A transient polarization grating method to study tumbling and bending dynamics of DNA

Abstract

A transient polarization grating (TPG) instrument was developed to investigate the tumbling and bending dynamics of various DNAs over the time range from 20 ns to 10 μs. This TPG experiment employs pulsed writing beams with orthogonal polarizations and a continuous-wave probe beam. Detection of the diffracted probe light is performed via a photon counting method. Methylene blue intercalated in DNA is used as the chromophore to create the gratings. TPG experiments performed on DNA molecules containing 200 base-pairs yield a relaxation time for tumbling that is in reasonable accord with prior work. This TPG experiment achieves a significant gain in signal-to-random-noise ratio over a direct photoinduced dicroism experiment, and eliminates an important source of systematic error that could significantly alter the tail of the decay curve, where bending and end-over-end tumbling dominate the relaxation. However, the proportionality constant between the diffracted signal and photo-induced dichroism in the sample is an additional unknown in the data analysis.