Studies On (Biomimetic) Biomolecules' Molecular Interaction And Behavior Mechanism Via Atomic Force Microscopy

In nature, biomolecules frequently form hierarchical structuresby intra- or intermolecular interactions to keep alive. Inspired by nature, scientists have filtered or synthesized many kinds of organic molecules, such as aptamers and peptoids. Undoubtedly, it's really meaningful to study these molecules'molecular interaction and behavior mechanism fordeveloping new functional materials.Peptoids are a class of biomimetic sequence specific polymers based on an N-substituted glycine backbone. The structure of a peptoid monomer is close to that of natural amino acids except that the side chains are appended to the amide nitrogen rather than the alpha carbon. Compared with polypeptides, peptoids lack both chirality and hydrogen-bond donors in the backbone. This difference results in a flexible chain with control over desired interactions through introduction of specific side chains. It also confers peptoids with excellent thermal and chemical stability. Synthesized via a solid-phase submonomer synthesis method from a chemically diverse set of cheap, commercially available building blocks, peptoids have an exact monomer sequence that can direct chain folding into higher order nanostructures.Atomic force microscopy (AFM), which is developed by Binning in 1986, is a type of scanning probe microscope with high spatial resolution. AFM can characterize sample's morphology in lots of media such as air and fluid with nanometer even atom level resolution. Besides, as AFM is very sensitive to force (pN level), it's also a perfect tool to test sample's molecular interaction. Thus, AFM is growing to be an important technique with wide application in biology and nanomaterial area.In this thesis, based on AFM, we mainly research about (biomimetic) biomolecules'molecular interaction and behavior mechanism. Firstly, we use single-molecule force spectroscopy (SMFS) to detect molecular interaction of peptoid-peptoid and thrombin-aptamer. Secondly, by using AFM nanoshaving and in-situ AFM, we study peptoids' chemical stability, height variety and self-repair. Finally, we also explore peptoids'surface controlled self-assembly.Chapter 1 IntroductionIn this chapter, we systematically introduce the work principle, work mode and characteristics of AFM. Then we emphatically introduce techniques of single-molecule force spectroscopy and AFM nanolithography, and their application in biology. Finally, we expound the research content and research significance of this thesis.Chapter 2 Directly investigating the interaction between aptamers and thromb-in by atomic force microscopyThough many studies have been reported about the interactions between the aptamers and thrombin by atomic force microscopy (AFM), the thrombins in those studies were all immobilized by chemical agents. Recently, we developed a new method using AFM to directly investigate the specific interactions between thrombin and its two aptamers without immobilizing the thrombin. The unbinding dynamics and dissociation energy landscapes of aptamer/thrombin are discussed. The results indicate that the underlying interaction mechanisms of thrombin with its two aptamers will be similar despite the structures of 15apt and 27apt are different in buffer solution.Chapter 3 Using single-molecule force spectroscopy to investigate the interaction of peptoid-peptoid and peptoid-micaPeptoids are a class of biomimetic sequence specific polymers. We synthesized a new kind of peptoid, which can self-assemble into three-dimensional porous networks on mica surface in Ca2+ solution. The mechanism of peptoid self-assembly is still unclear. By using single-molecule force spectroscopy, we investigate the interaction of peptoid-peptoid and peptoid-mica. We find that the interaction between peptoid and mica is stronger than peptoid with peptoid. Besides, the interaction between peptoid with mica will increase along with the increase of Ca2+ concentration. We also inferred the peptoid self-assembly process on mica.Chapter 4 Using atomic force microscopy to investigate the properties, self-repair and patterning of 2D membrane-like peptoid materialsTwo-dimensional (2D) materials are of increasing interest for use in filtration, sensing, nanoelectronics, and biomedical devices due to their unique properties. Peptoids are a class of biomimetic sequence-defined polymers for which certain amphiphillic sequences self-assemble into 2D crystalline materials with properties that mimic those of cell membranes. Here, we research these membrane-like materials' chemical stability, height variety with AFM. Besides, using in situ atomic force microscopy (In-situ AFM) to both dissect these membrane-like materials and image their subsequent behavior, we explore their ability to self-repair on a range of solid substrates. We show that, in a suitable range of pH, self-repair occurs on both negatively and positively charged substrates and can even occur in the absence of an underlying surface. Following dissection of pre-assembled peptoid membranes and upon introduction of a peptoid monomer solution, peptoids repair the damage by assembling at the newly created edges. The speed of the advancing edge depends on the edge orientation, reflecting the two-fold symmetry of the underlying peptoid lattice. Moreover, because the membranes are stabilized by hydrophobic interactions, if the solution contains peptoids possessing an identical sequence in the hydrophobic block but a distinct hydrophilic block, filling of the defects creates membranes that are patterned at the nanoscale. Consequently, we can utilize this ability to self-repair to create nm-sized patterns of distinct functional groups within a single coherent membrane.Chapter 5 Using atomic force microscopy to explore peptoid's surface controlled self-assemblyIt's really meaningful to develop functional materials by controlling molecule's self-assembly. We synthesized a new kind of peptoid, which can separately self-assemble into 2D membranes and nanofibers on mica surface and silicon dioxide surface. The peptoid's self-assembly is controlled by the surface. Using in situ atomic force microscopy (In-situ AFM), we explore peptoid's self-assembly process and kinetics. Besides, we discuss the mechanism of how surface control peptoid self-assembly. We find the difference of interaction force between peptoid with different surfaces is the main reason for peptoid form different structures. We show that pH also influent peptoid's self-assembly, both too high and too low pH will inhibit the self-assembly results. What's more, Ca2+ can also affect peptoid's self-assembly process on mica.