Wikipedia talk:USEP/Courses/JHU MolBio Ogg SP14/Group 81E

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Choosing an Article[edit]

Hi Ana! Which article would you like to work on? Out of the two that I assessed and the two that you assessed, I like base flipping best. Which is your first choice? Do you want to look at any other articles? I'd like to claim our article in the next couple days so make sure we get our first choice.  :) I don't know if there will be any competition for them or not. Magladem96 (talk) 01:05, 25 February 2014 (UTC)[reply]

Hi Jen! Base flipping sounds great and it was my first pick as well. Since it is not available now, there so much info we can add to Wikipedia. We should claim it then... I will look on the instructions to see what we have to do to claim our article, maybe email Dr. Ogg?Amontei2 (talk) 01:11, 25 February 2014 (UTC)[reply]
Great! Base flipping it is! Since it's not part of the original list, I'm not sure what we need to do? I will edit the program talk page where it was first listed to claim it there. I'm not sure what to do after that. Let me know what Dr. Ogg suggests. Thanks for emailing her! Magladem96 (talk) 13:47, 25 February 2014 (UTC)[reply]
Hi Jen! So I was checking on the Unit 6 and it says in order for us to claim our article we need to edit the table on the Article 81 page; however, since our topic is not listed on the table I have emailed Dr. Ogg and one of the OAs to check if we may edit the table or if that is something they will do. I just want to make sure I will not make any changes that I am not suppose to! I will keep you updated. Amontei2 (talk) 21:19, 26 February 2014 (UTC)[reply]
Hi! How about if we go ahead and create the DNA Base Flipping wiki page and then add that to the table for our group. I think we'll have to create it anyway... Do you want to create it? I'll also start working on the rationale. I'll post my thoughts here later on this evening. Then we can add your comments and edit it before we post it on our group page. Magladem96 (talk) 21:25, 26 February 2014 (UTC)[reply]
Hi! Yes, the OA responded to my message and I have edited the page and claimed our article. I have a test to take on another class and I will not start working on the rationale until Saturday night or Sunday morning. Sorry, but I will have something done by Sunday morning for sure. I will look over your comments and go from there. Talk to you soon! Amontei2 (talk) 22:24, 26 February 2014 (UTC)[reply]
Thanks Ana! Good luck on your test! Magladem96 (talk) 23:42, 26 February 2014 (UTC)[reply]

Preliminary Rationale for Base Flipping[edit]

HI Ana! Here's is my first attempt at our rationale. Please review, mark it up, add, delete, etc, as you see fit.  :) Right now, it's 185 words.

DNA base flipping is a mechanism in which a single nucleotide base in the DNA structure is rotated out from the DNA backbone by 180 degrees[1] so that an enzyme can perform work on it. Discovered in 1994[2], it has shown to be used in many biological processes[3]. Furthermore, studies have shown that DNA methylation, various DNA repair mechanisms, and events required for transcription and DNA replication are initiated by flipping of a DNA base out of the double helix.[4] [5]. As this will be our very first time working on Wikipedia, we are excited to make a substantial contribution on a topic that is non-existent today. Therefore, the fact that this topic is currently not available on Wikipedia (nor article content or stub), created a layer of interest and motivation for both of us. In addition, as discussed among our group, adding DNA base flipping information on Wikipedia, as a quality article, would also be beneficial to science students like us as quick reference guide during their studies. Another reason why we think this topic fits us well is because there are many scholarly articles available on base flipping, and it will give us the opportunity to elaborate on many aspects of it. Therefore, making this a great topic to develop with a vast amount of editing possibilities as new research unfolds and new discoveries are made in the future.

Information to be included on the article[edit]

  1. Definition of base flipping
  2. History behind its discovery
  3. What it consists of
  4. What are the mechanisms involved
  5. What studies have been done to this point
  6. Base flipping mutations
  7. Further researched topics.


Next Draft of Rationale[edit]

HI Ana! I really like how you expanded the rationale. Looks great! I changed a couple grammar things. My only other thought is that maybe we should make the information to be included a paragraph with a bulleted list instead of another section. I'm putting my thoughts in this new section so we can easily compare the two and see how they look. Let me know your thoughts. (This new section adds the references again. I'll make sure that when we finalize it, the references are correctly numbered.) Magladem96 (talk) 19:50, 1 March 2014 (UTC)[reply]

Hi Jen! What do you think now? I have also added some additional references on the bottom of things I found today. I agree with your changes, and I think they look good. Amontei2 (talk) 13:40, 2 March 2014 (UTC)[reply]
HI Ana! I don't think we should add the bibliography at the end. I think it's a great idea to keep a working list on this page for both of us to use and research (we should make a new subsection!), but I think it makes out rationale too long and we may not end up ending them as sources. Other than that, I think the rest of it looks great. Let me know what you think - if you'd really like to keep it in, we can do that too. After you respond, I'll post it on our group page and verify our inline references turn out correctly. Thanks! Magladem96 (talk) 17:38, 2 March 2014 (UTC)[reply]
Hi Jen! Sounds good, just post without the additional references, and we can leave them here so they are saved somewhere. I have started the "creating DNA base flipping" and I added to my watch list as it is one of the requirements of this week's assignment. Let me know if you have problems viewing it, but make sure you add to your watch list so you won't get a grade deduction.Amontei2 (talk) 12:01, 3 March 2014 (UTC)[reply]


DNA base flipping is a mechanism in which a single nucleotide base in the DNA structure is rotated out from the DNA backbone by 180 degrees[6] so that an enzyme can perform work on it. Discovered in 1994[2], it has shown to be used in many biological processes[7]. Studies have shown that DNA methylation, various DNA repair mechanisms, and events required for transcription and DNA replication are initiated by flipping of a DNA base out of the double helix.[8] [9]. As this will be our very first time working on Wikipedia, we are excited to make a substantial contribution on a topic that is non-existent today. Therefore, the fact that there is no information currently available on Wikipedia created a layer of interest and motivation for both of us. We also believe that adding DNA base flipping information on Wikipedia as a quality article would be beneficial to many science students as quick reference guide during their studies. Furthermore, there are many scholarly articles available on base flipping, and it will give us the opportunity to elaborate on many aspects of it. This is a significant topic to develop with a vast amount of editing possibilities as new research unfolds and new discoveries are made in the future.

The following list is a preliminary outline of the article. As we do additional research into this topic, this list may change and expand.

  1. Definition
  2. History behind its discovery
  3. Biochemistry
  4. Mechanisms involved
  5. Studies done to this point
  6. Base flipping mutations
  7. Additional topics as needed

The following list contains additional scholarly articles that may be used in the future

  1. Holz, Birgit, and Elmar Weinhold. "2-Aminopurine as a Fluorescent Probe for DNA Base Flipping by Methyltransferases." Nucleic Acids Research 26.4 (1998): 1076-1083. Web. 2 Mar. 2014. <http://nar.oxfordjournals.org/content/26/4/1076.short>.
  2. Arita, Kyohei, Mariko Aryoshi, Hidehito Tochio, Yusuke Nakamura, and Masashiro Shirakawa. "Recognition of Hemi-methylated DNA by the SRA Protein UHRF1 by a Base-flipping Mechanism." Nature 455(2008): 818-821. Web. 2 Mar. 2014. <http://www.nature.com/nature/journal/v455/n7214/abs/nature07249.html>.
  3. Patel, Premal, Motoshi Suzuki, Elinor Adman, Akeo Shinkai, and Pawrence Loeb. "Prokaryotic DNA Polymerase I: Evolution, Structure, and “base Flipping” Mechanism for Nucleotide Selection." Journal of Molecular Biology 308.5 (2001): 823-827. Web. 2 Mar. 2014. <http://www.sciencedirect.com/science/article/pii/S0022283601946194>.
  4. Banavali, Nilesh. "Partial Base Flipping Is Sufficient for Strand Slippage Near DNA Duplex Termini." Journal of American Chemical Society 135.22 (2013): 8274-8282. Web. 2 Mar. 2014. <http://pubs.acs.org/doi/abs/10.1021/ja401573j>.
  5. Matje, Douglas, Hongju Zhou, Darren Smith, Robert Neely, David Dryden, Anita Jones, Frederick Dahlquist, and Noberto Reich. "Enzyme-Promoted Base Flipping Controls DNA Methylation Fidelity." Biochemistry 52.10 (2013): 1677-1685. Web. 2 Mar. 2014. <http://pubs.acs.org/doi/abs/10.1021/bi3012912?journalCode=bichaw>.
  6. Matje, Douglas, Cody Krivacic, Frederick Dahlquist, and Norbert Reich. "Distal Structural Elements Coordinate a Conserved Base Flipping Network." Biochemistry 52.10 (2013): 1669-1676. Web. 2 Mar. 2014. <http://pubs.acs.org/doi/abs/10.1021/bi301284f?journalCode=bichaw>.
  7. Bianchi, Caterina, and Ronen Zangi. "Dual Base-flipping of Cytosines in a CpG Dinucleotide Sequence." Biophysical Chemistry 187(2014): 14-22. Web. 2 Mar. 2014. <http://www.sciencedirect.com/science/article/pii/S0301462213002184>

Unit 7[edit]

Hi Jen! Thanks for posting the article selection rationale. I am taking a look at Unit 7 and we should select one of our sandboxes to work on. Wanna use mine since we already have all those thread conversations saved? I guess we have to keep adding things on our sandbox so each other can edit as we go right?Amontei2 (talk) 01:16, 4 March 2014 (UTC)[reply]

Hi Jen! I started putting our references together as I am glancing over them. Cheng and colleagues is definitely a group we should target since they seem to be the pioneers in DNA base flipping studies. I have used my sandbox for that info so check it out when you get a chance and add anything else you find. Thanks Amontei2 (talk) 21:47, 4 March 2014 (UTC)[reply]
Sure - we can use your sandbox. I plan on spending this evening looking at the unit 7 stuff and doing more research for the base flipping topic. I'll add any new references to your list. Thanks for getting us started! Magladem96 (talk) 23:36, 4 March 2014 (UTC)[reply]
Sounds good, I will be adding some things during the day as well. Amontei2 (talk) 16:50, 5 March 2014 (UTC)[reply]

References[edit]

  1. ^ Grosjean, [edited by] Henri (2009). DNA and RNA modification enzymes : structure, mechanism, function and evolution. Austin, Tex.: Landes Bioscience. ISBN 978-1-58706-329-9. {{cite book}}: |first= has generic name (help); Cite has empty unknown parameter: |1= (help)
  2. ^ a b Roberts, Richard J. (June 1998). "BASE FLIPPING". Annual Review of Biochemistry. 67 (1): 181–198. doi:10.1146/annurev.biochem.67.1.181. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  3. ^ Brown, Tom. "Nucleic Acids Book". Retrieved 26 February 2014.
  4. ^ Huang, Niu (01/07/2003). "Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase" (PDF). PNAS. 100 (1): 68–73. Retrieved 03/01/2014. {{cite journal}}: Check date values in: |accessdate= and |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  5. ^ Grubmüller, Helmut. "DNA Base Flipping". Retrieved 26 February 2014.
  6. ^ Grosjean, [edited by] Henri (2009). DNA and RNA modification enzymes : structure, mechanism, function and evolution. Austin, Tex.: Landes Bioscience. ISBN 978-1-58706-329-9. {{cite book}}: |first= has generic name (help); Cite has empty unknown parameter: |1= (help)
  7. ^ Brown, Tom. "Nucleic Acids Book". Retrieved 26 February 2014.
  8. ^ Huang, Niu (01/07/2003). "Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase" (PDF). PNAS. 100 (1): 68–73. Retrieved 03/01/2014. {{cite journal}}: Check date values in: |accessdate= and |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  9. ^ Grubmüller, Helmut. "DNA Base Flipping". Retrieved 26 February 2014.

I moved your article[edit]

From "DNA Base Flipping" to DNA base flipping, to follow Wikipedia article title conventions. Klortho (talk) 03:39, 13 March 2014 (UTC)[reply]

Great! Thank you Klortho for all the help. By the way, we were able to identify an image that can use it for our project. Amontei2 (talk) 14:19, 14 March 2014 (UTC)[reply]

Moving your page to article space[edit]

Hi, I got your email, and tried to move the page from Draft:DNA base flipping to (article space) DNA base flipping, but unfortunately the old article already exists. I moved the old version to my sandbox, User:Klortho/DNA base flipping, but doing that leaves a "redirect page" in the old place, which will need to be deleted. Deleting pages needs an admin, so I added a delete request to it, but it might take a little while. Klortho (talk) 04:15, 24 March 2014 (UTC)[reply]

Hi Klortho!That old page was created by me, should I deleted? I though I could just "copy and paste" it on there once the article was ready. I wrote a paragraph there to avoid the page to be deleted again. Just let me know what you would like me to do and I will have it done today. Thank you for all the help. Amontei2 (talk) 10:03, 24 March 2014 (UTC)[reply]
Hmmm, I thought it would be deleted by now. Usually it happens very fast. The problem is, you *can't* delete it, and neither can I. It needs an admin. It's not a good idea to copy/paste the content of the new page there, because then you lose all the history, which is (rightly) considered important. I'll get Keilana or one of the other OAs to delete it. Klortho (talk) 11:53, 24 March 2014 (UTC)[reply]
It is done, see DNA base flipping. Congratulations on your new article! Klortho (talk) 13:33, 24 March 2014 (UTC)[reply]
Perfect! Thanks again!129.171.150.150 (talk) 15:01, 24 March 2014 (UTC)[reply]
Yes, thank you! Magladem96 (talk) 15:48, 24 March 2014 (UTC)[reply]

Unit 10 progress report log[edit]

  • Updated lead section with wiki-links and additional prose Magladem96 (talk) 01:53, 3 April 2014 (UTC)[reply]
  • The restriction endonuclease information was added as well as its appropriate citations. Amontei2 (talk) 00:02, 4 April 2014 (UTC)[reply]
  • Mechanism section updated for clarity Magladem96 (talk) 01:29, 4 April 2014 (UTC)[reply]
  • Discovery section updated for clarity Magladem96 (talk) 13:17, 5 April 2014 (UTC)[reply]
  • Updated Target recognition by restriction endonucleases section with appropriate wiki-links. Amontei2 (talk) 14:13, 8 April 2014 (UTC)[reply]

Unit 12 progress report log[edit]

  • Fixed wording in several sections
  • Added additional wiki-links to all sections
  • Added "See also" section
  • Added additional citations Magladem96 (talk) 02:11, 17 April 2014 (UTC)[reply]
  • Added Wikilinks to various sections
  • Formatted various areas of the NMR section, and added more information on what has been revealved about base flipping utilizing NMR technique.
  • Formatted DNA methylation section by reworking a large quote
  • Formatted Target recognition by restriction endonucleases section per reviewer 2 suggestions Amontei2 (talk) 01:14, 18 April 2014 (UTC)[reply]
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