Talk:Complementarity (molecular biology)

message: The last line of the article says: "tRNAs exhibit wobble, in which the third base of their anticodon does not follow the strict complementarity rules."
Wobble should be associated with degeneracy within the codons or genetic code, and not so much on complementarity.   I'm going to go ahead and remove this line from the article.   If you have a good reason to reinstate the line, then please respond here also.  --74.179.122.94 (talk) 14:47, 11 February 2010 (UTC)
thread_title: tRNA and wobble

message: See also complementary DNA. (Should these two articles get merged?) --Comment by User:Michael Hardy on main page.
*No. This area is a bit of a mess. Complement in genetics usually refers to something else entirely (as in complementation test).complementary DNA (cDNA) is specifically DNA generated from RNA. I'd like to draw attention to the page at Hybridisation (molecular biology) as well. I'm going to start tidying this stuff up. --Mike C | talk 12:12, 12 Apr 2005 (UTC)
thread_title: Page Merges planned

message: Hi there, this article was "adopted" by Johns Hopkins University course in Molecular Biology as a WikiProject. KevinBrownJHU and I are planning on editing it over the next few weeks. Possible areas to add/edit are:
*Overview/Introduction
*Principle of DNA base pair complementarity
*Complementarity in ds DNA
*Hybridization
*DNA repair function
*Regulatory functions
*Functions/Principles in Biotech
Reading through previous posts I am realizing that complementarity in terms of molecular biology and genetics overlap - looks like a challenge!
AjoneWiki (talk) 00:52, 23 October 2013 (UTC)
thread_title: Draft of Improvements

message: Hi,
The lead section follows style guidelines.  Sources reflect the content of each topic. The written language is succinct. Overall, you guys did a good job on explaining complementarity.
A table for Ambiguity codes would be easier to read. A diagram showing how A pairs with T (2 hydrogen bonds) and G pairs with C(3 hydrogen bonds) would help illustrate the concept of base pairing. It is also great if you can show how a strand is identical to the reverse complement of the other strand.  
For example
Forward ATGCATGC 
Reverse TACGTACG
Complement of reverse ATGCATGC
Chandler.c.ho (talk) 16:18, 7 November 2013 (UTC)
replies: text: Hi there, you gave me an idea of adding lines between the base pairs to indicate hydrogen bonds, I think it's a pretty good visual. Thank you! I am not sure if I want to add another table to explain the reverse complement concept, as the article might get too cluttered, what do you think Kevin? AjoneWiki (talk) 05:31, 13 November 2013 (UTC)
replies: text:  A visual might help with this concept. Hmm. We have the picture at the lead-in section that shows off most of this concept, but it has to be clicked on to see that detail. I think we can get rid of the ambiguity codes section from the page as it isn't really part of complementarity and more to do with reading or translation from a bioinformatics perspective. KevinBrownJHU (talk) 03:36, 21 November 2013 (UTC)
thread_title:  Review from Chandler.C.Ho

message: Looks like you guys are coming along well. One thing that struck me is that you talk about complementarity in terms of the "lock and key" metaphor, yet you focus exclusively on DNA and RNA. Enzymes and their substrates also fit the "lock and key" definition. I believe an important element of complementarity in molecular biology is the ability to reconstitute the whole from either half - for example, the ability to create a copy of a DNA molecule starting with either strand. I would expect an article on complementarity to include an extensive discussion of why this principle is so important in nature. Obviously the details of DNA replication are covered elsewhere, but it seems that an article on complementarity would be valuable at the information processing level. It's nice that you have the one illustration of two complementary base pair sequences, but you could easily expand this to illustrate replication, transcription, and even the basics of translation just using letter sequences. I would think that such "big picture" discussion would come before more complex subjects such as regulatory functions, anti-sense transcripts, etc. Also, although I think the Molecular Biology of the Gene is an excellent reference, I would suggest that you cite specific page ranges rather than the whole thing. Finally, you need to be careful to properly use the adjective "complementary" and the noun "complementarity". There are several cases in which you use the adjective when you should be using the noun.
Here's an interesting reference regarding complementarity in biology - Mazzocchi, Fulvio. "Complementarity in biology". EMBO Reports, May 2010; 11(5): 339-344. Hope that all helps. Don Brown (talk) 01:24, 19 November 2013 (UTC)
replies: text: Thanks for the feedback and the article. I can see how expanding the article in the direction hinted at in the lead in (about replication/correction) is a good thing to expand on for complementarity. I think some of it was covered in other parts of wikipedia, which is why links were made to some other articles. KevinBrownJHU (talk) 03:38, 21 November 2013 (UTC)
replies: text:  Thank you so much. The article you suggested is great. I love the idea to include proteins, why didn't I think of it? I also agree that it is a good idea to expand our reference list. Thank you! AjoneWiki (talk) 18:17, 21 November 2013 (UTC)
replies: text:  You guys have made some great progress! One minor observation is that you have a nice section on DNA complementarity that also includes a number of comments about RNA. I'd either change the title or consider breaking RNA off into a separate section. Don Brown (talk) 16:04, 27 November 2013 (UTC)

text:  One other suggestion would be to add a short introductory paragraph in the section on "Regulation". I lot of readers might not understand the whole concept of gene regulation, so a short orientation would be very helpful. Don Brown (talk) 19:38, 2 December 2013 (UTC)

text:  I know you guys are in wrap-up mode, but in re-reading today, I remembered how confused I was by the notion of 3' and 5' directions when I first learned about DNA and RNA. It might be worth explaining this directionality at least at a very high level, especially since it's included in one of the illustrations. Don Brown (talk) 14:20, 12 December 2013 (UTC)
replies: text:  Thank you for the feedback. We updated our wording to include RNA. For the regulatory section I added a very short introduction.AjoneWiki (talk) 01:35, 15 December 2013 (UTC)
thread_title:  Comments from donbinincom 

message: You are definitely making progress on this article.  I think you are on pace to have a great product by the end of the semester.  I would suggest adding something to the base complementarity section.  The idea of complementarity between DNA strands, DNA/RNA, and mRNA/tRNA during transcription and translation seem like important points that you could elaborate on, maybe through multiple subsections.  The idea of the genetic code traveling through these molecules ultimately leading to protein synthesis is an extremely elegant and interesting process.  While it would complicate things exceptions to the rule like rare bases, wobble concept, etc might add something as well.  What are the purposes of kissing hairpins?  You explain them but the reader is left wondering what they are used for. Do systems biologists use ambiguity codes and ambigrams?  Why are they used and who uses them?  Grabriggs (talk) 22:23, 19 November 2013 (UTC)
replies: text: You are making an interesting point about linking complementarity throughout transcription and translation. I thinking about how to make it more clear for th enon biologist. Thank you. AjoneWiki (talk) 18:21, 21 November 2013 (UTC)
replies: text: The improvements look great in your article!  I see you've added some explanation about how complementarity factors into transcription and translation.  The prose is improving and coming together.  Keeping a good flow between topics is a challenge on a big topic like this one.  It still bounces a little between topics.  Your reference list is growing and looks good, with one caveat.  I'm not sure how to cite the tables you have in references 12, 13, 14.  The links work, but not sure what standard protocol is for citing something like that.  Keep up the good work  Grabriggs (talk) 01:06, 3 December 2013 (UTC)
replies: text: Thanks. I'll see what I can do to smooth the transitions. AjoneWiki has done a lot of good work in fixing up the page so far. KevinBrownJHU (talk) 02:59, 5 December 2013 (UTC)
thread_title: Comments from grabriggs

message: Great job so far guys, let me know if you have any questions!
* The lead really needs to be expanded and use less technical language - it needs to be accessible to the average reader.
* DNA base pair complementarity needs to have citations.
* The entire regulatory section needs more links and glossing of technical language.
* Don't italicize names of specific proteins, either link them or leave them in plain text.
* It's unnecessary to use "figure 1", "figure 2", etc. Just explain the concept in the text and give a brief description in the caption of the image.
* One specific example of technical language - instead of saying "deltaG", explain the energetics.
* The last portion of the miRNA and siRNA section needs a citation.
* The ambiguity section needs a lot more glossing - I'm halfway to a molecular biology degree and I only vaguely knew what you were talking about. The average reader would be totally lost.
Good luck with the rest of your semester! Keilana|Parlez ici 18:15, 20 November 2013 (UTC)
replies: text: Thank you for your feedback! It so easy to forget that scientific language is too formal, and I really appreciate your comments.AjoneWiki (talk) 18:24, 21 November 2013 (UTC)

text: Worked on some of the issues with the page. Still need to decide if we should keep the ambiguity/ambigram material here, but for now added some stuff to help them fit in. Still need to work a bit on the lead section to make it a little less technical. KevinBrownJHU (talk) 03:42, 27 November 2013 (UTC)

text: I added a short section on cDNA as it's mentioned in the lead. I tried to keep it simple for the average reader. AjoneWiki (talk) 23:51, 27 November 2013 (UTC)
thread_title:  Comments from Keilana 

message: Hi Guys, your page looks like a vast improvement over the prior version.  Here are my comments.  
* Lead section
** The sentence that begins with "This line up between the sequences..." seems like it could be simplified.  For example, saying something like "This complementary base pairing allows cells to copy information from one cell to pass on to the next generation."  I wouldn't address the DNA repair with the sentence since you address it again two sentences later.  
** When discussing the degree of variation with complementarity ranging from "complete complementarity to none," would it sound better to say from "complete complementarity to no complementary?"
** The last sentence of this section states that most complementarity is seen between two sequences of DNA, but you talk about RNA  quite often in subsequent sections.  Just something to think about.  
* DNA Base Pair Complementarity section
** At several locations in this section, the term "respectively" is used when it is not necessary.  You normally want to use "respectively" if you provide two examples followed by conditions that apply to each.  For example, if you were talking about 2 species of bird and wanted to note that species A is blue and species B is green you could say "species A and species B are blue and green respectively."  But if you say "species A is blue and species B is green", then you would not use "respectively."
** If you can elaborate more on DNA replication, transcription and repair, the role of complementarity may be more apparent to the average, non-science reader.
*Regulatory Functions  and Bioinformatics sections     
** When I first started reading the subsections in these two sections, I thought I was on a different page than the complementarity page.  I believe that these sections are appropriate to have on this page, but I think you need to begin each subsection with talking about complementarity in these situations and then elaborate on what these are.  I'm not suggesting you do a complete re-write, I'm simply suggesting rearranging the order of presentation in each subsection so that when the reader gets to each section, their attention is still focused on complementarity- you discuss the role of complementarity in each, but it is not until later in the sections (for most).  I hope that makes sense. 
** I'm not sure if the Ambiguity codes section "works" in this article.  It doesn't really focus that much on complementarity itself.  I realize that it was in the prior version of the page; I just don't think this is the right page for it.  It's more suited for the base pair page.  
** I'm also not sure that the Ambigrams subsection belongs here as well.  All that this section is saying is that rather than using A,T,C and G that there are other designations that can be used.  The whole concept of complementarity does not change simply by using a different identifying code.  
Good luck on your final revisions!  The page looks very nice. Jfitz1974 (talk) 14:43, 5 December 2013 (UTC)
replies: text: Thank you for your comments. I changed the wording in the lead section, and the flow improved a lot.AjoneWiki (talk) 00:43, 15 December 2013 (UTC)
thread_title:  Comments from JFitz1974 

message: Hi, I can see that you guys have done a lot of work on this article since the last time I looked.  It is vastly improved!  
* I think you've done a great job of adding figures and tables, and that they really add value to the article.
* Lead is really good now 
** Written at the right level, I think.  
** It could still use a bit of copy-editing, though.  For example, (this is a bit minor, actually) in the last sentence you have, "While most complementarity is seen between two sequences of DNA, it is also possible for a sequence to have internal complementarity resulting in the sequence binding to itself in a folded configuration."  I think this conflates "sequence" with "molecule".  Even in a folded form of a single molecule, you still have complementarity of two sequences.  It's just that the sequences are in different places along the strand.
* The section "DNA base pair complementarity" should be renamed.  Maybe "DNA and RNA base pair complementarity", or maybe "Nucleotide base pair complementarity".  Since you talk about both DNA and RNA in this section, the current heading is wrong.
* Similarly, this kind of construction is awkward:  "involved in DNA complementarity: adenine, thymine (uracil in RNA), guanine and cytosine.".  The intro says specifically you are talking about DNA, but the parenthetical says RNA.
* I think you should highlight the significance of purines and pyrimidines.  Right now, you just mention them, but don't elaborate at all, and a casual reader might wonder what the significance is.  The fact that purines always "mate" with pyrimidines is crucial, and you could relate the type of molecule to the size difference.
* This sentence needs work:  "Following the principles of the genetic code translation allows to transform the code into cellular building blocks such as proteins".  Maybe it could be dropped.
* The "Antisense transcripts" section could start off with a layman description of exactly what antisense transcripts are.  Always keep in mind that your target reader is not a biologist.
* Regarding "kissing hairpins", I will admit that I am still confused by this.  I know what a hairpin loop is, and your figure is great for illustrating that.  But the way I read it, "kissing hairpins" actually involve *two* completely separate hairpin loops, and thus, four nucleotide strands, right?  I think this section, as it is written, is still pretty unclear.  I would suggest that you introduce the topic of hairpin loops in the section "miRNAs and siRNAs", and put the illustration there.  Then, if you want to talk about "kissing hairpins", you should move it to after "miRNAs and siRNAs", because I think it is probably less important.  This is just a suggestion -- don't feel that you *have* to accept it, if you disagree.
Great job!  Klortho (talk) 00:49, 9 December 2013 (UTC)
replies: text: Thank you for the review Klortho. These are great suggestions - I will definitely take them into considerations. How do you feel about the Ambigrams section? We got several comments that it might be out of scope, and I am honestly torn. Any feedback would be appreciated. AjoneWiki (talk) 23:23, 11 December 2013 (UTC)
replies: text:  I would like to thank you once again for the support you provided throughout the semester. I followed most of your suggestions, and changed the flow of the first section to highlight the role of the base pairs. I didn't remove the Ambigram section. AjoneWiki (talk) 17:43, 14 December 2013 (UTC)

text: Thanks for this information. I'm not sure why it seems like Kissing hairpins is talking about 4 sequences when it talks about two hairpins coming together, which, as the illustration under it shows, is just two sequences. I've added a small section about hairpins and other secondary structures to the article to introduce some of this stuff earlier than this specific section. KevinBrownJHU (talk) 02:02, 15 December 2013 (UTC)
thread_title:  Some more comments from Klortho 

message: Substituted at 12:08, 29 April 2016 (UTC)
thread_title: Assessment comment