Association Free Energy of DNA Oligonucleotides from Expanded Ensembles.

Expanded ensembles were used to obtain the association free energy, in which the number of ideal basepair contacts formed served as the order parameter, for DNA oligonucleotides of varying composition, chain length, and ionic strength. Although free energy profiles are unique to each sequence, all exhibit a pronounced response for low contact numbers dominated largely by an increase in system entropy. Short oligonucleotides with sequence periodicity exhibit a rather smooth free energy profile that increases in complexity as chain length increases. The complexity in non-periodic sequences arises even in short oligonucleotides. Taking intact dsDNA with an extent of reaction ξ = 1.0, the maximum of the free energy profile appears at ξ≈0.1, representing two to four basepair contacts. In terms of chain length, the free energy barrier of longer oligonucleotides is higher and slightly narrower, due to the ensuant sharpness of the single-to-double stranded transition. Low ionic strength conditions induce an instability along the sugar-phosphate backbone of DNA, resulting in a decrease of the free energy barrier toward molecular dissociation. [ABSTRACT FROM AUTHOR]