When we isolate RNA, we add acidic phenol so that DNA will go to the phenol phase and RNA keep in water phase. So both they are acid nucleic, why they have different characteristics? Addition, DNA can't be soluble in basic phenol. What is the role of pH here?
Thank you!
2007-01-19 18:17:36 · 3 answers · asked by tbn_love 1 in Science & Mathematics ➔ Biology
I'm not 100% but here is my guess.
Nucleic acids have a phosphate backbone but also nitrogenous bases.
DNA is a double helix and the bases are happily forming hydrogen bonds with each other. Thus in acidic environment the bases will not get much protonated. On the other hand, the phosphate groups will be protonated. Thus the molecule will not have a big net charge (assume 0) and it will become soluble in phenol which is not really polar and not very soluble in water.
RNA has most of the bases exposed (some participate in intramolecular base pairing) so they can get protonated, acquiring a positive charge. The overall positive charge (adding the charges of all the bases) will be high enough and the molecule will be too polar to dissolve in phenol.
When you go to alkaline conditions, the phosphate groups of DNA will be deprotonated, acquiring a negative charge and thus the DNA molecule will be heavily negatively charged. Thus it becomes too polar to dissolve in phenol.
For RNA purification you also have the problem that RNA hydrolyses readily under alkaline conditions; using alkaline conditions would result in compromising your sample.
2007-01-21 08:28:50 · answer #1 · answered by bellerophon 6 · 0⤊ 0⤋
Phenol is more acidic than alcohol. Think about it this way--when both give up their protons, which will be the more stable molecule? The phenol will be able to stabilize its negative charge over the aromatic ring (think resonance!), whereas in an alcohol, the negative charge can not go anywhere, just stay on the O- (not too stable). Therefore, the phenol can give up its proton more easily--it is more acidic!
2016-03-29 05:49:53 · answer #2 · answered by Anonymous · 0⤊ 0⤋
DNA and RNA is different. DNA is deoxy which means it would hydrolyse in phenol. So, it wouldn't be able to dissolve. The role of pH is to prevent hydrolysis.
It is difficult to isolate RNA because RNA is easily degraded. The exact reason I have forgotten.
2007-01-20 11:30:17 · answer #3 · answered by PIPI B 4 · 0⤊ 0⤋