RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

Abstract

The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes. Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two transient, on-pathway intermediates. Since these intermediates are degenerate with two to four alternative conformations per state, RNA quadruplex folding is a multi-pathway process with high conformational entropy.

Small molecule chaperones facilitate the folding of long non-coding RNA G

“…The folding and unfolding states of intramolecular rG4s without G4 ligands are multiple and complex (e.g. they are capable of forming hairpin, triplex and double hairpin states), which may explain the diversity of transitions obtained by FRET-renaturing assays (Figure S2) 44 .…”

Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes

“…[39][40][41][42][43][44][45] For nucleic acids, the three interaction site 4 (TIS) model, first formulated by Hyeon and Thirumalai, 46 provides a fine balance between accuracy and speed. Different variants of the TIS model have been exploited by us and others 26 to provide a quantitative description of ion-assisted RNA folding, [47][48][49][50][51] folding of Gquadruplexes, 52 and DNA mechanics and thermodynamics. 53 Encouraged by the wide range of applicability of our existing CG models, we develop COFFEE (Coarse-grained Force Field for Energy Estimation), a hybrid potential that integrates the SOP-SC model for folded proteins, with the TIS model for DNA.…”