Timed Pulses in DNA strand displacement reactions

Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays in gene expression and biological pathways, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based Strand Displacement Reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands we can finely control the delayed pulse output over a range of 10 hours. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially-appearing and self-erasing formation of DNA-based patterns.