Model speculation

Abstract

Recent development of microscopy technique, its related technique, and the fluorescence spectroscopy enables to produce the results about biomolecules, namely nuclear acids, proteins and lipids. Theoretical tools to analyze the result from experiment and to design the experiment are getting improved since the number of parameters which need to be concerned increases as the complexity of equipments. In this paper, the ‘model speculation’ scheme is defined and applied to the experimental results from fluorescence resonance energy transfer (FRET) which can monitor the reaction of biomolecules and fluorescence correlation spectroscopy (FCS) which measures the diffusion of biomolecules. ‘Model speculation’ scheme is defined as the method which enables to choose correct model before we try to find the proper fitting curve. Here the scheme is made of the model free method (maximum entropy method) and the transformation method. The bulk FRET measurement is performed to observe the reaction between the complement pair of short DNA fragments. The reaction kinetics cannot be decomposed mathematically into the first order reaction kinetics even with the hard sphere collision assumption. The maximum entropy method (MEM) is applied to decompose the kinetics, and the results show the two component first kinetics. This result is confirmed by the nonlinear fitting with the model of two exponentials. It is conjectured that the existence of transient variant form makes the occurrence of one component, and the simple approaching of two strands is for another one. To monitor the diffusion of proteins, the FCS is used, which gives the autocorrelation of intensity fluctuation as a result. The autocorrelation curve contains the information of diffusion time and the mean number of particles inside the confocal volume. In crowded media or in a cell, the diffusion of protein can be normal diffusion, or anomalous diffusion, or mixture of several diffusion components. To interpret the resu...