Jin Xu

Application of a novel IWO to the design of encoding sequences for DNA computing

Encoding and processing information in DNA-, RNA- and other biomolecule-based devices is an important requirement for DNA based computing with potentially important applications. To make DNA computing more reliable, much work has focused on designing the good DNA sequences. However, this is a bothersome task as encoding problem is an NP problem. In this paper, a new methodology based on the IWO algorithm is developed to optimize encoding sequences. Firstly, the mathematics models of constrained objective optimization design for encoding problems based on the thermodynamic criteria are set up. Then, a modified IWO method is developed by defining the colonizing behavior of weeds to overcome the obstacles of the original IWO algorithm, which cannot be applied to discrete problems directly. The experimental results show that the proposed method is effective and convenient for the user to design and select effective DNA sequences in silicon for controllable DNA computing.

Circular DNA logic gates with strand displacement.

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.

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA sub-tile strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

Fluorescent nanoparticle beacon for logic gate operation regulated by strand displacement.

A mechanism is developed to construct a logic system by employing DNA/gold nanoparticle (AuNP) conjugates as a basic work unit, utilizing a fluorescent beacon probe to detect output signals. To implement the logic circuit, a self-assembly DNA structure is attached onto nanoparticles to form the fluorescent beacon. Moreover, assisted by regulation of multilevel strand displacement, cascaded logic gates are achieved. The computing results are detected by methods using fluorescent signals, gel electrophoresis and transmission electron microscope (TEM). This work is expected to demonstrate the feasibility of the cascaded logic system based on fluorescent nanoparticle beacons, suggesting applications in DNA computation and biotechnology.

An Unenumerative DNA Computing Model for Vertex Coloring Problem

The solution space exponential explosion caused by the enumeration of the candidate solutions maybe is the biggest obstacle in DNA computing. In the paper, a new unenumerative DNA computing model for graph vertex coloring problem is presented based on two techniques: 1) ordering the vertex sequence for a given graph in such a way that any two consecutive labeled vertices i and i+1 should be adjacent in the graph as much as possible; 2) reducing the number of encodings representing colors according to the construture of the given graph. A graph with 12 vertices without triangles is solved and its initial solution space includes only 283 DNA strands, which is 0.0532 of 312 (the worst complexity).

One-Time-Pads encryption in the tile assembly model

Recent research has demonstrated that the ultra-scale computation by self-assembly DNA tiles could be implemented in the laboratory. One of the significant applications is the DNA-based cryptography systems. In this paper, we detail procedures for the DNA-based cryptography based on the One-Time-Pads (OTP) which is in principle unbreakable. In order to implement the whole encrypting and decrypting processes, we propose four tile systems: encrypting system, ciphertext extracting system, key extracting system and decrypting system. All the tile systems use Theta(1) input tiles and compute in Theta(n) steps according to the length of the input massage. The method of implementing the DNA OTP encryption extends the self-assemble tile models and achieves the real randomness in the DNA OTP.

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.

Research on Invasive Weed Optimization based on the cultural framework

Invasive weed optimization (IWO), which is inspired from the invasive habits of growth of weeds in nature, is a population-based intelligence algorithm. In this paper, the IWO is embedded into cultural framework as a population space of a cultural algorithm (CA), called cultural IWO. CA is mechanisms that incorporate generic knowledge sources obtained during the evolutionary process, which increases the efficiency of searching processes. Here, this situational knowledge and normative knowledge specifically designed according to the IWO evolution population are used to guide the evolution of the population, and they exploit the information sufficiently that the optimum individual carries and speed up the evolutionary process. The performance of the proposed method is evaluated by a number of test functions. Computational results reveal that the algorithm can be efficiently applied to the function optimization.

Binding assistance triggering attachments of hairpin DNA onto gold nanoparticles.

Here, we present a strategy to trigger monovalent attachments of thoilated hairpin DNA onto AuNP, assisted by molecular binding. Without binding helper strands, it is hard to control the attachments of thiolated hairpin DNA, because of spatial hindrances. By introducing a binding helper strand, the thiol-group can be brought into close proximity to the surface of AuNPs, which will greatly increase the local molecular concentration and attaching efficiency. In the experiments, the strategy is verified by the methods of DNA strand branch migration and dynamic assembly of AuNPs clusters. In addition, unique and complex AuNPs clusters with well-defined arrangements of DNA scaffolds are produced. Using this method, it is able to selectively manipulate and control different kinds and numbers of DNA attaching onto AuNPs. Our strategy also could be extended to assembling large complicated DNA/AuNPs programmable structures and nanodevices.

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.