DNA Origami Annealing: Folding Yield vs. Cooling Rate

DNA origami folds a long single-stranded scaffold into a target nanoshape by base-pairing it with hundreds of short synthetic "staple" strands, each of which must find its own correct binding site out of thousands of near-matches. That search only succeeds within a narrow thermal window around each staple's melting temperature — which is why real folding protocols anneal slowly from a hot, fully denatured bath down to room temperature over an hour or more, rather than cooling quickly. This simulator models a ~330-site scaffold lattice with per-site melting temperatures drawn from a realistic distribution, lets you set the cooling rate, Mg²⁺ concentration and starting temperature, and renders the lattice folding flat as staples hybridize correctly — or freezing into visible kinetically trapped defects when the bath is quenched too fast to give every site its chance.