Constructing Controllable Logic Circuits Based on DNAzyme Activity

Abstract

Recently, DNA molecules have been widely used to construct advanced logic devices due to their unique properties, such as a simple structure and predictable behavior. In fact, there are still many challenges in the process of building logic circuits. Among them, the scalability of the logic circuit and the elimination of the crosstalk of the cascade circuit have become the focus of research. Inspired by biological allosteric regulation, we developed a controllable molecular logic circuit strategy based on the activity of DNAzyme. The E6 DNAzyme sequence was temporarily blocked by hairpin DNA and activated under appropriate input trigger conditions. Using a substrate with ribonucleobase (rA) modification as the detection strand, a series of binary basic logic gates (YES, AND, and INHIBIT) were implemented on the computational component platform. At the same time, we demonstrate a parallel demultiplexer and two multi-level cascade circuits (YES-YES and YES-Three input AND (YES-TAND)). In addition, the leakage of the cascade process was reduced by exploring factors such as concentration and DNA structure. The proposed DNAzyme activity regulation strategy provides great potential for the expansion of logic circuits in the future.

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

“…DNA-based feedback cascades can significantly enhance signal propagation for reactions where target DNA concentrations are low [2][3][4][5][6][7][8][9][10]; however, these feedback cascades have a tendency to be 'leaky'. Any small amount of circuit instability has the potential to be amplified into a large amount of nonspecific background signal [11][12][13][14][15]. Previous studies have shown the effective use of porous membranes to control CNA reactions and minimize nonspecific molecular interactions [16][17][18].…”

Constructing DNA logic circuits based on the toehold preemption mechanism

“…[46][47][48] Compared with a monorail circuit, a dual-track circuit obviously increases the complexity of DNA strands which limits the expansion of DNA logic circuit. Second, the DNA strands used as inhibitory signals do not play a very specic or unique role in the DNA logic circuit, especially the XOR gate [49][50][51] in which the output suppression were realized by using complementary DNA strands as two different inputs. In this case, two complementary input DNA strands consume each other thus no output will be made.…”

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

“…In biological systems, the activity of the DNAzyme is also affected by its own structural changes. This feature is widely used to construct molecular logic gates [ 44 , 45 ], cascade logic circuits [ 46 , 47 ], and catalytic circuits [ 48 ]. In addition, expansive regulation [ 49 , 50 , 51 ] is a special way to regulate the catalytic activity of the DNAzyme that does not need to change the structure of DNAzyme.…”