Design And Research Of Programmable Molecular Models Based On Functional DNA

DNA molecular computing is an interdisciplinary knowledge-concentrated technology,which transcends the inherent structure of molecular biology and tends to a more perfect technical route.The DNA molecule as the operational carrier can be coded following certain rules according to the problem model so that the calculation object is mapped into the corresponding DNA strand to generate a data set.This emerging research field has made important progress in theory and experiment,but further exploration is needed in terms of algorithm design and model construction.The convergence of ideas from multiple interdisciplinary disciplines can often bring new ideas.The versatility of nucleic acid molecules provides source materials for the subtle control of nanostructures,which can be used to construct controllable computing processes by means of simulation and biotechnology.The thesis starts with the introduction of the research background and related research status in this field,showing that the comprehensive trend of DNA computing points to a more profound interpretation of molecular networks.The new analysis techniques and methods it arose have also made great contributions to expound complex systems.Among them,fluorescence detection technology has brought new dawn for observing the structure and behavior of specific molecules.In addition,DNA strand displacement technology brings flexible methods and reliable principles in the design of molecular networks.These methodology are the core prerequisites and technical support for this research.The search for intelligent nanomaterials and functional nucleic acids to construct novel logic gates that are easy to design,universal and stable has aroused great interest from researchers.In the class of functional DNA molecules,the triple helix structure has become one of the most fascinating materials for the construction of nanoswitches by virtue of its extraordinary characteristics.This study designed basic logical operations based on the conformational transformation of the DNA triplex in the first instance.The output of the Boolean signal is monitored by the fluorophore-labeled DNA strand,and graphene oxide（GO）is introduced to modulate the molecular signal,which together constitute a computing platform.The identification element was initially "locked" in the loop part of the three-strand functional hairpin.Only when the designated molecule is recognized,the triple helix structure is disintegrated and the single-stranded trigger probe in the middle is released.The complementary hybridization of the signal probe and the trigger probe to form a stable double-strand turns on fluorescence owing to the distance from the GO.The logic gate also provides a prototype for fluorescence detection device.This study integrates the specific response mechanism of the sensing unit and the signal conversion mechanism of the transducer unit,and uses the fluorescence signal as an output monitor to detect tetracycline.In this model,tetracycline aptamer was studied as identification elements,and a set of condition optimization carried out subsequently to further explore the feasibility,sensitivity along selectivity of the sensor.Novel nanomaterials and nucleic acid molecules are both promising tools that create new opportunities for molecular detection.The micro-processing system of modern semiconductor circuits is dependent on strategies organized on silicon chips to achieve the speedy transmission of substances or information.Similarly,in synthetic molecular circuits,the spatially localized architecture furnishes a different strategy,allowing for immobilized DNA molecules in close vicinity to each other,that of opening up a remarkable new area of inquiry for researchers.In this study,the Visual DSD modeling language was used to design and analyze the spatially organized DNA reaction network.The execution rules depend on the hybridization reaction caused by directional complementary nucleotide sequences.A series of DNA strand displacement calculations were organized on the locally coded travel track,and autonomous movement and addressing operations are gradually realized.The DNA nanodevice operates in this manner follows the embedded"molecular program",which improves the reusability and scalability of the same sequence domain in different contexts.Through the communication between various building blocks,the DNA device carrying the target molecule moves in a controlled manner along the programmed track,and finally the group transport and partition storage of dissimilar molecules were completed.DNA assemblies of distinct structures and forms are trying to take a giant stride forward towards DNA functional devices,bringing new prospects and perspectives.The epilogue of this thesis respectively summarized the innovations and shortcomings of the research results.It is expected that progress in this field will continue to promote the development of diversified innovations in other fields and contribute to different application scenarios.