Novel Development of Super-Resolution Force Spectroscopy and Applications in Biological Systems



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This dissertation focuses on applications of new techniques that are used to investigate interactions in biological systems. Atomic magnetometry and ultrasound have been extensively used as individual techniques in various physical and engineering fields. Their combination, however, has been rare. Super-resolution force spectroscopy (SURFS) was developed based on the integration of these two techniques, and it has unique biophysical applications in studying drug-DNA interactions and ribosomal translocations. I demonstrate that SURFS has a high force resolution of 0.5 pN by resolving the dissociation forces of 12 base pairs of DNA duplex and 11 base pairs of DNA duplex with the drug daunomycin. The SURFS technique was used to determine the positions of the ribosome on the mRNA at two distinct states. I found that from the post-translocation state (Post) to the subsequent pre-translocation state (Pre), the ribosome moves spontaneously by nearly half a nucleotide. The application of SURFS was expanded in biophysics. I was able to precisely resolve three small molecules binding with two DNA sequences, which were difficult to distinguish by using previous force spectroscopic techniques. The results indicate that the differential binding forces caused by drug binding correlate with enthalpy instead of free energy, thus providing an alternative physical parameter for optimizing chemotherapeutic drugs. Force-induced visualization (FIV) can determine the functional position of nucleic acids with single-nucleotide resolution by visually distinguishable states. The use of an adjustable mechanical force overcomes the variations of buffer conditions and analyte concentrations. Probing the mRNA movement during ribosomal translocation, and revealing the interacting sites and strengths of DNA-binding drugs were investigated. The experimental setup used to record and quantify data was achieved with an affordable and portable device coupled with a smart phone. Massive detections were achieved by simultaneously using acoustic radiation force. The simplicity of the method, low cost of the device, and high efficiency of the measurements have broad applications for FIV in biomolecular research.



Super-resolution force spectroscopy, DNA-drug, Ribosome motion, Force-induced visualization