Download MendeleyNMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.
Akinyemi, O., Kennedy, S.D., McSally, J.P., Mathews, D.H.(2026) Biophys J 125: 204-217
- PubMed: 41261770 Search on PubMed
- DOI: https://doi.org/10.1016/j.bpj.2025.11.026
- Primary Citation Related Structures:
9BXE - PubMed Abstract:
The conformational variability of RNA duplexes with internal loop 5'GAGU/3'UGAG was investigated by nuclear magnetic resonance spectroscopy (NMR) and all-atom molecular dynamics simulations (MD). It was previously found that the CG-flanked internal loop in 5'GACGAGUGUCA/3'ACUGUGAGCAG existed in a major conformation (I) characterized by U7 and U7 ∗ bulging into solution, A5 and A5 ∗ stacking, and G4-G6 ∗ and G6-G4 ∗ base pairs closing the loop. A minor conformation also existed with G-U pairs with a bifurcated hydrogen bond and A-G pairs with a single hydrogen bond (II). A maximum hydrogen bonding structure with wobble G-U pairs and two-hydrogen-bond A-G pairs (III) was not observed by NMR or MD. Here, flanking pairs A-U, U-A and G-C were substituted for the C-G base pair adjacent to the GAGU internal loop. NMR demonstrated changes in conformational preference depending on the identity of the flanking pair. Clustering of MD structures for C-G- and U-A-flanked duplexes showed transitions between conformations II and III with a greater fraction of the structures in conformation II, although the simulations started in conformation III. Additionally, U-A-flanked simulations contained 25% of structures in a state between conformations II and III. A-U- and G-C-flanked structures were in a single cluster whose centroid was conformation II. MD showed a dominance of structure II over III, in agreement with NMR for C-G closure, but in disagreement with other closures. MD starting in conformation I did not transition to II or III, with structures in a single cluster for all flanking base pairs except for G-C where 22% of the structures were defined by a C3'endo sugar pucker for G4 and G4 ∗ . Bases G4 and G4 ∗ were also syn around the glycosidic bond for all flanking pairs while G6 and G6 ∗ transitioned between syn and anti for C-G- and A-U-flanked simulations, consistent with NMR.
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States.
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