Is there a paper that describes a model-based suitable fit function to DNA or RNA UV melting curves from which not only melting temperature can be derived but also delta S and delta-H (and subsequently delta-G) like described in van't Hoff analysis. Eventually this should contain discrimination between intra and bimolecular reactions. Ideally the parameters should get directly out of the fit function.
Dear, try this book ( Method in Molecular Biology: Drug-DNA Interaction Protocols), I think you can find the information on the second chapter. Its a helpful book in this matter
I also has same problem. I checked the second chapter of above book, Drug-DNA interaction protocols, only discussed how to determine the Tm value of melting curve. There is no information of how to get the thermodynamic parameters. Any other expert can help on the question?
Hi Danny, I checked more reference, and I think the book, Nucleic Acid, has very clear answer about how to fit the melting curve to get the delta S and delta-H as well as the reason behind it.
Dear Zenaa and dear Haiquing,
unfortunately I do not have access to "Method in Molecular Biology: Drug-DNA Interaction Protocols)".
The book "Nucleic Acid", could you provide a ISBN on that.
I found some equations in literature from Richard Owczarzy: doi:10.1016/j.bpc.2005.05.006
For those who are interested, after studying the literature a colleague and me recently published some equations for thermal melting curves also for molecularity larger than 2. For details see the attached link or check out my profile.
http://www.sciencedirect.com/science/article/pii/S0301462215000757
This paper has the equations you are looking for. In the supplemental info the equations are in the appropriate syntax to be used directly in Igor Pro.
Article Imprint of Ancient Evolution on rRNA Folding
May I ask where you have the equations in the SI from? E.g. for 1-transition? f(x)=(0.1*A1)*((H1/(2*0.00198*((x+273)^2)))/(1+cosh((H1/(0.00198*(x+273)*(Tm1+273))*((x+273)-(Tm1+273))))))
I wonder especially where the cosh comes from? Is it mathematically equivalent to the equations comprising an exponential term instead?
See also: https://www.researchgate.net/publication/275154745_Manuscript_revised_melt-eqs-final
Data Manuscript revised melt-eqs-final
You are right, empirically tested by fitting cosh(x) on calculated example data created with (exp(x)+exp(-x))/2 here:
http://curvefit.tu-chemnitz.de/#/?591c9aa2468c6a0adc2ee4c7
I put your equation in our curve-fit web application:
curvefit.tu-chemnitz.de/#/?591ca063468c6a0adc2ee4c8
So you fit the derivative. Why dont you fit the original data including baselines?
Would you mind providing me a single of your thermal melting datasets (with 1 transition) and your obtained deltaH and Tm value? If yes, just put the data to curvefit.tu-chemnitz.de and press the export button and send me the URL. I'd like to fit it according to my workflow explained unfortunately only in german here:
https://www.researchgate.net/publication/299507018_Entwicklung_eines_webbasierten_Curve-fitting_Tools_fur_komplexe_Multiparameter-Funktionen
Conference Paper Entwicklung eines webbasierten Curve-fitting Tools für kompl...
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