Colloquium: Understanding RNA-Metal Ion Interactions: RNA Folding Pathways and Ion Selectivity

Ribonucleic acid (RNA) plays diverse and critical roles in cellular function. For most biological functions, RNA must fold into specific three-dimensional structures, and physiologically abundant monovalent (Na⁺ and K⁺) and divalent (Mg²⁺) metal ions are required to neutralize the negatively charged phosphate backbone and facilitate RNA folding^1,2. The discovery of ion-sensing riboswitches³ in bacteria revealed that RNA structures can specifically bind transition metal ions and even anions such as F^–, whose concentrations are multiple orders lower than that of Mg²⁺. The goal of my thesis is to understand the basic principles in RNA folding that lead to the specific binding of metal ions. To address this problem, I used riboswitches and introns as model RNA systems and studied their folding using computer simulations^4,5. I studied how these RNA systems fold in the presence of Mg²⁺ ions and at what stage in the folding process they distinguish between different metal ions and bind only to specific metal ions with high selectivity, even though there is a significant variation in the concentrations of different metal ions. I discuss the importance of the RNA folding intermediates, the inner and outer shell binding modes of solvated metal ions, and the local structure of the binding pocket in the selective binding of metal ions by RNA⁶. These results have implications for the design of RNA-based metal ion sensors and antibiotic discovery, as riboswitches are targets for discovering new antibacterial molecules.

1. Draper, D. E. A guide to ions and RNA structure. RNA 2004, 10, 335–343.
2. Hori, N.; Denesyuk, N. A.; Thirumalai, D. Ion condensation onto ribozyme is site-specific and fold-dependent. Biophys. J. 2019, 116, 2400–2410.
3. Kavita, K.; Breaker, R. R. Discovering riboswitches: the past and the future. Trends Biochem. Sci. 2023, 48, 119–141.
4. Mondal, D.†; Habibullah, S.†; Baidya, L.; Harariya, S. M. and Reddy, G., Transition Metal Binding Drives Folding of a Metalloregulatory Riboswitch by Modulating Conformational Flexibility at Helical Junctions (In Review) († equal first author).
5. Habibullah, S.†; Mondal, D.†; Kumar, S. and Reddy, G., Mg2+-Induced Multistep Folding of the Catalytic Group I Introns (Manuscript is in preparation) († equal first author).
6. Habibullah, S.; Baidya, L.; Kumar, S. and Reddy, G., Metal Ion Sensing by Tetraloop-like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion–RNA Inner-Shell Contacts J. Phys. Chem. B, 2024, 128 (46), 11389-11401.