# Thermodynamics of DNA double helix formation?

The entropy of a system decreases when 2 single stranded DNA molecules come together and form a double stranded molecule. For this to occur the total entropy of the universe must increase. Thus, heat is released when the double stranded molecule forms. My question is: Where does this heat come from?

• Creation of hydrogen bonds. – Mithoron Jan 18 '17 at 19:43
• Hydrogen bonds between the water that is released from the apolar DNA bases? – guest Jan 18 '17 at 19:50

## 1 Answer

The entropy of a system decreases when 2 single stranded DNA molecules come together and form a double stranded molecule.

Are you sure?

I would argue that association of two single-stranded DNA strands to form a double-strand is energetically favourable — for entropic reasons. This should be a combination of

1. the hydrophobic effect
2. the liberation of a few water molecules per base that are no longer needed in hydrogen bonding.

Point 2 is explained quickly. Upon association of two single strands, the characteristic Watson-Crick base pairs form and hydrogen bonds are established between the DNA bases. These hydrogen-bond donors and acceptors were previously associated with water molecules keeping them close to the DNA single strands and thus rather ordered. These water molecules are now liberated; and since there are at least two per base, this partial process is entropically favourable.

Point 1 may not be as clear as point 2, but it again boils down to the fact that water molecules are liberated from a rather well-defined structure. Large parts of DNA — the area around the bases — are not as hydrophilic as other parts of the molecule or water itself. While they still are somewhat polar, their interaction with water is not ideal. Thus, the ‘surface’ water molecules will form a kind of defined boundary around the molecule. This boundary becomes lesser overall if the surface to volume ratio decreases. And upon association, you have almost double the volume in practically the same surface (i.e. you have halfed your effective surface). Therefore again, a large number of water molecules are liberated.

If DNA association is entropically favoured, there is no need to invoke any heat.

• Your explanation is very clear. My teacher told us there is a decrease in entropy in the system (free single stranded DNA versus double stranded DNA). The release of water does increase the entropy of the system, but the decrease of entropy caused by the double strands is greater than this increase. But since the formation of double strands does occur spontaneously there has to be a release of heat. This heat then increases the entropy of the universe more than the decrease in the system, which is why the double strands are formed. This is also what my textbook states. – guest Jan 19 '17 at 9:58
• @guest You write: "But since the formation of double strands does occur spontaneously there has to be a release of heat." This is not correct. Endothermic reactions, which absorb (rather than release) thermal energy, can also occur spontaneously. – theorist Jan 19 '20 at 23:32
• @Jan According to this article (academic.oup.com/nar/article/43/17/8577/2414454 ), DNA pairing has an unfavorable (i.e., negative) $\Delta S$, even after accounting for water. This is in part because "water [is] fixed by the AT base pair in the minor groove and released upon dissociation of this group...." Having said that, this looks like a tricky problem (that this paper may not resolve), so if you're interested in exploring this further you should also read the articles that cite this paper. – theorist Jan 19 '20 at 23:36