Information processing based on DNA toehold-mediated strand displacement (TMSD) reaction

Abstract

We reviewed the recent research on information processing with the DNA toehold-mediated strand displacement reaction, including the basic principles and applications in logic circuit, analog circuit, combinational circuit, and information relay.

A nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit

“…A DTMSD reaction is a DNA strand hybridization reaction, which includes toehold association, branch migration and strand dissociation. 1 As shown in Fig. 1(a), the toehold domain is shorter than the displacement domain; therefore, toehold binding is unstable and is a reversible reaction.…”

“…In 1965, Gordon E. Moore, the co-founder of Intel (INTC), predicted that the number of transistors on a microchip would double every two years. Recently, the size of semiconductor devices has reached several nanometers, and the development of integrated circuits cannot continue to adhere to Moore's law 1 in the near future due to physical limitations. Against this background, advanced computers with smaller-sized subunits have become the chief objective of computation demand.…”

“…The application of semi-synthetic biology as a new semiconductor technology may lead to completely new storage and computing models, because DNA and RNA possess significant information storage and processing capabilities. 1 DNA is composed of four types of nucleotides, which can construct diverse DNA strands with complex structures. 2…”

Quantitative Analysis of In Situ Locked Nucleic Acid and DNA Competitive Displacement Events on Microspheres

“…The first involves the simultaneous addition of two or more distinct oligonucleotide targets to a probe system. This scenario is applicable to microarrays in which there are several potential yet heterogeneous targets. − The second and more studied − scenario involves prerequisite primary hybridization between single-stranded probes and primary targets to form primary duplexes, followed by the introduction of secondary or competitive targets to promote subsequent displacement of the original hybridization partner. To favor displacement of the primary target by a secondary target, a single-stranded segment or toehold outside the original duplex sequence is typically included as a sequence-specific “sticky” anchor to nucleate the formation of a secondary duplex with a competitive target while the primary target is still hybridized to the same sequence.…”

Bridge DNA guided assembly of nanoparticles to program chemical reaction networks

“…1 DNA holds great potential in programming chemical reaction networks thanks to its modularity, 2,3 predictability, 4,5 and addressability. 6,7 Particularly, programmed DNA guided assembly of nanoparticles is attractive for chemical reaction networks since it can control the relative stoichiometry or dimensionality, and directly visualize chemical reactions. 8,9 Thus, the construction of chemical reaction networks with programmable DNA allows the disclosure of chemical reaction processes with and without catalyst, further application in the design of novel molecular biosensors, 10,11 smart autonomous systems, 12,13 highly sensitive architectures 14,15 and unconventional computation.…”