Fast folding of RNA pseudoknots initiated by laser temperature-jump

RNA pseudoknots are examples of minimal structural motifs in RNA with tertiary interactions that stabilize the structures of many ribozymes. They also play an essential role in a variety of biological functions that are modulated by their structure, stability, and dynamics. Therefore, understanding the global principles that determine the thermodynamics and folding pathways of RNA pseudoknots is an important problem in biology, both for elucidating the folding mechanisms of larger ribozymes as well as addressing issues of possible kinetic control of the biological functions of pseudoknots. We report on the folding/unfolding kinetics of a hairpin-type pseudoknot obtained with microsecond time-resolution in response to a laser temperature-jump perturbation. The kinetics are monitored using UV absorbance as well as fluorescence of extrinsically attached labels as spectroscopic probes of the transiently populated RNA conformations. We measure folding times of 1-6 ms at 37 °C, which are at least 100-fold faster than previous observations of very slow folding pseudoknots that were trapped in misfolded conformations. The measured relaxation times are remarkably similar to predictions of a computational study by Thirumalai and co-workers (Cho, S. S.; Pincus, D.L.; Thirumalai, D. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 17349-17354). Thus, these studies provide the first observation of a fast-folding pseudoknot and present a benchmark against which computational models can be refined.     

Ion and solvent transport in polypyrrole: Experimental test of osmotic model

Ion and solvent transport in the conjugated polymer actuator material, polypyrrole doped with the immobile anion dodecyl benzene sulphonate, has been investigated by simultaneous cyclic voltammetry and Electrochemical Quartz Crystal Microbalance measurements. The purpose was to elucidate the precise nature of the mobile species during redox cycling, and to seek confirmation for the osmotic mechanism of actuation. Three testable aspects of the model were confirmed: The number of inserted H₂O molecules decreases with electrolyte concentration; at the same time the mechanism gradually changes from almost pure cation transport to ca. equal amount of anion transport; exchanging Br⁻ for Cl⁻ ions has only negligible effect at lower concentrations at equal osmotic pressures. Approximately, 4 H₂O molecules are tightly bound to each Na⁺ ion at concentrations <1 M. Paper presented at the International Conference on Functional Materials and Devices 2005, Kuala Lumpur, Malaysia, June 6 – 8, 2005.