Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

Abstract

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Specific Biosensing Using DNA Aptamers and Nanopores

“…The occupied fraction of 0.86 ± 0.03 indicates that the initial reduction from 1 to ≈0.86 is probably due to the imperfect DNA carriers while the rest from ≈0.86 to ≈0.64 is probably from the leaked output. Better purification of the DNA circuits components and optimized designs may improve the readout fraction range …”

Visual synchronization of two 3-variable Lotka–Volterra oscillators based on DNA strand displacement

“…[1][2][3] With the aid of DNA strand displacement, massive DNA circuits, including digital and analog circuits, have been designed and validated by experiments. [4][5][6][7][8][9][10][11][12][13] The outputs of the DNA circuit are represented by the concentrations of the DNA strands, but the detection of concentration is difficult or even impossible in some cases. For example, the structure of a DNA polymer is massive, complex, and unstable, such that detection of the concentration of the DNA polymer is impossible.…”

Implementing digital computing with DNA-based switching circuits

“…NA strand displacement reactions (SDRs) [1][2][3] have been employed to implement highly complex tasks such as molecular computing 4,5 , information processing [6][7][8] , and nanorobots [9][10][11] . In molecular computing, molecular circuits operate by the action of orthogonal molecules 12 .…”

“…Recent advances in modular molecular design and programmable reaction dynamics have led to the development of SDRbased Boolean logic gates with unparalleled complexity 5,13,[17][18][19] . However, limitations associated with logic gate circuits emerges, which hinders the scale-up for practical achievable computational tasks as follows.…”

“…However, limitations associated with logic gate circuits emerges, which hinders the scale-up for practical achievable computational tasks as follows. (i) Typical approaches to increase the scalability involves the combination of basic gates such as AND and OR 5,13,20,21 , which nevertheless increases the use of gates [22][23][24][25][26] . (ii) Using uniform motif and implementing AND and OR gate with different threshold concentrations have shown high modularity and potential for constructing complex computing networks.…”