High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping

Structured RNAs play critical roles in cellular functions, underlying the life cycle of RNA viruses, and serve as blueprints for new artificial machines. These RNAs must fold on themselves to form complex 3D structures which underlie their function. Folding occurs in two steps: initially forming a secondary structure defining helices, junctions, and loops through base pairing, followed by potential long-range tertiary contacts among these elements. There is significant variability in the structure and stability of tertiary contacts. Some contacts are single adenines that transiently dock into the minor groove of a helix. On the other hand, some contacts involve multiple base pairs and are stable enough to lock the entire RNA into well-defined 3D conformations essential to its function. Understanding the thermodynamics of these tertiary contacts is crucial for decoding the folding of biological RNAs into functional forms. Despite their importance, methods to measure tertiary contact thermodynamics are low-throughput or technically challenging, requiring specialized instruments. Here, we introduce a new quantitative dimethyl sulfate mutational profiling with sequencing (Q-DMS-MaPseq) approach that leverages Mg2+ titrations to measure the thermodynamics of tertiary contacts in a high-throughput manner. Utilizing a nanostructure model system with a tetraloop/tetraloop receptor (TL/TLR) tertiary contact, we conducted a 16-point Mg2+ titration and computed the [Mg2+]½ which aligns with prior findings. The titration revealed conformational changes upon Mg2+ addition, allowing consistent GAAA tetraloop binding, in agreement with earlier structural models of the apo TLR. Comparing our [Mg2+]½ values with known ΔGs 100 known TL/TLR mutations revealed that Q-DMS-MaPseq provides high-quality measurements, suggesting it is a rapid, reliable, high-throughput technique for assessing RNA tertiary contact thermodynamics, paving the way for massively parallel energetic measurements of RNA folding.