The Study Of Intermolecular Interactions Based On Single-molecule Mechanical Fingerprint Of Helical Structures

Helical structures are widely existent in nature.Many synthetic and biological molecules can form helical structures,such as DNA,polysaccharide,peptide and virus,in which their functions are closely related to helical structures.Such as the double-helical structure of DNA(ds DNA)can store a large amount of genetic information,and can form a surface(e.g.,minor or major groove)to allow other molecules(such as protein)to bind with it specifically.The study on the structure and function relationship and the factors that affect the function of helical structures is very important for materials design and the tuning of biological functions.Atomic force microscopy(AFM)-based single molecule force spectroscopy(SMFS)is a powerful method for investigating the conformational transition of molecules and the intermolecular interactions.Here SMFS was used to study the interactions of polycyclic aromatic hydrocarbons(PAHs)and protein with ds DNA,the effect of tannin and its derivatives on the assembly and disassembly of RNA in tobacco mosaic virus(TMV),according to the changes of mechanical fingerprints of helical structures.The possible anti-cancer(or anti-virus)mechanism of those small molecules were discussed.Furthermore,the nanomechanical properties of a new type of supramolecular helix stabilized by pure non-covalent interactions were studied,for the first time,and the mechanical fingerprint was obtained.In chapter 2,based on the mechanical fingerprint of ds DNA,we studied the interactions of helical and planar PAHs with ds DNA.The results show that both types of molecules bind to ds DNA trough intercalation,and the binding ability for planar molecules icreases with the increase of the number of aromatic rings that is NQ>BQ>Q,and for helical molecules is P6>4H>M6>P7>M7.The binding ability of helical molecules is generally greater than that of planar molecules.In addition,the result of circular dichroism spectrum shows that ds DNA could stabilize the chiral structure of 4H and induce the transition from racemic to single chiral structures.In chapter 3,we investigated the interactions between ds DNA and human papillomavirus(HPV)16 L1 coate protein.To do that we constructed a plasmid containing HPV 16 L1 protein target gene using genetic engineering technology,expressed and purified the L1 protein.Then we studied the binding of HPV 16 L1protein to ds DNA under dynamic(dialysis)and static conditions using AFM.We found that under dynamic condition,ds DNA-binding can hinder the assembly of L1.Under static condition,L1 tends to bind at the ends of ds DNA.Finally,according to the change of mechanical fingerprint of ds DNA,we found that HPV 16 L1 protein can condense ds DNA and form loop structures,and the binding strength is around 22p N.In chapter 4,we used SMFS to pull the helical RNA out of the groove formed by the TMV protein coat.By comparing the changes in the mechanical fingerprints before and after the addition of tannin,we studied the influence of tannin on the interactions between RNA and coat protein in the TMV.Our SMFS results show that tannin can enhance the interactions between RNA and coat protein and inhibit the disassembly of RNA from TMV protein coat.In addition,we also found that the size of tannin can affect the pathway of antivirus.The results of cycling stretching-relaxation experiment show that tannin can inhibit the reassembly of RNA on to the protein coat of TMV.Finally,according to the AFM imaging and photon correlation spectroscopy,we found that tannin can cause the aggregation of TMV particles.These results reveal the possible antiviral mechanism of tannic acid and its derivatives,i.e.,tannin can inhibit the assembly and disassembly of TMV,in addition tannin can cause TMV aggregation and inhibit its infection of plant cells.In chapter 5,we choose a thermal responsive supramolecular helix as a model system to study the nanomechanical properties of a new type supramolecular helix stabilized by only non-covalent interactions at the single-molecule level using SMFS and established the mechanical fingerprint of its helical structure.We found that when the supramolecular helix was stretched,the plateau-containing force curves can be produced and the force of the plateau is about 30 p N.The rupture force of the helical structure depends on the loading rate,which indicates the process occur in a nonequilibrium state.From the cyclic stretching-relaxation experiment we found that the force-induced unwinding process is reversible in the time scale of SMFS experiment,and there is almost no energy dissipation in the process.Finally,we used thermal shape-fluctuation analysis to study the axial mechanical properties of the supramolecular helix and obtained the information of persistence length and modulus.We found that the supramolecular helix exhibits very low static flexibility(P_L=222nm)but quite high dynamic flexibility(P_L=1.1 nm),which is different from those helical structures(e.g.,ds DNA)stabilized by both covalent and supramolecular interactions.