biostudies-literatureSarkar RScience and Engineering Research BoardNational Institute of General Medical SciencesNIGMS NIH HHSDepartment of Biotechnology, Ministry of Science and Technology, India6479-6490https://www.ebi.ac.uk/biostudies/studies/S-EPMC8988897biostudies-literatureUnknown125(24)Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions. A mechanism is proposed for the role of experimentally discovered site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers in bacteria. This mechanism is observed with atomistic simulations performed in a physiological mixed salt environment at a high temperature. The simulations were validated with phosphorothioate interference mapping experiments that help to identify crucial inner-sphere Mg²⁺ sites prThe journal of physical chemistry. BChelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.PMC8988897R01GM110310BT/12/IYBA/2019/12SRG/2020/001295R01 GM110310Sarkar RHennelly SPSanbonmatsu KYJaiswar ARoy SOnuchic JNfalseChelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions. A mechanism is proposed for the role of experimentally discovered site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers in bacteria. This mechanism is observed with atomistic simulations performed in a physiological mixed salt environment at a high temperature. The simulations were validated with phosphorothioate interference mapping experiments that help to identify crucial inner-sphere Mg²⁺ sites pr2021-01-01T00:00:00Z2021 Jun2026-05-31T06:00:52.593Z2025-02-19T01:55:17.165ZS-EPMC89888973410671910.1021/acs.jpcb.1c02467