Programmable Digital Computing System Based On DNA Strand Displacement Reaction

As the main genetic material of organisms,DNA molecules follow the principle of precise base complementary pairing,and they possess good orthogonality,designability of molecular structure and controllability of reaction dynamics.DNA molecules have become one of the most potential materials for molecular calculations.In particularly,DNA-based strand displacement reaction systems also follow these simple and precise design rules,providing important tools for constructing complex digital circuits that operate at room temperature.In recent years,DNA computing using the strand displacement reaction has been able to achieve a variety of functions,including early use to solve NP problems,large-scale digital calculations,game decision-making,and even pattern recognition of handwritten notes.Although the logic gate circuit based on the DNA strand replacement reaction has reached a high level of complexity,how to increase the calculation speed and how to further expand the actual achievable computing tasks are still challenging.Based on the DNA strand displacement reaction,this thesis designed a DNA switching circuit to achieve fast digital calculations,and further designed a programmable gate array platform,and combined them to achieve large-scale and diversified digital calculations.Finally,it was planned to use the precise spatial addressing ability of DNA origami to construct a molecular reaction network on the surface of DNA origami,which could reduce the requirements for DNA sequence design through spatial isolation and construct a programmable logic operation network.The main research contents are as follows:First,the DNA digital operation circuits are all based on logic gates,and the circuits are more complicated.As the number of DNA strands participating in the reaction increases,the operation speed and signal-to-noise ratio are both limited.We have constructed a modular DNA molecular switch.In terms of chemical nature,logic gate circuits show different energy variation trends for four input combinations.In contrast,the gradual decrease in the free energy of all the input combinations that produce the output in a switching circuit is very similar.It's faster.Based on this,The DNA switch circuit could experimentally realize multiple circuit structures and functions,including simple logic operations,fan-in and fan-out structures,complex combinational logic circuits,full adders,and 4-bit radical operations.The calculation time of all circuits was within 10 minutes,showing the fastest complex DNA digital calculation so far.Second,using the high orthogonality and scalability of the DNA strand replacement reaction,we have developed four types of addressable dual-rail logic gates(AND,OR,NOT,and XOR),each of which has six,which can be connected freely through wiring instructions to form a complex computing network.At the same time,four output units were constructed in the dual-rail logic circuit for signal reading.By permuting and combining 24 different dual-rail logic gates,arbitrary functions such as addition,subtraction,and multiplication can be realized.And at high concentrations,large-scale calculations containing up to 500 DNA strands have been achieved.It provides an example for the design of reliable large-scale molecular circuits.And it opens up a new direction for the use of DNA or other molecules to develop biochemical machines with stronger computing capabilities.Third,the DNA origami platform is an ideal platform for molecular confinement environmental regulation.A molecular array of hairpin structure for programming was constructed on the surface of DNA origami,and logic gates and signal transmission lines were created by arranging the DNA hairpins on the array to realize the programming of chemical reaction spatial paths and realized different logic functions.Subsequently,a logical operation network with complex operation capabilities was constructed for the combination of logical functions to realize multi-functional operations on the molecular array.The signal propagation across transmission lines of different lengths and directions were demonstrated through a single-molecule total internal reflection fluorescence microscope.This subject combined interface DNA computing with single-molecule fluorescence monitoring technology to provide a new idea for constructing scalable large-scale DNA computing circuits.In summary,this thesis takes the DNA strand displacement reaction as the main body to construct a modular DNA molecular switch,showing the fastest complex DNA digital operation so far.It provides new ideas for the challenge of long computing time in the field of DNA computing.At the same time,four types of addressable dual-track logic gates are designed.Through separation and multi-stage assembly,the interacting molecules can be reduced in one reaction.From a chemical point of view,the use of divide-and-conquer methods reduces the interacting molecules in each reaction system,reduces the number of strand displacement reactions used to implement logic operations,and solves the problem of difficulty in expanding the scale of DNA circuits.