Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics

Abstract

Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs, and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering, through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs, and may explain their distinct recognition by protein partners.

Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

“…An important step forward in understanding RNA structure is the consideration of ensembles as the best descriptors of flexible systems ( Plumridge et al 2019 ; Liu et al 2021 ). Folding behavior and intermolecular interactions of single-strand RNA molecules have implications in biopharmaceutical drug development, including rational design and predicting delivery properties ( Costales et al 2020 ), as single stranded antisense oligonucleotides (ASOs) have been approved as drug products starting in 1998 ( de Smet et al 1999 ).…”

Modeling concentration-dependent phase separation processes involving peptides and RNA via residue-based coarse-graining

“…Results are shown in red circles, blue squares, and black triangles for COCOMO, the Regy et al . 2020 33 model, and experimental values 50, 52 , respectively. Different salt concentrations were reflected by varying the Debye length, κ , in Eq.…”

“…As observed for proteins, the Rg and Plength values are most sensitive to the choice of 𝐴𝐴 0 and 𝜀𝜀 𝑏𝑏𝑡𝑡𝑏𝑏−𝑝𝑝𝑡𝑡𝑡𝑡𝑡𝑡𝑜𝑜 values, while the choice of 𝑘𝑘 𝑡𝑡𝑏𝑏𝑎𝑎𝑡𝑡𝑎𝑎 and 𝑘𝑘 𝑏𝑏𝑡𝑡𝑏𝑏𝑏𝑏 showed much smaller effects (Figure S2). 50,52 , respectively. Different salt concentrations were reflected by varying the Debye length, 𝜅𝜅, in Eq.…”

“…Orientational correlation factor (OCF) for polyAde-30 (B), and polyU-30 (E) at 100 mM salt concentration is also shown. Results are shown in red circles, blue squares, and black triangles for COCOMO, the Regy et al 2020 33 model, and experimental values50,52 , respectively. Different salt concentrations were reflected by varying the Debye length, 𝜅𝜅, in Eq.…”

Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA

“…To assess the force fields, we compare this property for oligo-Us. The experiment 44 reports L P ≈ 1.9 nm for U 30 at 100 mM KCl. Computed L P from rU 15 on the other hand shows notable differences among force fields.…”