Nucleic Acid Chemical Reaction Reaction Networks For Biological Analysis

With the continuous discovery and identification of tumor markers,biosensors are becoming more and more critical in promoting the development of medical diagnosis and treatment.However,lacking of sensitivity,detection range and detection efficiency of biosensors limits its further application in bioanalysis.Due to the specificity and sequence programability of its complementary base pairing,combining with the predictable kinetics and biocompatibility,DNA nanotechnology has great potential application for constructing high-performance biosensors.Aiming to be based on the interdisciplinary field of nanotechnology and analytical chemistry,this thesis using the superior controllability and functionality of DNA nanotechnology(including structural nanotechnology and dynamic nanotechnology)to solve the existing technical problems in analytical chemistry,such as sensitivity and detection range.Around the goal,the thesis mainly carried out the following work:(1)The ultrasensitive switch is the critical important to achieve the nonlinear dynamic behaviors of the biology,while the cooperative allosteric is the main strategy to construct the ultrasensitive switch.Based on cooperative mechanism,biologies can response small changes of input signals and transfer to significantly changes of output signals.Then,this mechanism can be employed to construct biosensors with ultrasensitive responses that solve the problem of small changes of input signals in analytical chemistry.Here,the high specificity of DNA aptamer for ligand combined with DNA strand displacement reaction were used to construct a ligand-responsive nonlinear DNA input/output(I/O)controller.Based on the programmable property of DNA,the numbers of binding sites and the lengths of linking domain were designed to tune the nonlinear range of DNA I/O controller,resulted in a range of 1.08~1.44.In addition,a nonlinear DNA chemical reaction network was developed using a strategy of multiple cooperative allosteric centers,which laid the theoretical and experimental basis for designing of chemical reaction networks with complex dynamic behaviors and the development of ultrasensitive biosensors.(2)Small biomolecules are important markers in molecular diagnostics,and quantitative analysis of these molecules is the essential goal for the development of biosensors.Here,biosensor with ultraresponse to biological small molecules sensor was designed and developed by introducing sequestration mechanism,which includes a signal module and a non-signal module.Through the adjustment of the affinity of the non-signal module(concentration of depletant),dual adjustment of the sensitivity and response range of the biosensor is achieved.Moreover,Combining with the structural DNA nanotechnology,an ultraresponsive integrated chip was designed for designed for multiplex and high-throughput analysis of small biological molecules,which provides research ideas for the miniaturization and universality of the biosensors.(3)However,the difficulty of the current biological detection and analysis lies in the dependence on the signal equipment,which makes most biosensors stay in the laboratory stage.Here,based on the dissipative structure of the enzyme cascaded reaction network and the kinetic adjustment of DNA chemical reaction network,a spatiotemporal pattern with kinetic regulation was constructed.And,the patterns were signed as a visual signal of small molecules.This work serves as a candidate for the visual analysis of biology,further provides a boost for the promotion of molecular diagnostics.In summary,this thesis focuses on the study of the dynamic behavior of DNA CRNs and focuses on solving the detection problems in analytical chemistry.It has developed a special detection based on ultrasensitive switches with nonlinear I/O behavior,adjustable detection range,and visualization performance.We believe that the further integration of DNA chemical reaction networks and analytical chemistry will definitely provide new opportunities for the development of DNA nanotechnology and analytical chemistry,as well as new technical means for precise diagnosis and prognostic analysis of molecules.