Past exam of the chemistry B course of the University of Cambridge / 2025 / Paper 1 / B5 / c / i

There are three natural states: an unfolded single strand, a monomeric DNA hairpin, and an intermolecular self-duplex. A useful parsing of the sequence is $\mathrm{T}|\mathrm{CGACT}|\mathrm{CAAC}|\mathrm{AGTCG}$. The two five-base arms are reverse complements. They can form a hairpin with a five-base-pair stem, a four-base CAAC loop, and a dangling 5′ T.

Two copies can instead pair their arms intermolecularly. The self-duplex has two five-base-pair regions, a central noncomplementary internal region, and dangling T residues; it is not a perfectly paired 15-base-pair duplex. Low temperature favours pairing. At relatively low strand concentration, the unimolecular hairpin avoids the association-entropy cost of a dimer; at sufficiently high concentration, intermolecular pairing becomes more favourable. At high temperature, the unfolded state predominates. Actual crossover temperatures require salt conditions and sequence thermodynamics.