Designs And Applications Of Framework Nucleic Acid-Based Molecule Recognition Probes

With the rapid evolution of DNA nanotechnology,nucleic acids have been utilized as building block materials to create various well-defined nanostructures.Apart from the advantages of nucleic acid,the DNA nanomaterials also hold significance properties,such as structural order,intrinsic biocompatibility,multi-functionalization integration capacity,and nanoscale addressability.Benefiting from the growth of DNA nanotechnology,DNA nanomaterials have been applied in biochemistry,analytical chemistry,biomedicine,and material science.As a classical three-dimensional(3D)nanostructure,framework nucleic acids(FNAs)have attracted much attention in different fields.Except for the design and synthesis of FNAs,various chemical groups(such as functional units and fluorescent dyes)can be modified on the predesigned sites of FNAs substrates and thus realize precise organization at molecule level.More importantly,these FNA-based scaffolds are readily translated to biomolecular signal transduction in various settings as a result of their high spatial order and excellent addressability.Hence,FNAs are extensively used as universal unit to design molecule recognition probes for biosensors.In this thesis,we designed a series of FNAs molecule recognition probes thanks for the topological and mechanical properties of FNAs.Based on those recognition probes,we developed various smart and sensitive biosensors for clinic applications.(1)Based on the topological properties of FNAs,a family of topological ligands were constructed.Combined with DNA nanotechnology,we quantified the interaction force between the ligands and receptors on the surface of cells.The precise engineering of topological complexes formed by the tetrahedral DNA frameworks(TDFs)were readily translated into effective binding control for cell patterning and binding strength control and thus used for cell sorting.Those ligands pave the way for the development of versatile design of topological ligands.(2)Inspired by biological process,we constructed a bridge probe based on TDFs.Based on the mechanical properties,the bridge probes achieved optimal secondary structure.Combined with electrochemical techniques,this bridge probe was employed for detection 2019-n Co V biomarkers.Moreover,this platform achieved limit of detection(LOD)of 1 copy and response range of five order of magnitudes.(3)We developed a TDF-nanoruler strategy for engineering of biosensor interface.The nanoscale precision distance control was realized with the TDF-based system to obtain the highest fluorescence enhancement of plasmonic substrate.Combining with DNA hybridization chain reaction,we established a low-cost,highly sensitive and selective plasmonic chip for trace mi RNA detection.TDF nanoruler chip provided a broad dynamic range for mi RNA detection with LOD of 10 a M and a single mismatch selectivity.This mi RNA sensor was directly employed for the analysis of biological samples,such as cell extract and xenograft tumor samples.This TDF sensor was also applyed to test the mi RNA in PCa(prostatic cancer)patient serum and showed a good agreement to the Gleason Score.Thus,our TDF nanoruler-engineered approach holds great promise for developing biosensors to detect the other targets with great potential for clinical applications.