Solution Structures of Flexible RNA Molecules in Mono- and Divalent Salt

Abstract

Cells transmit and process genetic information using single-stranded RNA (ssRNA); these molecules realize their function through dynamic structural changes such as folding, association with binding partners, and conformational switching. Disordered, un-basepaired states of RNA play a key role in these dynamic structural transitions, yet most relevant measurements of single-stranded oligonucleotides have focused on DNA. Thus, we measure and compare the conformations of chemically similar ssRNA and ssDNA oligonucleotides lacking secondary structure. SAXS curves and smFRET efficiencies of rU40 and dT40 in 100mM NaCl are well-described by a simple wormlike chain model. We detect subtle but significant differences between the contour and persistence lengths of rU40 and dT40 that agree with predictions based on relative sugar pucker preferences of the two nucleotides. To compare the polyelectrolyte properties of ssRNA and ssDNA, we report persistence lengths derived from smFRET data acquired over a wide range of ionic conditions. We find that the apparent charge screening efficiency of divalent magnesium is anomalously large compared to monovalent sodium in both ssRNA and ssDNA. This strong interaction between divalent ions and disordered RNA presents an important problem for polyelectrolyte theory and challenges our understanding of how ions influence RNA folding.