Timed Pulses in DNA Strand Displacement Reactions

Abstract

Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, 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 h. 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 the 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.

Temporally controlled multistep division of DNA droplets for dynamic artificial cells

“…DNA programmability also facilitates the temporal control of chemical reactions. For example, DNA computing reactions have been demonstrated, such as the chemical oscillation of DNA concentrations [27][28][29] , temporal logic circuit 30 , and timing-controlled generation of chemical signals 31,32 . Moreover, the programmability of DNA has been utilized not only for controlling chemical reactions but also for controlling the physical dynamics of mechanical DNA-based nanostructures [33][34][35] .…”

“…Here, we coupled the mixed DNA droplet with non-equilibrium chemical reactions; the time delay of division triggers (Figure 1a) realized timing and pathway control of DNA droplet division (Figures 1b-1d). We used temporal control of DNA reactions based on RNA degradation with a ribonuclease H (RNase H), which has been used in many dynamic DNA reactions such as DNA oscillators 27 , DNA bistable switch 49 , logic computation 50 , DNA walker 51 , and timers for DNA strand displacement reactions 31,32 ; however, there is no report on temporal control of LLPS droplets with the RNase H reaction. Finally, we present a molecular computing element to compare the concentrations of microRNA (miRNA) sequences (called molecular comparators) as an application of the timing-controlled division of DNA-droplet-based artificial cells.…”

Designer DNA Strand Displacement Reaction toward Controlled Release of Cargos

“…Thus, thanks to the nature of DNA and the variety of DNA motifs available, there are many stimuli that have already been used to generate a dynamic DNA nanotechnology system, which include pH, light, temperature, enzymatic reactions, strand displacement, and aptamer (7)(8)(9)(10)(11)(12). Amongst these stimuli for designing dynamic DNA nanotechnology system, the toeholdmediated strand displacement reaction (TMSDR), which has been used for DNA circuits (13)(14)(15)(16)(17), biosensors (4,5,18), release system (19,20), reconfigurable nanodevices (21)(22)(23) is particularly attractive. Indeed, the TMSDR operates by using a single strand DNA (trigger strand) with higher affinity to displace another strand in a DNA duplex (incumbent) and does not require any other external stimuli (Figure S1).…”

Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a

“…However, the reliance on external additions of fuel DNA strands or protein enzymes limits their applicability in vivo. In contrast, the field of DNA nanotechnology provides promising approaches, particularly through nonenzymatic signal amplification methods. , DNA amplifiers based on a hybridization chain reaction (HCR), − toehold strand displacement reaction (TSDR), , and catalytic hairpin assembly (CHA) − have emerged as strong contenders, leveraging their nonenzymatic and isothermal characteristics for amplified detection of intracellular miRNA. Despite their potential, most of these DNA amplifiers face challenges such as inefficient penetration of the cell membrane, susceptibility to intracellular nucleases, and slow reaction dynamics, which limit their usefulness in imaging low-abundance miRNAs. , …”