Profile of RNA Helices: Brownian Dynamics Simulations

Bends in nucleic acid helices can be quantified in a transient electric birefringence (TEB) experiment from the ratio of the terminal decay times of the bent molecule and its fully duplex counterpart (T-ratio method). The apparent bend angles can be extracted from the experimental T-ratios through the application of static (equilibrium-ensemble) hydrodynamic models; however, such models do not properly address the faster component(s) of the birefringence decay profile, which can represent up to 80% of the total birefringence signal for large bend angles. To address this latter issue, the relative amplitudes of the components in the birefringence decay profile have been analyzed through a series of Brownian dynamics (BD) simulations. Decay profiles have been simulated for three-, five-, and nine-bead models representing RNA molecules with central bends of 300, 600, and 900, and with various degrees of associated angle dispersion. The BD simulations are in close agreement with experimental results for the fractional amplitudes, suggesting that both amplitudes and terminal T-ratios can be used as a measure of the magnitudes of bends in the helix axis. Although the current results indicate that it is generally not possible to distinguish between relatively fixed and highly flexible bends from single T-ratio measurements, because they can lead to similar reductions in terminal decay time and amplitude, measurements of the dependence of the fractional amplitudes on helix length may afford such a distinction.