Improved Data Analysis Method Of Single-molecule Experiments Based On Probability Optimization

The single molecule manipulation method has been widely applied in the study of conformational dynamics of biomolecules,such as DNA unzipping and protein folding/unfolding.In a single molecule manipulation experiment,the molecule is stretched by force and the extension is measured with nanometer resolution.From the measurement of force and extension,conformational transition of the molecules can be detected.Dynamic parameters can be obtained by fitting a theoretical model to the analytic expression of the measurement distribution.If there is no analytical expression,a model-dependent simulation can be used to compare with the experimental results,which is usually done roughly by adjusting the parameter to minimize the difference intuitively.Both methods require the distributions of unfolding force,lifetime,et al.Because the conformational transition dynamics of a single molecule is a stochastic process,a lot of measurements need to be done to obtain an accurate distribution.However,the time required for single-molecule measurement is limited by the fact that the molecular chain is subject to stress and the damage of the molecule itself.With limited experimental data,it is hard to obtain an accurate distribution.In this case,the kinetic parameters are also difficult to obtain,even rough estimations.Here we propose a systematic algorithm to obtain the optimized parameters based on the measured time trace directly.We assume that the measured time trace has maximal probability to appear among all possible time traces.In the algorithm,the kinetic parameters are optimized to maximize the probability of the measured time trace.The optimized parameter values are good estimates of their real values.We use the most widely used Bell’s model and dynamic simulation of two-state transitions to demonstrate the algorithm.Then we apply this algorithm to the single molecular manipulation experiment of a DNA hairpin and calculate the unfolding rate of a-catenin protein by our algorithm.With the development of magnetism technology,we can exert torque and mechanical force to DNA at the same time.At present,there has been extensive research on the dependence of DNA torsion on ion concentration and the dependence of DNA elasticity on temperature.However,there has been few experimental studies on the relationship between DNA twist and temperature.In this part,we preliminary exploration temperature dependence of B-DNA twisting by freely orbiting magnetic tweezers(FOMT).During the experiment,the force of the cylindrical magnet in the FOMT was measured,two kinds of DNA samples were designed and prepared,and the temperature heating was tested.Then we write the data processing program.This section is intended to serve as a reference for follow-up research.