Talk:Nucleic acid thermodynamics

— Preceding unsigned comment added by Super randome user (talk • contribs) 09:52, 10 April 2018 (UTC)

Derivation of Melting Temperature Wrong
Hej guys, I have some questions marks in my head about this section of the article. Especially about this sentence:

"[A], [B], and [AB] will be equal, and equal to half the initial concentration of double-stranded nucleic acid, [AB]initial."

and then you conclude that

$$T_m = -\frac{\Delta G^\circ}{R\ln\frac{[AB]_{initial}}{2}}$$.

But if [A]=[B]=[AB] then $$\ln{\frac{[A][B]}{[AB]}} = 0$$ and nothing else.

The other question mark is about the units of the equilibrium constant:

$$K=\frac{[A][B]}{[AB]}$$

If [A], etc. is in mol/l then K has the unit mol/l  and hence

$$K=ln\frac{[A][B]}{[AB]}$$

does not make sens.

Super randome user (talk) 09:56, 10 April 2018 (UTC)

Incorrect (?) Definition Melting Temperature
The definition cited by this Article (SantaLucia1998) assumes a two-state model of DNA-hybridization (ds vs ss). This model is the basis for the nearest-neighbor model of SantaLucia, but does not completely reflect the nature of hybridization. There exist intermediate states of hybridization where only a partial hybridization between two strands took place (also called "hybridization cores"). Usually, the definition only includes a statement about the single-stranded strands and does not comment on the state of the remaining DNA. I changed it in the paragraph but I did not find a proper source for this. — Preceding unsigned comment added by 192.124.248.157 (talk) 14:08, 14 January 2013 (UTC)

An article showing that the hybridization is not a two-state process: http://www.pnas.org/content/104/3/712.full. The "nucleation" process of the hybridization might also be added to the article. — Preceding unsigned comment added by 192.124.248.157 (talk) 14:33, 14 January 2013 (UTC)

I'm finding melting temperature defined as: Primer Melting Temperature (Tm) by definition is the temperature at which one half of the DNA duplex will dissociate to become single stranded and indicates the duplex stability >> http://www.nfstc.org/pdi/Subject04/pdi_s04_m01_02_b.htm OR melting temperature (Tm) is the temperature at which one-half of a particular DNA duplex will dissociate and become single strand DNA >> http://www.nfstc.org/pdi/Subject04/pdi_s04_m01_02_b.htm They contradict one another... — Preceding unsigned comment added by 184.66.166.197 (talk) 05:43, 24 August 2013 (UTC)

I
I know this section is small, but the DNA section does not actually talk about DNA melting in terms of why it happens. So perhaps this should be placed within DNA. I tried looking at Wikipedia what was the point of DNA melting but there was nothing Tourskin 01:52, 4 February 2007 (UTC)

Proposal to merge
I feel the information from melting temperature can go in here as a subsection. In addition, I feel the article title "melting temperature" is too vague to only be refering to the DNA phenomenon. -Madeleine 01:13, 23 March 2007 (UTC)
 * I agree; the name "melting temperature" is innapropriately vague, and "DNA melting" makes a far better title. In terms of content the two articles overlap and would be more approproiate as one. - Zephyris Talk 09:21, 4 April 2007 (UTC)
 * Merger has been done. -Madeleine 17:52, 6 April 2007 (UTC)


 * I might get use to people deleting my info if only they gave proper reason - so why was the info regarding the use of DNA melting deleted? The composition of the nucleotides determines the melting temperature. Well whoopee doo for finding that one out but doesn't that mean that mutations (which are weaker in bonding due to their abnormal positioning and hence bonding) will melt easier? Tourskin 21:47, 12 May 2007 (UTC)


 * I removed it because it was wrong and unreferenced. Mutations do not have "weird structures" -- a point mutation might start with a single nucleotide mismatch, but those are rapidly detected and repaired to form a stable bonded double-helix structure, and subsequent rounds of DNA replication match each base with its complement. Perhaps your wording was wrong, perhaps you were thinking of an obscure related technology that I have heard of, but you didn't give a reference and I'm not going to help you with this, because you're being rude. I find it disturbing that you apparently made this scientific page on wikipedia claiming a statement of fact that was in merely based on your own speculations. Madeleine 22:14, 12 May 2007 (UTC)

Rude? Exactly how was I being rude? You don't know me and I don't know you. It is a fact that mutations have weaker bonds - think about it if you replace a base which was suppose to bond with 2 hydrogen bonds ad then mutate it to bond with a base with three, it will not bond as effectively. Its analagous to trying to use a UK socket for an American or a European Plug. I don't need your help regarding referencing, who ever mentioned that I needed it? What do you expect me to do beg for your assistance? Keep your arrogant help.Tourskin 22:49, 12 May 2007 (UTC)

Move page to "DNA denaturation"
I think this is the more general term, since it's used for chemical denaturation as well as heat, although the article still should refer to "melting" of course and there will be redirect. Any comments / objections? Madeleine 20:16, 20 May 2007 (UTC)


 * I have no objections. Tourskin 22:48, 20 May 2007 (UTC)


 * DNA denaturation is the correct term, is it not? In terms of accepted nomenclature, "melting" is an inaccurate term. I remember being taught as an undergraduate (many moons ago now) that the concept of "melting temperature" is just a common misconception of the abbreviation "TM"; the actual term being "median temperature". Argh 01 (talk) 09:20, 12 May 2011 (UTC)

dissociation or separation ?
The 'separion' inserted long ago. Insertad with 'urea' addition. In fact urea act during dissociation. Also urea buffer is used to DNA separation. (Separation is error here separation of DNA in urea buffer on chromatography columns...) Dissociation is more correct term. Xook1kai Choa6aur (talk) 04:19, 31 August 2009 (UTC)

Typical melting temperature
Could someone add a typical melting temperature or a range (maybe for some typicals strands). 77.11.52.78 (talk) 17:40, 12 January 2010 (UTC)FiratO77.11.52.78 (talk) 17:40, 12 January 2010 (UTC)


 * The melting temperature depends on the base composition as well as the length of the DNA sequence. So there is no fixed melting temperature or a narrow melting temperature range. — Preceding unsigned comment added by 192.124.248.157 (talk) 14:36, 14 January 2013 (UTC)

Merge
This article, now titled Nucleic acid thermodynamics, was the result of a merge between DNA denaturation (the former title of this article), Nucleic acid hybridization, and Annealing (biology). I'd like to note that I made an error in one of the edit summaries: the second edit after the page move, at 17:07, 9 April 2010, was actually the merge from "Annealing (biology)" and not "Nucleic acid hybridization". Antony-22 (talk) 21:02, 13 April 2010 (UTC)

Hybrid
Forgive me, I'm not familiar with the concept in this specific context.

However, I have the impression that the hyperlink to hybrid hasn't got much to do with what we're talking about here.

212.126.224.100 (talk) 15:30, 9 May 2011 (UTC)


 * I agree. If "hybrid" is accepted usage I think it's unfortunate. Also, the section seems unclear - it seems to imply that "hybrids" are not complementary at every base pair, yet refers to "complementary" strands.
 * lifeform (talk) 05:24, 22 May 2012 (UTC)


 * Good catch. I have fixed it.  Antony–22 (talk⁄contribs) 16:33, 22 May 2012 (UTC)

Extending the scope of Nearest-neighbor model
The scope Nearest-neighbor method has been extended beyond melting temperature context. The extension include the possibilities of non-Watson-Crick pairings (mismatches) with appropriate reference.

FysBio (talk) 15:06, 27 March 2013 (UTC)