Circular DNA Logic Gates with Strand Displacement

Abstract

Circular DNA logic gates were constructed on the basis of DNA three-way branch migration. In this logic system, circular DNA was used as a basic work unit and linear single-strand DNA was used as input and output signals. Making use of the circular structure, most of the DNA-specific recognition regions were designed in a single DNA ring. Depending on accurate DNA sequence recognition and highly effective strand displacement, the logic gates yielded correct results. In addition, the positions of gold nanoparticles (AuNPs) were detected as an alternative approach to determine logic results. Thus, the accurate and tunable control of DNA/AuNPs may be applied widely in DNA nanotechnology.

Lineal DNA logic gate for microRNA diagnostics with strand displacement and fluorescence resonance energy transfer

“…AND logic is represented by the situation where the output of the gate occurs only when both inputs are present. The AND logic gate queries two microRNAs to determine whether both of them are present [10]. The AND gate in our system consists of SA, SF, SQ and SM.…”

“…Various DNA logic gates have been developed [7][8][9][10][11][12]. Wang et al designed a series of DNA logic gates based on toehold-mediated strand displacement and Gquadruplex that can autonomously control the coalescence and release of PPIX in vitro, an important molecule in photodynamic diagnosis and therapy [8].…”

“…Willner et al designed a series of logic gates using DNA scaffold, which are activated by either adenosine monophosphate or cocaine [9]. Xu et al constructed a circular DNA logic gates through ligase-assisted strand displacement to detect the position of gold nanoparticles [10]. Until now, there has been no consensus for the best logic gate design method in terms of simplicity and robustness.…”

Towards biomolecule-based information processing using engineered nanopores

“…The presence of the two inputs (DNA and dye) was necessary for the labelled logic gate DNA strand to generate an efficient FRET signal. A large variety of DNA logic gates have been reported [85,23,77,96,54,48,99]. Ran et al [70] have implemented simple logic programmes based on short DNA strands (either double or single stranded), where DNA was used to encode propositions, queries and implications.…”

Role of Density Functional Theory in “Ribocomputing Devices”

“…The concept of DNA molecular computation was demonstrated by Prof. Leonard Adleman, in which the ability of synthetic DNA oligonucleotides were used to solve a seven-point Hamiltonian path problem by performing a sequence of logical operations [19]. Since then, the possibility of developing a new generation of molecular logic gates and molecular computers based on the advantages of DNA molecules has started [20][21][22][23][24][25][26][27][28][29]. The DNA molecules were chosen as they are amenable to well-regulated, programmable folding, and have the unique ability to store genetic information.…”