Rational Design of Cascade DNA System for Signal Amplification

Abstract

System leakage critically confines the development of cascade DNA systems that need to be implemented in a strict order-by-order manner. In principle, ternary DNA reactants, composed of three single-strand DNA (ssDNA) with a strict equimolar ratio (1:1:1), have been indispensable for successfully cascading upstream entropy-driven DNA circuit (EDC) with downstream circuits, and system leakage will occur with any unbalance of the molar ratio. In this work, we proposed “splitting-reconstruction” and “protection-release” strategies on the potential downstream circuit initiator derived from upstream EDC to guide the construction of EDC-involved cascade systems independent of system leakage derived from unpurified reactants. Both the reconstructed and released downstream circuit initiators were in compliance with the principle of the cascade AND logic gate. Using these two strategies, two cascade systemsEDC2-4WJ-TMSDR and EDC3-HCRwere developed to carry out the designed order, which did not require that the ratio of 1:1:1 be maintained. Furthermore, the inherent property of the upstream EDC could transfer into the downstream circuit, endowing the developed cascade systems with a more powerful signal amplification ability for the sensitive detection of the corresponding initiator strand. These two strategies may provide new insights into the process of constructing EDC-like circuit-involved high-order DNA networks.

Enhanced DNA Entropy-Driven Circuit by Locked Nucleic Acids and Simulation-Guided Localization

“…DNA circuits are a type of biological computing system that can realize signal amplification via a DNA strand interaction or enzyme catalysis . Advanced strategies such as “reconstruction” and “cascading” significantly improved the DNA circuits and enhanced the signal amplification . Enzyme-free signal amplification circuits are more suitable for a variety of application scenarios, such as living cell imaging .…”

AND-Logic Cascade Rolling Circle Amplification for Optomagnetic Detection of Dual Target SARS-CoV-2 Sequences

“…AND-logic gates output signals only when both inputs are present, which bring high specificity and accuracy, and are widely adopted in biosensing strategy design. − Currently, nucleic acid AND-logic operations are typically achieved through the formation of multicomponent nucleic acid nanostructures consisting of input sequences. , However, such nanostructures are limited in sensitivity by the Poisson distribution when low concentrations of both target molecules are recognized with a high concentration of the capture probe. As a consequence, the concentrations of input sequences required for, e.g., competitive strand-displacement recognition, are normally equal to or higher than the nanomolar level for logic gate operations. − Suffering from the low abundance of targets in clinical samples, the nanomolar detection range fails to provide distinct signals, leading to false-negative results.…”

“…13−15 Currently, nucleic acid AND-logic operations are typically achieved through the formation of multicomponent nucleic acid nanostructures consisting of input sequences. 16,17 However, such nanostructures are limited in sensitivity by the Poisson distribution when low concentrations of both target molecules are recognized with a high concentration of the capture probe. As a consequence, the concentrations of input sequences required for, e.g., competitive strand-displacement recognition, are normally equal to or higher than the nanomolar level for logic gate operations.…”