Nearest Neighbor Parameters for Estimating RNA Folding Stability with In Vivo-like Conditions
- 1University of Rochester
Abstract
RNAs regulate gene expression and cellular processes, often relying on specific conformations for function. RNA folding is hierarchical and sequence-dependent, with nearest-neighbor thermodynamic models commonly used to predict secondary structure. Current models were developed using optical melting experiments in 1 M NaCl, which does not represent the cellular environment. To address this, we developed a new model in Advanced Dulbecco's Modified Eagle Medium (Adv. DMEM), which mimics mammalian extracellular ionic composition. This in vivo-like model provides RNA folding parameters for helical base stacks and loop motifs. Optical melting experiments revealed helical stacks, particularly tandem G-U pairs, are less stabilizing in Adv. DMEM. Loop parameters were generally destabilizing but highly dependent on both sequence and loop type, with internal loops displaying idiosyncratic behavior. Structure prediction benchmarking revealed minimal differences overall, except for tRNAs, which showed improved prediction reliability and enhanced cloverleaf stability. Notably, tRNAs lack internal loops, suggesting further studies in Adv. DMEM could refine secondary structure predictions. This in vivo-like parameter set is included in the RNAstructure software package. Grounding these parameters in a physiologically relevant environment, we improve the biological relevance of RNA secondary structure predictions and establish a foundation for studying RNA folding under in vivo conditions.
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BibTeX
@misc{hiltke2026nearest,
title = {{Nearest Neighbor Parameters for Estimating RNA Folding Stability with In Vivo-like Conditions}},
author = {O. M. Hiltke and E. Kierzek and M. Prochota and M. Rachwalak and M. Miaro and T. Shabangu and S. Gorczynska and R. Kierzek and D. H. Mathews},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.04.749202},
url = {https://www.biorxiv.org/content/10.64898/2026.09.04.749202v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Nearest Neighbor Parameters for Estimating RNA Folding Stability with In Vivo-like Conditions
AU - O. M. Hiltke
AU - E. Kierzek
AU - M. Prochota
AU - M. Rachwalak
AU - M. Miaro
AU - T. Shabangu
AU - S. Gorczynska
AU - R. Kierzek
AU - D. H. Mathews
PY - 2026
DA - 2026/09/04
PB - bioRxiv
DO - 10.64898/2026.09.04.749202
UR - https://www.biorxiv.org/content/10.64898/2026.09.04.749202v1
AB - RNAs regulate gene expression and cellular processes, often relying on specific conformations for function. RNA folding is hierarchical and sequence-dependent, with nearest-neighbor thermodynamic models commonly used to predict secondary structure. Current models were developed using optical melting experiments in 1 M NaCl, which does not represent the cellular environment. To address this, we developed a new model in Advanced Dulbecco's Modified Eagle Medium (Adv. DMEM), which mimics mammalian extracellular ionic composition. This in vivo-like model provides RNA folding parameters for helical base stacks and loop motifs. Optical melting experiments revealed helical stacks, particularly tandem G-U pairs, are less stabilizing in Adv. DMEM. Loop parameters were generally destabilizing but highly dependent on both sequence and loop type, with internal loops displaying idiosyncratic behavior. Structure prediction benchmarking revealed minimal differences overall, except for tRNAs, which showed improved prediction reliability and enhanced cloverleaf stability. Notably, tRNAs lack internal loops, suggesting further studies in Adv. DMEM could refine secondary structure predictions. This in vivo-like parameter set is included in the RNAstructure software package. Grounding these parameters in a physiologically relevant environment, we improve the biological relevance of RNA secondary structure predictions and establish a foundation for studying RNA folding under in vivo conditions.
ER -