase, and perhaps also illustrating DNA nicks’ function in genetic recombination (mentioned in your last sentence).

Figure: As mentioned by Ye, using figures directly from a scientific article may be violating the publishers' copyright. Therefore, it is better to draw your own figure or plot. As to selection of image, the figure you are choosing is not the most informative and illustrative as you can find from similar journals. I think an image about DNA nicks’ role in DNA mismatch repair or an image about topoisomerase releasing DNA supercoils would compensate your writing in a better way.

Reference: the number of reference is reasonable. As I found out that it is difficult to find a comprehensive review just focusing on DNA nicks, I think it is even more necessary for expanding your research to a wider range of journals for better understanding. As to formatting, the in-text labels are well located, but the reference list at the bottom of the page is a bit messy. First, there are redundant citations (number 2 and 3). Then, some of the citations do not have an active external link. I think the most consistent and reliable method for citation is using the citation box, and searching for the journal by its DOI or Pub Med ID (Details are shown in Ye’s workshop slides).

Overall presentation: your group has grasped the major areas relating to the topic, and your page has been a great improvement comparing to the original page. As mentioned, some parts need elaboration, and the flow of the entire writing needs to be improved. One important thing: you need to put a statement on the existing DNA nick Talk paging indicating your work on this topic for class project. I noticed that someone from University of Western Ontario has claimed the page on October 9th, 2015. This could be a conflict of interest since you both are working on this page for a class project.

Houq (talk) 18:09, 22 October 2015 (UTC)

DNA Nick Peer Review 4
Group 8 Review- DNA Nick

The structure of the introduction seems to have no build-up or story. It went directly in defining a nick rather than setting a tone speaking about DNA and other DNA “abnormalities”. By this, I mean that they could list different DNA crossings then move to highlight nicking.

The diagram shown in the formation illustrates varying types of nicks, but no explanation as to what causes each type of nick- conditions, advantage effects etc. This could tie into how nicking alleviates the energy created by intersecting states and to what degree each nicking helps.

Speak briefly (sentence or two) about DNA mismatch before going on to mismatch repair. Currently, the overall structure could be refined. As it is, it seems to be of defining different categories rather having a flow in writing.

Further explain the reparation of nick. Try to make it simpler and if possible, use a diagram to aid in the explanation (just a synopsis).

Define abbreviations before using them. Do not assume that everyone is in the field.

Give more examples. Use; “such as” and “for example”, to better explain concepts. — Preceding unsigned comment added by Kevon.stanford (talk • contribs) 17:55, 22 October 2015 (UTC)

Suggestions from ChemLibrarian
Good job! Here are my suggestions.

ChemLibrarian (talk) 17:54, 23 October 2015 (UTC)
 * 1) Remember to delete the heading Introduction when you move the article to the formal space. The lead section doesn't need that. It's great that you incorporated the original content into your article.
 * 2) The Notes and References section can just be References.
 * 3) Please fix the format of your reference 2,3, 6,9 -11. They are all journal articles. But you did not cite them correctly. I see you did it correctly with the reference 4 - 5. But if you do need help with formatting citation. Please watch the tutorials below. If you try to link to sources, please make sure your link doesn't contain any umich specific components because you want general public have access to the page you link.

Review from GSI
Good job done in editing and modifying the article. Here are few suggestions to make it better.

1. A reaction scheme showing the mechanistic details of the formation of phosphodiester bond by ligase would simplify the the content and give the reader a better visual comfort in reading the article.

2. The section on Repair of Nicks can be improved by highlighting two different types of Nick ligation. One type is known as Nick idling, where the polymerase actively preserves ligatable nick. The other type is Nick translation, where the combine process of DNA polymerase and flap endonuclease allow the sysmtem to progress along DNA until the nick is reached.

3. The section Role in mismatch repair can be written as a subsection under the broader heading Biological Applications/Implications.

Soumigchem (talk) 03:21, 24 October 2015 (UTC)

Merger discussion
The article Nic site appears to be covering material already covered in Nick (DNA) and Bacterial conjugation. Mccapra (talk) 07:34, 13 January 2019 (UTC)
 * ✅ Klbrain (talk) 22:03, 12 February 2020 (UTC)