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Branching DNA machines based on transitions of hairpin structures

We constructed a DNA machine, the state branches of which depend on input DNA oligomers. The machine is a single DNA oligomer consisting of two hairpin structures connected by a single-stranded section. The input DNA oligomers can invade a hairpin's stem via branch migration, opening the hairpin. The branching state is represented by which of the hairpins is opened. This paper describes the design of the DNA machine, an analysis of secondary structure transitions, and experimental results.