Talk:Aminoallyl nucleotide

Reasons to move

The article talks only about aminoallyl-modified nucleotides and not about the aminoallyl group in general. --Kupirijo 02:09, 3 December 2006 (UTC)

I've completed the page move, as requested. -GTBacchus^(talk) 05:48, 8 January 2007 (UTC)

Additional information

Myself and Mishasubz plan on adding additional information into this article and would like some input as to what would be important/not mentioned on the article itself and not talked about in our points. We are both new to the Wiki community and have been slowly learning through the educational program.

Our talking points are as follows:

expand how they are used in

cDNA (describe each in detail)

PCR nick-translation

random-primed labeling

primer extension.

DNA microarray, which measures the level of gene expression

Pros/cons of aminoallyl nucleotides use in DNA labeling

Expanding information on the four known aminoallyl nucleotides, AA-dUTP/UTP and AA-dCTP/CTP with images

Would Biotin-16-Aminoallylcytidine-5'-Triphosphate fall in the article?

We embrace any input, please check my sandbox as we are editing there. Crandel5425 (talk) 03:18, 12 March 2014 (UTC)

unit 8 notes/comments/ideas

HI Randel

should we add a protocol on how to label with aaNTPs? if so, what do you think about this one

http://www.pangloss.com/seidel/Protocols/amino-allylRT.html — Preceding unsigned comment added by Mishasubz (talk • contribs) 07:03, 24 March 2014 (UTC)

Hi Misha, I've edited and revamped it a bit. I'm going to read over some of our links and include them into this article. I'll need your links to what you were trying to cite. I'll include them when I can. Looking better every time! Crandel5425 (talk) 19:17, 24 March 2014 (UTC)

Review by Graeme Bartlett

I see that several useful sections have been added. The lead section did not get changed, but it would be a good idea to improve that. The very first sentence should say what the topic is (see WP:Lede). We need a clear explanation of what an aminoallyl group is, and a diagram that numbers the atoms in the pyrimidine ring. A clearer explanation of the abbreviation of "aa-dUTP" would also be welcome.

The picture is not labelled correctly. what you have is a triphosphate. The original picture was an amionoallyluracil molecule and not correctly labelled either, and not an example of what the article is talking about, so at lest you took that off.

When you do section headings such as "Aminoallyl Nucleotide List" the subsequent letters should be in lower case, eg "Aminoallyl nucleotide list", but not only that we don't need the topic repeated, so this could just appear as "List". The style for this can be read in WP:Heading (this is really a minor issue easily fixed). WP:List can tell you how to format a list using "*" at the front of each line. However there is already more than just a list here, but a few facts are included. It is preferable to use complete sentences, so it will be good to expand each one into a sentence if you can. When writing using full sentences with correct English grammar. I like it how you have included all the abbreviations, but they are inconsistent with the lead, is the prefix aa- or AA- ? Also is N6-([6-Aminohexyl]carbamoylmethyl)adenosine 5′-triphosphate an aminoallyl nucleotide? It there a deoxythymidine derivative, or a purine derivative?

I would like to see the Reaction section increased to Reactions with more than one reaction! There area many terms in this section that should be linked such as cyanine. Any technical term should be linked as we cannot expect our average high school educated reader to know what all these things or concepts are.

I would also like to see a section covering the synthesis of these substances. Another missing section is history. How did there discovery and use come about? Are there other related labeling substances? Or are there other useless derivatives?

One plagiarism issue is the last sentence in the Reactions section which seems to be copied from http://www.trilinkbiotech.com/cart/scripts/prodList.asp?idCategory=84. also in https://www.tebu-bio.com/index.php?module=tech-info&id_cms=331&type_cms=3 in the Indirect RNA labelling section.

In the post synthesis section I am pretty confused. What is this about? Also is Biotin-labeling anything to do with this. Graeme Bartlett (talk) 07:31, 30 March 2014 (UTC)

Thanks Graeme for your incite.

• I'm not familiar with programming or editing with the programs recommended to create molecular images. Is there a way I can recruit a knowledgeable person who can create said diagram - I could use MS paint!
• Will make necessary corrections for the current image.
• Will fix the "list" to something more informational as you described.
• Will cross link in the reaction section - adding other reactions is difficult as finding information has become increasingly challenging with pay walls and proprietary information.
• We haven't been able to find anything about synthesis of these nucleotides unfortunately - still looking for that information.

Regards Crandel5425 (talk) 19:39, 8 April 2014 (UTC)

Comments From BigA726

For the leading section, it would be a good idea to actually describe what an Aminoallyl nucleotide is. Its a great idea to include what it does, but a specific explanation of what it is would be great.

For the section labeled "Reaction," there's no actual description of the reaction that takes place. It would be nice to see a description of a general mechanism or maybe a picture of how the reaction would take place. Also, the last statement needs to be cited. You may want to spell out "Nucleoside Triphosphates" once in the article before using the acronym, it might help with understanding where the term comes from.

The Uses section needs to be cited more. "5-(3-Aminoallyl)-Uridine(AA-UTP) is more effective for high density labeling of DNA than pre-labeling DNA [cite]. The amine group in aminoallyl-modified nucleotides is reactive with dyes such as the cyanine series, HiLyte Fluor, or Alexa Fluor dyes that HAVE been modified to be amine-reactive." The next sentence is a run on sentence. "Usually used" could be changed to "commonly used" which might roll off the tongue a bit better. Also, the last part of the sentence should be its own sentence. (Ex. A common problem with this method comes from the reaction of the dye with the buffering agent usually used for the storage of the nucleotides. Instead of utilizing this method, a carbonate buffer is used in its place.) The next sentence down needs a bit of work. "Some other" should be changed to perhaps "another" or "a number of other." Also, i think the addition of the thought "typically uracil" would be in parentheses. I think the last part of that sentence is supposed to read "is a mix of..."

In the last section, it might be good to describe what post-synthesis labeling is. after DNA Microarray, the proper use of the word is "cheaper." Under Biotin-labeling, "Biotinylation, a process by which biotin covalently attaches to a protein, IS used ..." "to detect A protein ..." What is "nice translation"? "Works really well" may be seen as a personal view and may not be completely biased. It would be more effective to probably say, "is commonly used" or some variation on that. (not to say it doesn't work very well, but if you were to stick with that statement, it would be effective to include specific information or statistics on why or how much better it is). In the cDNA section, the last sentence needs to be redone. In the DNA Microarray section, the article is a source that would need to be paid for in order to read it. However, just from the abstract, it gives a small explanation of how processes are more efficient and are cheaper than current procedures. You should explain what makes these procedures more effective instead of just stating that they are.

From your sources, your 9th source isn't free and i was not able to access the article other than an abstract on pubmed. Also, from the abstract, i didn't get any of the information that you cited in the article from it. The fourth source is just an order form page. It doesn't really give much factual information. The second source is another that i can't see the article for free unless i sign up for a site. — Preceding unsigned comment added by BigA726 (talk • contribs) 00:43, 1 April 2014 (UTC)

Hi BigA726,

Please see my response to Graeme for much of what was already addressed.

Much of the sources we will begin to find will not be free and we base information from what access we have and their abstracts. Link 4 will be fixed - should have been a pdf link.

Regards, Crandel5425 (talk) 19:48, 8 April 2014 (UTC)

Comments from Androidhu

I agree with BigA726 that it would be good if you start your first section by defining (chemically and structurally) what Aminoacyll nucleotide is, rather than by starting your section by how it is used.

With regard to the next section, you need to add more contents to describe what 5-(3-Aminoallyl)-2’-Deoxyuridine(AA-dUTP), 5-(3-Aminoallyl)-2’-Cytidine (AA-CTP), 5-(3-Aminoallyl)-2’-Deoxycytidine (AA-dCTP)are as you already described about other types.

For the Reaction section, it would be helpful if you can include actual reaction equation or picture to illustrate the reaction process.

For the Uses section, maybe it's a good idea to make a hyperlink to key terms (e.g. PCR, nick translation, primer extension, etc.) so that readers can access to what these terms mean. Also, it would be good if you can elaborate on "these labeled NTPs are helpful due to their application in molecular biology labs where radioactive labeling is not allowed or is banned" with citation. The next two paragraphs should be backed up with valid citations as well.

With regard to the Post-synthesis section, I agree with BigA726 that there should be a definition/explanation of what "post synthesis" means. It would be great if you can provide more context or specific examples for the readers (e.g. what kind of problems are avoided by post-synthesis?) You already provided some explanations on some sub types of labeling (cDNA, microarray, etc.) and should complete this section by explaining the other sub types as well with valid citations. Androidhu (talk) 22:27, 3 April 2014 (UTC)

Hi Androidhu,

Please see my responses to Graeme and BigA for already covered information.

The "list" soon to be edited section has been really hard to fine specific information on each as pay walls and proprietary information is hard to get over.

the hyperlinks will be addressed

regards, Crandel5425 (talk) 19:53, 8 April 2014 (UTC)

Unit 11 Deacon C comments

This is a nice page and is addressed in a way such that a user is pleasantly surprised by the fashion in which a normally chemistry related topic is made to seem biological.

The comments I have are mostly stylistic in nature and don't really affect the content of the article as much as the way it is organized.

• Header: I would take out the particulars of the molecule (maybe after cytosine in line 3) in the header and move this to the synthesis section.

• History: I would move the uses and first paragraph of post synthesis into the history section as it continues to explain the rationale for this type of research. Otherwise, this is a very nice section.

• Synthesis: Anything about the reactivity of the molecule should also be moved into the synthesis section including the different types of aminoallyl nucleotides. I think that a diagram with the carbons labeled would be nice. There are lots of free chemical drawing software programs or you could just copy your drawing, paste it into paint, label it and then put it back into your article; it would make it easier for the layperson to understand it.

• Post synthesis: I guess you are still building out this part and will either put descriptions or links into the article. Just a piece of information: the online ambassador told me there should be no "bolding" in the article, except that which occurs naturally at subject heading, etc.. I had to remove a lot of it in our article.

• Vendors: A list of some vendors for these type of probes would be helpful.

• Pictures: If you could add some pictures of the glowing molecules, people would go crazy for it.

♠ Deacon C (talk) 19:42, 10 April 2014 (UTC)

thanks so much for the input, specially about adding vendor information. Will definitely do soMishasubz (talk) 08:48, 13 April 2014 (UTC)

Unit 11 discussion

hi Randel,

We good some really helpful feedback from last week. I am going to work on this today and see what I can improve.

Please review my additions and advice of improvements. I am having a hard time finding diverse information of this topic, most of the information i find is repeated in our already listed references thanks Mishasubz (talk) 09:02, 7 April 2014 (UTC)

Sorry I haven't had a chance to fully look at the work added on your end. I'll be able too hopefully today - latest tomorrow. I also replied to your email. Check out some articles allotted by companies or email them for specific journals and articles. I've contacted sigma aldrich and was able to find the synthesis articles from them. Crandel5425 (talk) 13:55, 14 April 2014 (UTC)

wow that is great! where did you post those articles? are they under the reference list?Mishasubz (talk) 17:40, 19 April 2014 (UTC)

https://www.gelifesciences.com/gehcls_images/GELS/Related Content/Files/1314735988470/litdocCyScribe_20110830223750.pdf.... check out this article, I was wondering what do you think about using figure 1, shows an outline of labeling cDNA.Mishasubz (talk) 09:30, 21 April 2014 (UTC)

This link looks very promising! I will comb though it as well. Crandel5425 (talk) 00:57, 22 April 2014 (UTC)

Review by Neelix

This article is coming along very well. Here are some recommendations for further improvement:

1. Nothing in the lead should need to be cited because the lead serves as a summary of the rest of the article; anything in the lead should already exist in the body and be cited there.
2. Be straightforward and direct. For example, there is no need for the words "can be referred to as" in the first sentence of the lead; the article should simply start with "Aminoallyl nucleotide is a primary amino group linked..."
3. Pay attention to punctuation and grammar. The last sentence of the lead is missing a period, "a useful labeling techniques" mixes singular and plural, etc.
4. Sections should consist of more than one paragraph each.
5. There should be no unsourced information; all information should be followed by a citation.
6. Only the title of the article in the lead should be bolded; other bolding should be removed.
7. The format issues in the "Post-synthesis" section should be addressed, such as the "[cite]" and the indented phrases that are sometimes followed by periods and sometimes not.

You are making some great progress with this article. Feel free to leave a message on my talk page if you have any questions about the recommendations above. Neelix (talk) 02:49, 14 April 2014 (UTC)

Hi Neelix,

Thank you for some great recommendations, please advice further. I have made changes to your suggestions Mishasubz (talk) 19:19, 19 April 2014 (UTC)

Will alter the lead topic and clean up the rest. Very difficult to find information on this topic. Crandel5425 (talk) 00:59, 22 April 2014 (UTC)

Comments from Lisawisa

"Aminoallyl nucleotide can be referred to as…" sounds a bit awkward. Simply stating "aminoallyl nucleotide is etc etc" flows better and makes the definition sound more concrete. It might be useful to wikilink to amino and ester group as well. The description of the naming convention might be too technical for the lead. It might fit better at the end of the synthesis section or as it's own section.

Hopefully this will be cleared up after Tuesday Crandel5425 (talk) 01:04, 22 April 2014 (UTC)

The history section needs more citations. The first two sentences need to have something to back up those claims with. "Just recently" is pretty ambiguous; is last year, decade, etc?

Again, "aminoallyl nucleosides may be synthesized" sounds as if you're unsure. "Aminoallyl nucleosides are synthesized" is more definite. You might want further explain the synthesis as well, it feels pretty bare bones as it is. Both sources for this section are closed access, so I couldn't find out more on my own. Labeling the molecules in the drawing would be helpful to understand the basics with a quick look.

Yes, very hard to find information on this topic, trying our best. The synthesis was based off only the abstracts of articles behind pay-walls, as well as the other parts of this topic. Crandel5425 (talk) 01:04, 22 April 2014 (UTC)

The list section might fit better at the end of the article. The other sections are arguably more important and should come before it. Consider renaming the category to something more descriptive, such as "List of commonly used aminoallyl nucleotides." Try to say something about each of them as well; as it stands it really doesn't add much to the subject.

Will consider your idea or just delete the list all together. Still undecided. Crandel5425 (talk) 01:04, 22 April 2014 (UTC)

The last sentence of the reaction section needs a citation.

Again, the entire uses section needs citations. I'm sure you got this information from your sources, but you have make it explicit. Try to get in the habit of citing your sources as you write, it's a lot easier than trying to go back and remember what source you used for everything. The example protocol is a good link, but it doesn't really fit in the uses section; it's more about making a probe rather than why you would use it. It would fit better in the reaction section or it's own external links section at the end of the article.

The grammar and punctuation in the post-synthesis section needs to be cleaned up. I'm assuming "aRNA" is a typo. The format for the section also needs to be consistent. Capitalize the first word of each one (cDNA being the exception) and follow with a semicolon. It may sound nit-picky, but it's a simple thing that makes it look a lot nicer. Also consider arranging it into a bulleted list rather than just an indentation.

The article as a whole could use more wikilinking. Terms such as in situ hybridization, cDNA, and NTP could all use links. When you do link, make sure to do it for the first time that term is used; cyanine, HiLyte Fluor, and Alexa Fluor are first brought up in the reaction section without links, and then have links in the uses section. When deciding what to link, ask yourself "is this something that someone without an extensive scientific background would know?" If the answer is no, consider linking to it. Lisawisa (talk) 06:04, 15 April 2014 (UTC)

Thank you for the informative feedback! will work on itMishasubz (talk) 20:13, 19 April 2014 (UTC)

Looking better! There are still grammatical, spacing, and punctuation errors, particularly in the uses section. The uses section is also pretty technical, I'm not sure someone without a good science background would understand it. I don't think you should include the vendors, it doesn't really add any information. It could almost be considered promoting them (which would be against Wikipedia's policies), especially because you're just linking to their catalog. Lisawisa (talk) 21:28, 29 April 2014 (UTC)

Thanks Lisawisa, I'll remove the vendors. Did not your reply to Misha Crandel5425 (talk) 21:21, 1 May 2014 (UTC)

Link issue

Hey Misha I noticed some of the links you added aren't being referenced correctly. I didn't want to step on any toes to fix the issue, I figure I'd bring it to your attention first. Before trying to fix it myself and likely messing it up. Let me know what I can do to help with this small issue. Crandel5425 (talk) 13:57, 23 April 2014 (UTC)

thanks Randel, took care of it!Mishasubz (talk) 20:56, 26 April 2014 (UTC)

Link issue

Hey Misha I noticed some of the links you added aren't being referenced correctly. I didn't want to step on any toes to fix the issue, I figure I'd bring it to your attention first. Before trying to fix it myself and likely messing it up. Let me know what I can do to help with this small issue. Crandel5425 (talk) 13:58, 23 April 2014 (UTC)

Review by martinhyou 4.28.2014

Hello, Here is my review for the article:

Introduction

• I like the information in the introduction. It is pretty straightforward and to the point.
• One thing I would suggest different is to switch the second and third sentence. I think the sentence about what it is used for is more relevant to the initial reader who may not be as familiar within the topic. Also, the second sentence goes more into the structure, which is what the rest of the introduction focuses on, so it would transition better.

Will consider the change Crandel5425 (talk) 00:41, 29 April 2014 (UTC)

Thanks for the tip, i agree that the transition is smoother.

Randel, i have made the change, let me know otherwiseMishasubz (talk) 02:19, 30 April 2014 (UTC)

I think what happened was that I had made the change, and then you flipped it back. I have corrected this again. Per Martinhyou's input. Crandel5425 (talk) 13:46, 30 April 2014 (UTC)

History

• Changed some grammar by adding , and ;
• Great history section! I would add a picture though. Possibly of the heatmap with DNA microarray that you can take straight from that Wikipedia page.

Will edit grammar, however adding a picture might clutter the article, or make it easier to understand. Will consider Crandel5425 (talk) 00:41, 29 April 2014 (UTC)

Synthesis

• I would add onto this section a little bit with more information. For example, is Heck coupling the only means of producing aminoallyl nucleosides? Why is it necessary for the nucleoside to form into a nucleotide by phosphorylation? More elaboration into the single pot synthesis with other halogens? How do you obtain the substrate in the first place and where?  Just some ideas. Not necessarily needed to go into all of them!

a lot of your comments and questions cannot be answered as the pay wall prevents this information from being uncovered. Phosphorylation may not be needed, will consider editing for correctness. Crandel5425 (talk) 00:41, 29 April 2014 (UTC)

Interesting. That's fine then. Just some suggestions :) Martinhyou (talk) 17:30, 29 April 2014 (UTC)

Reaction

• There should be a citation for the last sentence of this paragraph.

Will add citation Crandel5425 (talk) 00:41, 29 April 2014 (UTC)

Uses

• There are quite a few grammatical errors with sentences, spacing, periods, and citation locations. Please fix these.
• The information should be in paragraph format, but they seem like notes. It would be good to transition from one another within the section.
• I like the information that is here though. Going over the uses, advantages, disadvantages, and other areas is great!

I have worked on the general formatting as you suggested, please let me know if there is still work needed, thanks!Mishasubz (talk) 18:11, 30 April 2014 (UTC)

In General

• Looks like there are a lot of citations used throughout. From looking at the references section, some of the citations (such as 6 through 11) may not be formatted properly? Not quite sure.
• I think the overall jargon could be a bit improved upon especially in sections such as “Uses.”
• Good job though! Hope my review helps

Martinhyou (talk) 21:59, 28 April 2014 (UTC)

Review by Keilana

Hi guys, great job so far. Here are my comments as you finish things up. Let me know if you have any questions!

• I saw a few spelling/grammar errors throughout, so a thorough copyedit would be really helpful.

Anything specific? I noticed 3 spelling errors.Crandel5425 (talk) 16:18, 2 May 2014 (UTC)

• The lead is still at a really high level of writing, some more glossing there would be helpful to the lay reader, if you can.
• A more thorough caption for the heat map would be good.

The point of the heat map image is to show what it is and that aminoally nucleotides are used in it. Why would we need a more thorough caption; I feel it takes away the point of the article. Crandel5425 (talk) 16:18, 2 May 2014 (UTC)

• The second paragraph of Synthesis needs at least one citation.

Will use the initial citation in the section. Crandel5425 (talk) 16:18, 2 May 2014 (UTC)

• Starting a paragraph with "Concerns with labeling:" doesn't follow usual Wikipedia style. You have two options here, you can either create a subsection for concerns or you can just make that a sentence (e.g. "There are some concerns about using aminoallyl nucleotides to label")
• The spacing in some sections is weird - check to make sure you only have one blank line in between your paragraphs.

Will correct.Crandel5425 (talk) 16:18, 2 May 2014 (UTC)

• The sample protocol should be explained with a citation in that section. You could also put the link in an "external links" section.
• The last paragraph of "Uses" needs a citation. The source is not cited, thanksMishasubz (talk) 08:20, 6 May 2014 (UTC)
• I'm a little concerned about the number of brands you're mentioning - take a readthrough of WP:PROMO.

That's all I've got. Good luck! Keilana|^{Parlez ici} 15:57, 2 May 2014 (UTC)

Thank you for the review. I'll correct what I've commented on. Crandel5425 (talk) 16:18, 2 May 2014 (UTC)

moved out of unassessed

1/15/17 DennisPietras (talk) 02:01, 16 January 2017 (UTC)