Amino Acid Specific Effects on RNA Tertiary Interactions: Single-Molecule Kinetic and Thermodynamic Studies.

Abstract

In light of the current models for an early RNA-based universe, the potential influence of simple amino acids on tertiary folding of ribozymal RNA into biochemically competent structures is speculated to be of significant evolutionary importance. In the present work, the folding-unfolding kinetics of a ubiquitous tertiary interaction motif, the GAAA tetraloop-tetraloop receptor (TL-TLR), is investigated by single-molecule fluorescence resonance energy transfer spectroscopy in the presence of natural amino acids both with (e.g., lysine, arginine) and without (e.g., glycine) protonated side chain residues. By way of control, we also investigate the effects of a special amino acid (e.g., proline) and amino acid mimetic (e.g., betaine) that contain secondary or quaternary amine groups rather than a primary amine group. This combination permits systematic study of amino acid induced (or amino acid like) RNA folding dynamics as a function of side chain complexity, pKa, charge state, and amine group content. Most importantly, each of the naturally occurring amino acids is found to destabilize the TL-TLR tertiary folding equilibrium, the kinetic origin of which is dominated by a decrease in the folding rate constant (kdock), also affected by a strongly amino acid selective increase in the unfolding rate constant (kundock). To further elucidate the underlying thermodynamics, single-molecule equilibrium constants (Keq) for TL-TLR folding have been probed as a function of temperature, which reveal an amino acid dependent decrease in both overall exothermicity (ΔΔH° > 0) and entropic cost (-TΔΔS° < 0) for the overall folding process. Temperature-dependent studies on the folding/unfolding kinetic rate constants reveal analogous amino acid specific changes in both enthalpy (ΔΔH⧧) and entropy (ΔΔS⧧) for accessing the transition state barrier. The maximum destabilization of the TL-TLR tertiary interaction is observed for arginine, which is consistent with early studies of arginine and guanidine ion-inhibited self-splicing kinetics for the full Tetrahymena ribozyme [ Yarus , M. ; Christian , E. L. Nature 1989 , 342 , 349 - 350 ; Yarus , M. Science 1988 , 240 , 1751 - 1758 ].