Research On Logical Calculation Model Based On DNA And Restriction Endonuclease

DNA carries genetic information and plays an important role in building molecular machines.DNA molecules have such natural characteristics as specificity,high parallelism and microcosm.In the process of information storage and processing,it has shown great advantages and attracted extensive attention from scholars.DNA molecules are widely used to design and construct various functional structures and devices,such as DNA computers,DNA sensors,DNA chips,DNA molecular probes and molecular beacons.Toehold-mediated DNA strand displacement has been widely used to construct DNA devices,including sensors,machines,and circuits,because it enables dynamic control of the displacement reactions.DNA strand displacement technique is characterized by the tendency of the molecular hybridization system to stabilize the energy level,and by introducing input strands of different lengths and sequences to induce and control the strand displacement reaction,thereby releasing another DNA strand.In the traditional strand displacement systems,the toehold and the branch migration domain are covalently connected,and the pre-exposed toehold region is an essential prerequisite for activating a further cascade reaction.Therefore,it would be great advantageous to be able to control the generation and the removal of toehold dynamically.In this study,restriction endonuclease with specific recognition function were introduced into DNA strand displacement as the input of the DNA circuit.A variety of logic gates were designed and controlled by controlling the generation and removal of the toehold.Furthermore,a majority molecular circuit was constructed.The research contents are as follows:The toehold generation mechanism and the toehold removal mechanism based on restriction endonuclease were studied for the construction of molecular logic gates.The length of the toehold region was controlled by adjusting the cleavage site of restriction endonuclease through reasonable DNA sequence design.The experiment method of polyacrylamide gel electrophoresis(PAGE)was used to verify the conclusion that the optimal toehold length was 5nt.By comparing the experimental results of reaction systems with different enzyme concentrations,we draw the conclusion that the optimum concentration was 1 ?M.A variety of logic gates based on the toehold generation and removal mechanism were designed,and based which a majority molecular circuit was constructed.NUPACK was used to simulate the DNA sequence design.A series of logic gates such as YES gate,NOT gate,AND gate,OR gate and NOR gate were constructed.The experimental design was verified by polyacrylamide gel electrophoresis and simulated by Visual DSD.Compared with previous molecular logic gates,the design of this paper is rapid,easy to operate and has good expansibility,which provides the possibility for large-scale circuit design.