Viscosity Measurement of Biological Fluids Using Optical Tweezer

Abstract

Hydrogen bonds play an important role in RNA structure and dynamics. Fluctuations in base pair openings could be the starting point of unfolding processes or could indicate potential docking sites for ligands or proteins. The effects of hydrogen bond formation and breaking kinetics in RNA base pairs on the linear and coherent third order infrared spectra of small UUCG tetraloops in solution can be described by Markovian, not necessarily Gaussian, fluctuations. We have simulated these spectra using the stochastic Liouville equations. Slow fluctuations are described phenomenologically. Fast fluctuations are characterized by an N-state jump model for hydrogen bond configurations, where N depends on the specific tetraloop. Bases in the RNA strands that exhibit high levels of fluctuation are isotope labeled and the chemical exchange 2DIR spectra are calculated. The existence and evolution of the resultant cross peaks at different waiting times provides information on the coupling interactions between base pairs in the loops, which will be used to help characterize unfolding mechanisms of the RNA strands.