Observation of a Change in Bend of an RNA Kissing Complex Using the Angular Dependence of Fluorescence Resonance Energy Transfer

Abstract

We report on the observation of a change in the bend angle of an RNA kissing complex upon Rop binding using single-molecular-pair FRET. The angular relationship between the dyes, rather than the distance between them, is shown to be responsible for the observed change in energy transfer. It has long been thought that Rop increases the bend angle of the R1inv-R2inv complex upon binding, but this has never been directly observed. In contrast, we find an increase in FRET upon the addition of Rop that is shown via modeling to be consistent with a decrease in the bend angle of the complex of $-15^{\circ}\pm7^{\circ}$. The model predicts FRET from dye trajectories generated using molecular dynamics simulations of Cy3 and Cy5 attached to $5'$ terminal cytosine or guanosine on RNA. While FRET is commonly used to observe global changes in molecular structure attributed to changes in the distance between dyes, it is rarely, if ever, used to elucidate angular changes. Subtle global changes in molecular structure upon binding are generally difficult to discern using NMR or crystallography, but FRET is well suited to observe these changes because of its sensitivity at interdye distance around the Förster radius, $R_F\approx5$ nm. While FRET is often referred to and used as a "molecular ruler" for distances around $R_F$, for dye pairs that have minimal rotational freedom, FRET can also be used to observe changes in structure for which there is no significant change in distance between the dyes. This is the case for the R1inv-R2inv kissing complex studied here. This complex is derived from the RNA I - RNA II complex in E. coli. RNA II is a primer for replication of the ColE1 plasmid, its function is modulated by interaction with RNA II. Rop is known to stabilize the complex, and it is also known to bind kissing complexes in a structure, but not sequence, dependent fashion.