DNA Self-assembly Principles For Optimizing Hybrid Chain Reaction And Their Application Patterns In SERS Biosensor

Deoxyribonucleic acid(DNA)is essential as the carrier of genetic information for all forms of life,and is also used as important biomarkers for medical diagnostics.Based on the intrinsic properties,such as good biocompatibility,chemical stability and programmability,and easy to be chemically synthesized and modified,DNA have been concerned as a construction material in nanotechnology.The nanotechnological applications of DNA have grown exponentially from static structures to dynamic device over the past years.As an isothermal nucleic acid amplification technique,hybridization chain reaction(HCR)has become interesting tool in the development of biosensors.Unfortunately,HCR-based methods still face many challenges in biosensing applications.In this thesis,the principles of DNA self-assembly were proposed to optimize hybrid chain reaction,and their application patterns in biosensor were established.The main work includes the followings:(1)One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator.Here,we systematically analyze the sources of leakage and refine leak-resistant rule.The transition threshold of the energy barrier is proposed as a testing benchmark of leak resistance DNA hairpins.We further extend the strategy for specific signal amplification of miRNA homologs.Significantly,it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification,and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.(2)In recent years,nonlinear HCR systems have been developed with good detection sensitivity,however exponential growth mechanisms are still limited.We use only two smart super-hairpin species with leak-resistant switches that automatically program nonlinear DNA self-assembly when target strand exists as key.The kinetics and thermodynamics of toehold-mediated strand displacement reveal the critical elements of the designed modality of the smart super-hairpin species,and the leak-resistant behaviors and morphologies of the grown dendrimers are separately verified.This work advances our understanding of toehold-mediated strand displacement kinetics and thermodynamics and innovates anti-leakage mechanism by introducing switches.This simple approach has the potential to serve as general guideline for programming nonlinear DNA self-assembly,facilitating its future applications in biosensing and bioimaging.(3)The traditional HCR occurs through random diffusion of DNA hairpins.In that case,the reaction kinetics is limited.Inspired by the mechanism of cell recruitment molecules,we characterize the binding patterns and kinetics of chitooligosaccharides interacting with DNA duplex.DNA self-assembly are accelerated by chitooligosaccharides-chaperoned floating bridge in the aqueous mixture.This finding would provide a strategy for rapid and sensitive detection of biosensors based on DNA hybridization chain reaction.(4)Currently,HCR-based bioanalytical methods are still challenging.Surface enhanced Raman spectroscopy(SERS)is an increasingly important tool in the detection biomolecules.Based on the characteristics of SERS and HCR,the bifunctional SERS substrates are constructed for DNA self-assembly separation and signal extraction,and further the application patterns are proposed to improve the performance of biosensors based on hybrid chain reaction.