Conformational Designs And Applications Of Stereochemically-Defined Framework Nucleic Acids

Most of the natural products in nature have delicate conformations,so they can interact with their own biological receptors to exert corresponding biological functions.As one of the most fundamental concepts in organic chemistry,conformational factors significantly affect the physical properties,chemical reactivity,and biological activity of molecules.After more than 40 years of development,DNA nanostructures with near-atomic precision of almost any size and shape can now be constructed at the nanoscale.Due to the advantages of near-atomic precision,excellent programmability,addressability,and biocompatibility,DNA nanostructures are easy to perform conformational design and obtain unique properties.Nowadays,the conformational design of DNA nanostructures has been applied to many fields such as bionics,biomonitoring,and drug delivery.Nonetheless,the precise design of nucleic acid structural conformation is still a major challenge in the field,and the universal law needs to be further studied.In this thesis,the important role of conformational design in DNA nanostructures was investigated from multiple dimensions.The functional optimization of the framework nucleic acids is achieved through intramolecular conformational design,intermolecular conformational design,and conformational design in composite nucleic acid nanostructures.(1)Here,we developed a spectrum of fluorescent probes by enclathrating organic dyes into the hydrophobic cavities inside the amphiphilic DNA frameworks(DNA frameworks,DNFs).The formation of a hydrophobic confinement space was induced by the conformational design of the fine orientation of the alkyl chains on the edge of the DNA framework.Based on hydrophobic confinements,a series of fluorescent probes with tunable shape,size,and the internal chemical environment were constructed and successfully applied in super-resolution fluorescence imaging.Single-molecule fluorescence experiments showed that the dyes inside the hydrophobic cavity were protected by the DNA framework,thus exhibiting non-linearly enhanced brightness and photostability compared to free dyes.In addition,the photostability of fluorescent probes varied with the size,shape,and internal chemical environment of the DNA framework.A variety of hydrophobic fluorescent dyes can be individually wrapped or mixed in the interior of the DNA framework,and finally,44 colors of fluorescent probes could be achieved,covering from the visible light to the near-infrared(NIR)region.We further demonstrated that the monovalent probe could be used for DNA-based point accumulation for imaging in nanoscale topography(DNA-based point accumulation for imaging in nanoscale topography,DNA PAINT)super-resolution imaging,and the localization accuracy of the DNF-imager(σ_x=13.7±0.27nm,σ_y=14.72±0.29 nm)was better than the localization accuracy of traditional single-stranded DNA(ss DNA)(_x=15.78±0.32 nm,_y=17.58±0.35 nm).This work provided a general pathway for the construction of high-performance molecular probes,which have great potential for applications in the fields of single-molecule tracking,multiplexed imaging,and super-resolution imaging in biological environments.(2)Inspired by the assembly methods of chiral macromolecules in nature,a self-assembly method based on the intermolecular conformational design was proposed to construct a series of chiral supramolecular structures by monomer end rotation.By employing the same monomer,the precise control of the pitch and chirality of DNA helix structures could be achieved only by rotating the angle of the monomer joint.Through cryo-electron microscopy and other characterization methods,we confirmed that the DNA helix structure conformed to the theoretically designed three-dimensional conformations.This method enriched basic strategies for DNA structure design and provided new ideas for supramolecular assembly.(3)By combining DNA as a surface modifier to modulate the growth behavior of inorganic nanocrystals,we designed a stellate gold nanoparticle to achieve conformational regulation of the composite structure and used it as a self-correcting Raman probe for in vitro neurotransmitter quantification.The conformation of stellate gold nanoparticles with sharp surface morphologies and a 1-nm hollow interior nanogap provides a structural basis for the construction of self-correcting Raman probes.After applying the stellate gold nanoparticles for the label-free detection of four neurotransmitters(dopamine,norepinephrine,epinephrine,and serotonin),the linearity in the tested concentration range was significantly improved after internal reference-based signal calibration.The developed stellate-like gold nanoparticles hold great potential for the quantitative in vitro and in vivo SERS assay.