[ecoli]

Would the melting point of DNA be affected by the presence of an organic solvent?

My guess is no because there would be no difference between the H bonds formed between, say, ethanol and water. H-bonds contribute little to the stability of DNA of nucleic acid structures anyway...

I can't think of any other properties that may affect the melting temperature.

thanks.

[Psycho]

The ratio of GC to AT base pairing, an increase in GC base pairs means there are more hydrogen bonds (3 instead of 2 in between A and T) and that will increase the melting point.

Also if DNA is free in a solution the dielectric constant of the solvent will effect the strength of the charges and therefore its melting temperature.

[ecoli]

[quote name='Psycho']The ratio of GC to AT base pairing, an increase in GC base pairs means there are more hydrogen bonds (3 instead of 2 in between A and T) and that will increase the melting point.[/QUOTE]

The increased stability from GC content is due much more to Pi orbital stacking than due to Hydogen bonding.
H-bonds play less role in stability than stacking van der waals forces (this iss what my textbook says).

[/quote]Also if DNA is free in a solution the dielectric constant of the solvent will effect the strength of the charges and therefore its melting temperature.[/QUOTE]
so I'm assuming that water has a higher dielectric constant, because of the partial charges? Will the partial positive charge shield the anionic phosphates more than ethanol would?

In that case, would the melting point under ethanol be lower?

[DrDNA]

A couple of things that are missed in some discussions about DNA duplex stability.
The H bonds dictate specificity to a great extend (along with stability).
Pi-Pi stacking interactions aka nearest neighbor effects contribute greatly to DNA stability. For example, CGA will have different stability than ACG.
There is also an increase n entropy, exclusion of a LOT of water from the helix core as the two strands come together.
Ionic strength of the solvent but also ions in the solvent. For exmple, increasing NaCl conc increases melting temp. Also, other ions, such as Mg++, Ni++, etc.
The concentration of the DNA in the solution effects the melting temperature. Higher concentrations have higher melting temps.
Organic solvent CAN effect stability. For example, you can add DMSO and still do many things like pcr. It increases pcr effeciency by lowering stability of GC rich regions which could otherwise cause problems.

I believe that adding ethanol will raise the Tm because ions are not dissolved well in ethanol. Should force them together. EDIT: lowers solubility which should be kind of like raising concentration.

[Transdecimal]

What's the pH of DNA?

[DrDNA]

Transdecimal said:

What's the pH of DNA?

DNA doesn't have a pH. pH refers to aqueous solutions.
DNA DOES have several different pKa values. At certain pH values, different funtional groups on the DNA strand will accept protons and/or donate protons (their pKa for protonation or deprotonation).

For example, the pKa for protonation of a PO4- group....and the various different pKa values for protonating and deprotonating the various different ring and exocyclic nitrogens on the bases (A, C, G, T).

If you type "pKa nucleobase" or pKa DNA" in Google, you will probably find a whole lota info about this.

[ecoli]

DrDNA said:

I believe that adding ethanol will raise the Tm because ions are not dissolved well in ethanol. Should force them together. EDIT: lowers solubility which should be kind of like raising concentration.

Hold on though... adding a positive ions like Sodium raises the melting point, because they shield negative charges on the phosphate groups. This decreases the anion interactions and increases the stability of DNA, thus raising the melting point. Because the ions come out of solution

If adding a non-polar organic solvent should decrease the solubility of these ions, like you said, then adding ethanol should decrease the melting point of DNA.

I think the answer is that the Tm is raised... but I'm not sure for what reason.

edit: My notes said this: pyrimidines and purines 'stick out' more in ethanol than in water, which decreases the stability... which would also decrease the Tm. Is that affect caused by the polarity differences?

[DrDNA]

To summarize,
I believe that it can be broken down as follows:

DNA is about 3 things: nucleation, zippering and unzippering

The ability of the DNA to form a nucleation complex is the rate limiting step: the probability of two ss DNA molecules simply banging into each other in the correct orientation.

then Zipper <--> Unzipper (equilib)

So, the answer should lie in how the solvent (EtOH) efects the above.

Mobility and motion in the solvent (to form a nucleation complex)
H bonding (EtOH vs HOH, between solvent molecules, between the DNA ds and also between ss DNA (including partially formed zippers) and the solvent)
Solubility of the DNA (less in EtOH)
Solubility of ions in soln (Na+Cl-....)
Entropy (how will adding EtOH effect entropy?.....normally, an increase in disorder occurs as relatively ordered water is excluded from the helix core into the surrounding soln as the DNA zipper comes together)
pKa (easier or harder to protonate/deptrotonate the ring and exocyclic Ns in EtOH)
The ability of the solution ions to associate with the phosphates
The organic solvent may make the pi pi interactions stronger.
Stability of ss DNA in ethanol vs stability of ds DNA.

[shubhu]

Actually I have a question rather that's does anybody knows what is the dissociation constant of DNA?