Talk:Uracil

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Quick question, under the Reactions sections... when an olefin reacts with elemental Bromine it forms an anti-addition product with the pi bond. i think that first picture is incorrect. but i don't have the means to correct it. the alkene should be trans-brominated under those conditions. right?

1 Reason for Uracil and not Thymine in RNA
2 Recent Updates
3 The other neucleotide, neucleoside, etc should be like this!
4 Suppliers links
5 Old references, cleanup

[edit] Reason for Uracil and not Thymine in RNA

I added this section after reading this: http://www.madsci.org/posts/archives/dec97/879354206.Bc.r.html It's not exactly a peer review journal, but it makes sense. Nonetheless, if anyone has any references pertaining to this, they should really be added. Oh, I also corrected someone's contribution that stated that uracil degraded into cytosine, rather than the other way around. Fish-Face 23:40, 21 January 2006 (UTC)

Great stuff, Fish-Face, I was asking myself that very question and sure enough, you contributed it about 24 hours prior!! Thanks for the info. Nhandler 05:42, 22 January 2006 (UTC)

No problem; glad to be helpful :) My Biology teacher found this out after I and another student asked her. Incidentally, I found two pages that have a more official appearance. Firstly: http://www-saps.plantsci.cam.ac.uk/records/rec284.htm and secondly: http://normlife.com/documents/original/the_use_of_thymine_instead_of_uracil_in_dna.htm The latter appears to have several typos and other mistakes, however. I'm not going to add these references as the latter could be unreliable due to its other mistakes, and the former, although professional looking, somehow doesn't have as much credence as I think a source should. Altogether, it seems a reasonable body of evidence, though. If anyone knows better, they should add citations as they see fit; I've not really had much involvement in edits necessitating such.

Fish-Face 15:19, 22 January 2006 (UTC)

This section needs some work and is not entirely correct. For example, "Uracil can be produced by the degradation of cytosine, so if it were present in DNA, the genetic code may be corrupted undetectably", doesn't make sense, especially since there are enzyme, which specifically look for uracil in DNA to fix it. Now if the question were "Why not Uracil in DNA?" then it makes some sense. I'll try to clean it up a bit, but there is not really a clear cut answer to this question, however there are many possible reasons. Hichris 17:53, 22 February 2006 (UTC)

I've cleaned up the section a bit and clarified a few things. I removed the methylation info, since people are easily confuesd between methylating DNA and methylating a base. One non methylated base in a stand of DNA is not likely to cause a great deal of nuclease susceptability anyway. Hichris 20:28, 22 February 2006 (UTC)

This table looks interesting, but it does need some annotation before it goes back into article. maveric149

 ACD/Labs0216022041

 8  8  0  0  0  0  0  0  0  0  1 V2000
   0.2863   -2.2800   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.2863   -3.6100   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.4381   -1.6150   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.4381   -4.2750   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   2.5899   -2.2800   -0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   2.5899   -3.6100   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.4382   -0.2850   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   3.7417   -4.2750   -0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 1  2  2  0  0  0  0
 1  3  1  0  0  0  0
 2  4  1  0  0  0  0
 3  5  1  0  0  0  0
 4  6  1  0  0  0  0
 5  6  1  0  0  0  0
 7  3  2  0  0  0  0
 8  6  2  0  0  0  0

M END

This table looks like a dump of a MOL file containing the atomic coordinates of the Uracil molecule. This would be perfect content for my wiki, the Computational Chemistry Wiki, if someone would give the details of how the geometry calculation was carried out, and perhaps include the hydrogen atoms as well. Ed Sanville 21:38, 7 November 2005 (UTC)

Also, I have recieved the following question, which I do not have the answer to. If somebody else can help this man out, I believe it would be a good gesture for a good cause:

Respected sir I am indian farmer Igrow mango fruit and exporting UK i see our nearest grap farm they use uracil as growth regulators can i use uracil PGR. please inform me by mail my mail adress gittu99@yahoo.com thank you girish patel

Ed Sanville 21:38, 7 November 2005 (UTC)

[edit] Recent Updates

Glad to see this article is getting worked on quite a bit, a couple of issues I'd like to mention. I believe the synthesis section should be moved later in the article. Uracil is a biomolecule and while synthesis is of interest, the biochemistry is much more important and more likely to be why people look up the article.

The references are nice, but they should be in order. Right now it goes 1 then 10 then 8, it may be preferable to just make each footnote citation a link to the citation on the bottom instead of numbers (that way they don't have to be constantly changed!)Hichris 03:06, 9 May 2006 (UTC)

I think the synthesis should be moved up back, too. It should be in order of depth: first what a curious middle schooler needs, then enough for a high school student cramming for their chemistry finals, and then finally what a graduate student might need for there primary thesis. Kr5t 02:46, 21 May 2006 (UTC)

the recent changes in my mind are not an improvement. The current article seriously lacks internal links and therefore impossible to follow for a general reader. Also the table should be trimmed down because most of it does not have actual information. V8rik 16:58, 31 May 2006 (UTC)

[edit] The other neucleotide, neucleoside, etc should be like this!

We should at least explain a little about tautomers and such! In fact, the adenine page has two pictures of tautomers of adenine, a sure source of confusion. I'll add a link to this page, with the observation that it explains alot of tautomers and such, in addition to being a related substance. Kr5t 02:46, 21 May 2006 (UTC)

[edit] Suppliers links

The place and format of supplier links has been disputed, please see User Talk:213.188.227.119 and RfC on Commercial Suppliers. --Dirk Beetstra 07:49, 30 May 2006 (UTC)

[edit] Old references, cleanup

Because there was a dispute about the link to a commercial supplier in this text, I have gone through the text, tried to find where this ref (ref. 2) was. Since I could not find it, I started to replace the refs with ref-tags, and clean up the section in that way. Three references are gone, in case I missed some, the old ones are down here:

1 Garrett, Reginald H.; Grisham, Charles M. Principles of Biochemistry with a Human Focus. United States: Brooks/Cole Thomson Learning, 1997.
2 [www.sigmaaldrich.com Sigma Aldrich]
3 National Institute of Standards and Technology http://webbook.nist.gov
4 Lee,J.K.; Kurinovich, Ma. J Am Soc Mass Spectrom.13(8), 2005, 985-95.
5 Goto, et al. "Fungal and bacterial regioselective hydroxylation of pyrimidine heterocycles." Tetrahedron, 53(18), 6421-6432; 1997.
6 Chittenden, G.J.F.; Schwartz, Alan W. Nature.263,(5575), 350-1.
7 www.madsci.org
8 Horton, Robert H.; et al.Principles of Biochemistry. 3rd ed. Upper Saddle River, NJ: Prentice Hall, 2002.
9 Zorbach, W.W. Synthetic Procedures in Nucleic Acid Chemistry: Physical and Physicochemical Aids in Determination of Structure. Vol 2. New York: Wiley-Interscience, 1973.
10 Brown, D.J. Heterocyclic COmpounds: Thy Pyrimidines. Vol 52. New York: Interscience, 1994.
11 Hildalgo, A; et al.'J Agric Food Chem.53(2),2005, 349-55.
12 Mashiyama, S.T; et al.'Anal Biochem. 330(1),2004, 58-69.
13 Brown, E.G. Ring Nitrogen and Key Biomolecules: The Biochemistry of N-Heterocycles. Boston: Lluwer Academic Publishers, 1998.
14 Pozharskii, A.F.; et al.Heterocycles in Life and Society: An Introduction to Heterocyclic Chemistry and Biochemistry and the Role of Heterocycles in Science, Technology, Medicine, adn Agriculture. New York: John Wiley and Sons, 1997.
15 Kochetkov, N.K. and Budovskii, E.I. Organic Chemistry of Nucleic Acids Part B. New York: Plenum Press, 1972.