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Abstract DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.
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This content will become publicly available on June 1, 2025
Leak-resilient enzyme-free nucleic acid dynamical systems through shadow cancellation
DNA strand displacement (DSD) emerged as a prominent reaction motif for engineering nucleic acid-based computational devices with programmable behaviours. However, strand displacement circuits are susceptible to background noise, known as leaks, which disrupt their intended function. The ill effects of leaks are particularly severe in circuits with complex dynamics, as leaks in them amplify nonlinearly, resulting in rapid circuit degradation. Shadow cancellation is a dynamic leak-elimination strategy originally proposed to control the leak growth in such circuits. However, the kinetic restrictions of the method incur a significant design overhead, making it less accessible. In this work, we use domain-level DSD simulations to examine the method’s capabilities, the inner workings of its components and, most importantly, its robustness to the practical deviations in its design requirements. First, we show that the method could stabilize the dynamics of several catalytic and autocatalytic dynamical systems heavily affected by leaks. Then, through several probing experiments, we show that its design restrictions could be significantly relaxed without impacting the circuit function by simply adjusting the circuit parameters. Finally, we discuss several ideas to tackle the practical challenges in applying the method to arbitrary DSD circuits, paving the way for future experimental work.
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- Award ID(s):
- 2113941
- PAR ID:
- 10534931
- Editor(s):
- x
- Publisher / Repository:
- Royal Society
- Date Published:
- Journal Name:
- Journal of The Royal Society Interface
- Edition / Version:
- 1
- Volume:
- 21
- Issue:
- 215
- ISSN:
- 1742-5662
- Page Range / eLocation ID:
- 1742-5662
- Subject(s) / Keyword(s):
- DNA strand displacement
- Format(s):
- Medium: X Size: 2MB Other: pdf
- Size(s):
- 2MB
- Sponsoring Org:
- National Science Foundation
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