Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Abstract

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.

DNA Kirigami Driven by Polymerase‐Triggered Strand Displacement

“…A Klenow fragment was employed as the polymerase for the PTSD reaction, which has excellent strand displacement activity in a dNTP‐rich, 37 °C environment. [ 25 ] As shown in Figure 2b, agarose gel electrophoresis demonstrated the detachment of the staple from the upper left corner of RO1 when both Klenow and dNTP were added (Lane 3). In the absence of either Klenow or dNTP, band migration could not be observed (Lane 1: purified RO sample with primer; Lane 2: sample of Lane 1 with dNTP).…”

“…In our previous work, we systematically validated polymerase‐triggered DNA strand displacement (PTSD) reactions, by which a sequence pattern recognition network was constructed requiring a less complex sequence design than an equivalent network based on the classical toehold‐mediated DNA strand displacement. [ 25 ] Typically, the PTSD reaction substrate is a DNA complex containing a 3′ end toehold. A primer binds to the toehold of the substrate and triggers the reaction.…”

Cofactor-assisted three-way DNA junction-driven strand displacement

“…16,30,34,38 Moreover, fuzzy DNA strand displacement or CRISPR-mediated strand displacement with toehold-free DNA that utilized enzymes were proposed to construct DNA networks. 39,40 One of the basic requirements for smart nanodevices is the ability to respond to a variety of external stimuli. 41,42 The above strategies for regulating strand displacement are mainly based on DNA or a certain factor, which restricts the development of multi-responsive systems.…”

“… 16,30,34,38 Moreover, fuzzy DNA strand displacement or CRISPR-mediated strand displacement with toehold-free DNA that utilized enzymes were proposed to construct DNA networks. 39,40 …”

Versatile CRISPR-Cas12a-Based Biosensing Platform Modulated with Programmable Entropy-Driven Dynamic DNA Networks

“…As an enzyme-free dynamic DNA reaction network, entropydriven catalysis (EDC) is based on the toehold exchange and branch migration reactions between ssDNA and dsDNA complexes driven by configurational entropy, which has shown great potential in bioanalytical applications. 26 During a typical EDC cycle, the presence of a target nucleic acid strand could trigger the release of a ssDNA strand with amplified concentrations, through which some key bioanalytical mechanisms, such as input converter 27 and signal amplification, could be achieved. With the further combination of responsive DNA structures such as aptamer structures, the responsive target range of the EDC process could expand from nucleic acids to non-nucleic acid targets.…”