Yafei Dong

Logic Nanoparticle Beacon Triggered by the Binding-Induced Effect of Multiple Inputs

Recently, the toehold-mediated DNA strand displacement reaction has been widely used in detecting molecular signals. However, traditional strand displacement, without cooperative signaling among DNA inputs, is insufficient for the design of more complicated nanodevices. In this work, a logic computing system is established using the cooperative binding-induced mechanism, based on the AuNP-based beacons, in which five kinds of multiple-input logic gates have been constructed. This system can recognize DNA and protein streptavidin simultaneously. Finally, the manipulations of the logic system are also demonstrated by controlling programmed conjugate DNA/AuNP clusters. This study provides the possibility of detecting multiple input signals and designing complex nanodevices that can be potentially applied to the detection of multiple molecular targets and the construction of large-scale DNA-based computation.

Control of gold nanoparticles based on circular DNA strand displacement

In this study, DNA strand displacement is utilized to control the aggregation of DNA/gold nanoparticles (AuNPs) based on circular DNA, in which DNA/AuNP conjugates are captured and released by adding different DNA signal strands. Using this strategy, single DNA/nanoparticle building blocks are capable of assembling into complex structures of two and three circular DNA/nanoparticles. The existence of these structures is demonstrated by gel electrophoresis and transmission electron microscopy (TEM) analysis. This advance has potential applications in controlling, transporting and detecting DNA/AuNP conjugates with subsequent manipulation of the structure and function of these assemblies.

Development of DNA computing and information processing based on DNA-strand displacement

DNA computing, currently a hot research field in information processing, has the advantages of parallelism, low energy consumption, and high storability; therefore, it has been applied to a variety of complicated computational problems. The emerging field of DNA nanotechnology has also developed quickly; within it, the method of DNA strand displacement has drawn great attention because it is self-induced, sensitive, accurate, and operationally simple. This article summarizes five aspects of the recent developments of DNA-strand displacement in DNA computing: (1) cascading circuits; (2) catalyzed reaction; (3) logic computation; (4) DNA computing on surfaces; and (5) logic computing based on nanoparticles guided by strand displacement. The applications and mechanisms of strand displacement in DNA computing are discussed and possible future developments are presented.

DNA Sequential Logic Gate Using Two-Ring DNA

Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize before and after triggering sequences of DNA signals. By taking advantage of a loop-open mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by interlocked two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems.

A parallel type of DNA computing model for graph vertex coloring problem

A DNA computing model for solving graph vertex coloring problem is proposed in this article. To illustrate the capability of the DNA computing model, a 3-colorable graph with 61 vertices was constructed as an example. Using this model, more than 99% of false solutions were deleted when the initial solution space was established and finally all solutions of the graph were found. Because these operations can be used for any graph with 61 vertices, the searching capability of this model could be up to 0(359). This searching capability is the largest among both electronic and non-electronic computers after the DNA computing model (with searching capability of 0(220) ) proposed by Adlemans research group in 2002.

The Application of DNA Nanoparticle Conjugates on the Graph’s Connectivity Problem

A DNA computing algorithm is proposed in this paper which uses the assembly process of DNA-AuNP (DNA Au nanoparticle) conjugates to solve an NP-complete problem in the Graph theory, the connectivity problem, and a 3D DNA self-assembly algorithm model are also established. According to the algorithm we need to design the special DNA-AuNP conjugates which will assemble based on a specific graph, then a series of experiments are performed to get the final answer. This biochemical algorithm could reduce the complexity of the connectivity problem. The biochemical experimental technologies are mature and available, which will provide a practical way to validate the practicability and effect of DNA self-assembly algorithm model.

Logic Gates Based on Circular DNA Strand Displacement and a Fluorescent Agent

We constructed a three-input OR logic gate based on a single-strand DNA circle and a two-input AND logic gate measuring fluorescence signals produced by strand displacement to detect the outputs. The simple, cost effective OR and AND logic gates produced the expected results, demonstrating their feasibility for future use in DNA computing. Fluorescently labeled DNA oligonucleotide inputs were initially hybridized with a quencher strand, which was displaced when the input strands hybridized to circular DNA.

A Half-Subtracter Calculation Model Based on Stand Displacement Technology

In this work, we construct a half-subtracter calculation model with the principle of complementary base pairs and the technology of fluorescence labeling through the combination of INH and XOR calculation model. We implement the calculation process of a half-subtracter utilizing the strand displacement technology that two DNA signal strands as the input signal and the intensity of fluorescence as the output signal. The sequence of strands used in the experiment is designed by NUPACK. The simulation experiment is constructed with Visual DSD which is convenient to analyze the experiment results. The results show that the model performs well with high stability and feasibility and decreases the complexity of calculation.