Metal ion induced heterogeneity in RNA folding studied by smFRET

Abstract

More than two decades investigating nucleic acids and ribonucleic acids (RNA) by single molecule Förster Resonance Energy Transfer (smFRET) have passed. It turned out that sample heterogeneity in structure and function of RNA molecules as well as folding intermediates, kinetic subpopulations, and interconversion rates of conformational states of RNA biomolecules, all of which are usually hidden in ensemble type experiments, are often observed characteristics. Besides proteins, metal ions play a crucial role in RNA folding and dynamics, as well as RNA/RNA or RNA/DNA interactions. RNA molecules form discrete conformational intermediates before reaching the native three-dimensional fold, whereby metal ions guide the folding pathway by changing the energetic barriers between local and global minima in the energy landscape. Here we review recent advances in the characterization of the role of metal ions in folding and function of nucleic acid structures by means of smFRET. Subsequently, the workflow of smFRET data analysis is described and exemplified by the metal ion-depending folding and dynamics of the group IIB intron from S. cerevisiae and RNA-RNA binding kinetics of this ribozyme's 5'-splice site formation.

Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts

“…Our FRET trajectories capture binding and unbinding events across various K + and Mg 2+ concentrations. Consistent with previous experiments, IBS1 (un)docking and Mg 2+ coordination are coupled, resulting in Mg 2+ exchange rates on a timescale of milliseconds to seconds, thus accessible to camera-based detection 15,16 . We find that Mg 2+ association and dissociation from the EBS1*/IBS1* contact are linked to very subtle conformational changes within the duplex, indiscernible by FRET.…”

“…Hence, exon unbinding is characterized by multiexponential decays from one degenerate FRET state, conceptually known as kinetic heterogeneity. Heterogeneity is common to many nucleic acid interactions and increases the complexity of the kinetic analysis 16 . Here, we have shown how to dissect such a state degeneracy and elucidate its molecular origin.…”

“…As ion coordination is transient though, designated binding pockets are often only partially occupied and exon dissociation is thus kinetically heterogeneous 15 . Particularly, Mg 2+ is known to induce such kinetic partitioning by interacting with RNA directly (inner-sphere coordination) or via a water molecule (outer-sphere coordination) [16][17][18] .…”

“…As metal ions direct folding and catalysis, heterogeneity is inherent to many RNAs 16,22 . RNA folds hierarchically into a set of interconnected topological modules.…”

Mechanism of Lithium Cation Hopping between Tetragonal Thiophene Cages

“…[1][2][3][4][5][6][7][8][9][10][11] In particular, lithium-based energy-storage systems have recently attracted much attention due to their high energy densities and relatively cheap production costs. A first step towards obtaining such a knowledge is to reveal the local structure in the vicinity of an ion.…”