Improving RNA nearest neighbor parameters for helices by going beyond the two-state model

Abstract

RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson–Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson–Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.

Stability of an RNA•DNA–DNA triple helix depends on base triplet composition and length of the RNA third strand

“…buffer species and pH, salt identity and concentrations, polyamines, solvent, molecular crowding agents, temperature and equilibration time) and type of assay used to measure relative stabilities (24–26,40,48–50). Similar study-to-study variations have been observed for the stability of D•D–D base triplets and base pairs in dsRNA, both of which vary greatly depending on neighboring base triplets or base pairs (46,51,52). These results reinforce the importance of experimentally testing each computationally predicted triple helix, given the number of factors that can influence the overall stability of a triple helix.…”

Estimating uncertainty in predicted folding free energy changes of RNA secondary structures

“…One source of systemic error is that optical melting experiments are analyzed assuming two-state behavior. Our previous work shows that this leads to errors in the Watson-Crick parameters (Spasic et al 2018). Another source of systematic error is that the nearest neighbor model is incomplete.…”

Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement

“…The U exc in Equation (1) represents excluded volume interactions between two CG beads, and the P, C, and N beads are treated as spheres with van der Waals radii (r) of 1.9 Å, 1.7 Å, and 2.2 Å, respectively. The U bp , U bs , and U cs in Equation (1) are the base-pairing (between Watson-Crick and wobble base pairs), base-stacking (between nearest-neighbor base pairs), and coaxial stacking (between two discontinuous neighbor helices) interactions, respectively, and the strength of them was derived from sequence-dependent thermodynamic parameters and the corresponding experimental data (Xia et al, 1998;Spasic et al, 2018). The last term U el in Equation ( 1) is an electrostatic potential corresponding to electrostatic interactions between phosphate groups (a charge of -e for each P bead at its center), which are ignored by most existing predictive models for RNA 3D structures (Hajdin et al, 2010;Rose et al, 2011;Shi et al, 2014b;Schlick and Pyle, 2017).…”