Title: Single-molecule studies of RNA aptamer binding
Description: Aptamers are structured oligonucleotides, primarily RNA, that bind ligands with high specificity and affinity. They have been found by artificial in vitro selections, and in natural mRNAs. To avoid the biases and limits of selection experiments, and to investigate the heterogeneity of binding kinetics, it is desirable to apply direct single-molecule techniques to study aptamer binding. While single-molecule techniques have greatly illuminated the dynamics of phenomena which occur at short time scales of milliseconds to minutes--notably folding, conformational change, and to a lesser extent, catalysis--they have suffered from a technical gap, in not capturing behavior occurring at long time scales of minutes to days, and a functional gap, in not facilitating critical studies of binding. These two deficiencies are linked, in that binding at the low concentrations required for single-molecule experiments is likely to occur on a long time scale, as on rates are concentration dependent. In addition, high affinity may be achieved at least in part by slow off rates. This dissertation seeks to address this particular missing combination of function and time scale.

In this dissertation, a single-molecule approach for observing binding under equilibrium conditions on the long time scales of hours to days is developed. The approach is applied to a highly optimized artificially evolved RNA species, the Class V aptamer. The finding of great uniformity in the binding kinetics of Class V is quite striking, given the oft-noted ruggedness and complexity of the RNA folding landscape, and the heterogeneous kinetics of catalysis of small model ribozymes.