Guiding the folding pathway of DNA origami

Probing the assembly process that occurs when single-stranded DNA is folded into desired shapes by ‘DNA origami’ shows that it can be guided by controlling the strengths of local and long-range interactions, enabling more reproducible synthesis. More control for DNA origami DNA origami is a promising self-assembly technique for the production of molecular components designed to assemble into a single stable structure, but misfolding can be problematic when targeting larger or more complex structures. Katherine Dunn and colleagues have now probed the assembly process and show how assembly can be directed towards desired structures, particularly by controlling the strengths of local and long-range staple interactions within the system. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis so that DNA origami can continue its rapid development as a nanofabrication technology. DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short ‘staple’ strands 1 , 2 , 3 , 4 . Its guiding design principle is that the target structure is the single most stable configuration 5 . The folding transition is cooperative 4 , 6 , 7 and, as in the case of proteins, is governed by information encoded in the polymer sequence 8 , 9 , 10 , 11 . A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield 2 . Although adjusting assembly conditions 2 , 12 or following empirical design rules 12 , 13 can improve yield, well-folded origami often need to be separated from misfolded structures 2 , 3 , 14 , 15 , 16 . The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond fo