Talk abstracts
Talk on Friday 01:15-01:30pm submitted by Edric Choi
Kinetic modeling of chemical probing data enables extraction of intrinsic nucleotide energetics
Edric K. Choi (Chemical and Biological Engineering, Northwestern University), Ritwika Bose, Anthony M. Mustoe, Julius B. Lucks
Abstract:
Chemical probing has long been indispensable in studying RNA structures within diverse biological systems, leading to significant insights into RNA functionality. However, the full potential of chemical probing data from these experiments remains obscured due to the complexities of interpreting raw reactivity data. Here we address this limitation by developing a conceptual framework for interpreting reactivities that is analogous to the framework used in analyzing hydrogen exchange experiments for protein structures. Using this model, we show that raw reactivities, r, are a non-linear convolution between intrinsic RNA structural information, denoted K, and experimental parameters related to probe modification kinetics. We validate the model through non-linear fitting of time-course DMS probing experiments conducted on the extensively studied Salmonella fourU thermometer at a range of temperatures. Analysis of extracted K values show that they exhibit Arrhenius-like temperature dependence, allowing us to extract an effective ΔG value from the K values for each nucleotide. These extracted ΔG values are significantly correlated with published NMR-derived base pair dissociation energies (R2 = 0.78) and ΔΔG (R2 = 0.54), supporting that they represent physical measurements of base-pair stability. We suggest a path forward for further study for a deeper understanding of the aspects of RNA structure being revealed by this analysis. These findings demonstrate the capability to extract nucleotide-resolution RNA structure thermodynamic parameters from RNA chemical probing experiments, and a framework for analyzing reactivity data that can be extended into a robust standard for comparing RNA structures across varied experimental conditions.
Keywords: RNA chemical probing, Nucleotide thermodynamics, Quantitative data analysis