Scalable Logic Circuits with Multiple Outputs and an Automatic Reset Function Based on DNAzyme-Mediated Branch Migration

Abstract

A scalable logic platform made up of multilayer DNA circuits was constructed using Pb2+, Cu2+, and Zn2+ as the three inputs and three different fluorescent signals as the outputs. DNAzyme-guided cyclic cleavage reactions and DNA toehold-mediated strand branch migration were utilized to organize and connect nucleic acid probes for building the high-level logic architecture. The sequence communications between each circuit enable the logic network to work as a keypad lock, which is an information protection model at the molecular level. The multi-output mode was used to monitor the gradual unlocking process of the security system, from which one can determine which password is correct or not immediately. The autocatalytic cleavage of DNAzyme makes the biocomputing circuit feasible to realize the reset function automatically without external stimuli. Importantly, the logic platform is robust and can work effectively even in complex environmental samples.

Single-Molecule Resettable DNA Computing via Magnetic Tweezers

“…In addition, a complex DNA circuit was exemplified in this study that can be reset during measurements. Some previous studies make efforts toward resettable DNA computing using fluidic mixing methods, pH-/aptamer-controlled DNA tweezers, , a digestion–ligation method, DNAzyme-mediated branch migration, and strand displacement oscillators . In comparison to these methods, the real-time control, changeable buffer, and label-free properties in this design are greatly beneficial to applications in detecting biomarkers such as microRNA. , …”

Constructing DNA logic circuits based on the toehold preemption mechanism

“…The scalability and accuracy of DNA logic circuits in molecular computing and information processing have been extensively demonstrated. [11][12][13][14][15][16][17][42][43][44] Especially, nucleic acid-based constitutional dynamic networks provide versatile means to design computing circuits of enhanced complexity and advance the processing and scaling of DNA computing systems. 45 However, existing circuits have some problems that cannot be ignored.…”

DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate

“…Notably, catalytic nucleic acids (DNAzymes or ribozymes) [ 30 , 31 ] have had prominent applications in logic calculation [ 32 , 33 , 34 , 35 ], micromolecular detection (virus, miRNA) [ 36 ], biosensors [ 37 , 38 , 39 ], and signal amplification [ 40 ] in recent years because of their characteristics of specific recognition and high-efficiency catalysis. The DNAzyme is an enzyme that relies on and is affected by metal ions.…”