Biochemical Logic Circuits Based on DNA Combinatorial Displacement

Abstract

DNA, as an excellent nano-engineering material, contributes to a new computing model, namely, DNA computing. This model is a type of biological computing, which takes advantage of the high density and high parallelism of molecules. One of the current methods of implementing DNA computing is to construct DNA circuits, among which the toehold-mediated DNA strand displacement technique is an important method. The hybridization of toehold domains provides the start position and accelerates the branch migration process. Toehold-based DNA combinatorial displacement is a practical method for designing and implementing DNA circuits. In this paper, we designed and simulated a multiplexer using the DNA combinatorial displacement mechanism to verify its practicability. Additionally, we improved and optimized the existing logic INHIBIT gate by leveraging the DNA combinatorial displacement mechanism so that the DNA strands in the entire chemical reaction network (CRN) system are capable of coexisting in large quantities. Moreover, we applied this improvement to the demultiplexer. Our method provides more capabilities to larger and more complicated DNA integrated circuits. INDEX TERMS Combinatorial strand displacement, logic gate, CRN, DNA computing.

An Operational DNA Strand Displacement Encryption Approach

“…As a new approach in dynamic DNA nanotechnology, DNA Strand Displacement Reaction (SDR) has particular advantages such as being enzyme free and self-assembly. SDR has attracted considerable attention in recent years and has been widely applied to build various molecular systems [ 19 ] (it should be noted that the materials (DNA single strands) required for DNA strand displacement experiments are first designed by researchers, then commissioned to manufacture, and finally assembled into DNA molecules (complex structure)). A DNA SDR can be described as a molecular dynamic process ( Figure 1 ), where a single-stranded DNA molecule is combined with a double-stranded DNA molecule through short complementary single-stranded DNA domains (called toeholds; see and ), and a new stable double-stranded DNA molecule will be formed and a new single-stranded DNA molecule released from the original double strand.…”

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.…”

Programmable DNA-Based Boolean Logic Microfluidic Processing Unit

“…To simplify the CRN of DNA used in logic gates, Zhu et al . proposed a method that reduces three sequential steps . However, the complex CRNs involved in DNA biocomputing need to be further optimized for combinational logic demonstrations.…”