Construction And Performance Research Of Biological Computational Model Based On DNA Nanotechnology

With the advent of the "post-Moore era",the development of modern electronic computers based on silicon chips reachs a bottleneck.The new DNA computing model constructed from DNA materials attracts more attentions due to its advantages of high parallel computing ability and highdensity storage,which provides a possibility to solve the problem.However,the current DNA computing mode relies on the complementary pairing of bases between multiple DNA single strands,which requires manual intervention,complex computation and decoding by fluorescence detection and other means.Therefore,the calculation result is not very convincing.The nanostructure constructed by DNA nanotechnology has uniform size,good addressability and programmability.It realizes the precise arrangement of single DNA strand on the nanostructure,which has become the template for the design of DNA logic gates and DNA circuits.However,how to design a DNA computing model based on DNA nanotechnology which reduces human intervention and decodes simple is still a challenge.To solve this problem,this paper proposes a DNA computing model based on the nanostructure constructed by DNA origami,which can realize the DNA computing with a small amount of human intervention,and only requires atomic force microscopy(AFM)to decode the results.The research content can be divided into the following two parts:1.The solution of Hamiltonian pathHamiltonian path is a famous NP-complete problem in graph theory,which requires a large number of operations,so it is difficult to solve on the electronic computer.Adleman et al.successfully solved the seven-node Hamiltonian path using DNA computing,but the computation process and result are complex and not intuitive.Therefore,this paper proposes a DNA computing element based on DNA nanotechnology to solve this problem.The DNA computing element uses a rectangular DNA origami with uniform size as a template,then streptavidin(SA)is modified on the template surface to encode the node information in the graph,and the staple chains is extended on the two short edges of the template to form a sticky end to encode the path infoemation in the graph.Each node in the graph corresponds to a DNA computing element.All the DNA computing elements corresponding to all nodes in the graph are mixed together for calculation,and all the path relationships in the graph are solved by using the parallel computing capability of DNA.Then the solution of Hamiltonian path is solved by using magnetic bead screening and AFM decoding.2.The solution of Euler pathEuler path is also a famous mathematical problem in graph theory.Euler path can be solved by using the DNA computing model,but there are also problems mentioned above.In this paper,DNA nanotechnology is combined with the proximal exchange cascade based on hybrid chain reaction(HCR)to form a DNA computing element to solve this problem.The DNA computing element takes rectangular origami as a template,uses hairpin structure of the template surface to encode the path in the graph,and then selects some hairpins on the template to initiate the path calculation process.The parallel computing power of DNA computing is used to traverse all path combinations in the graph,and then AFM decoding is used to find the solution of Euler path.