MSc student working with Dr. Jocelyne Vreede on the effect of methylation on RNA under force.
Double-stranded RNA (dsRNA) has proven to play essential roles in antiviral immunity, gene regulation, and RNA interference, while its biological activity is closely linked to its structural and mechanical properties.1 RNA molecules are extensively modified after transcription, with N6-methyladenosine (m6A) representing the most abundant internal modification in eukaryotic RNA.2 Although m6A has been widely studied for its effects on RNA metabolism, immune recognition, and host–pathogen interactions, its influence on the mechanical behaviour of dsRNA remains incompletely understood.3
Recent molecular dynamics simulations conducted by the Computational Chemistry Group demonstrated that m6A methylation induces only subtle changes in dsRNA conformation while largely preserving force-extension behaviour and the stability of the dimers, suggesting that stretching experiments are relatively insensitive to structural effects stemming from methylation. This indicates that alternative perturbations, may be more effective in revealing the impact of m6A on dsRNA dynamics. Previous experimental studies using ‘magnetic tweezers’ support this hypothesis by demonstrating that rotational stress can induce conformational transitions which are unobserved during simple stretching.4,5 Therefore, the proposed project aims to investigate how m6A methylation influences the torsional mechanics of dsRNA using microsecond simulations to characterise the equilibrium state, followed by steered molecular dynamics to study the dsRNA under force.6,7
(1) Fire, A.; Xu, S.; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; Mello, C. C. Potent and Specific Genetic Interference by Double-Stranded RNA in Caenorhabditis Elegans. Nature 1998, 391 (6669), 806–811. https://doi.org/10.1038/35888.
(2) Roundtree, I. A.; Evans, M. E.; Pan, T.; He, C. Dynamic RNA Modifications in Gene Expression Regulation. Cell 2017, 169 (7), 1187–1200. https://doi.org/10.1016/j.cell.2017.05.045.
(3) Dominissini, D.; Moshitch-Moshkovitz, S.; Schwartz, S.; Salmon-Divon, M.; Ungar, L.; Osenberg, S.; Cesarkas, K.; Jacob-Hirsch, J.; Amariglio, N.; Kupiec, M.; Sorek, R.; Rechavi, G. Topology of the Human and Mouse M6A RNA Methylomes Revealed by M6A-Seq. Nature 2012, 485 (7397), 201–206. https://doi.org/10.1038/nature11112.
(4) Heller, Iddo.; Dulin, David.; Peterman, E. J. G. . Single Molecule Analysis : Methods and Protocols; Humana Press, 2024.
(5) Rashid, Z. M.; Klein, M.; van Heesch, T.; Quack, S.; Smitskamp, Q.; America, P. P. B.; Rivas, P.; Albers, M. A.; Paulus, J.; Vreede, J.; Grossmann, T. N.; Dulin, D. TAV2b Peptide Derivatives Underwind and Stabilize Double-Stranded RNA upon Binding. J. Am. Chem. Soc. 2026, 148 (8), 8298–8309. https://doi.org/10.1021/jacs.5c18586.
(6) Mohr, B.; van Heesch, T.; Pérez de Alba Ortíz, A.; Vreede, J. Enhanced Sampling Strategies for Molecular Simulation of DNA. WIREs Computational Molecular Science 2024, 14 (2). https://doi.org/10.1002/wcms.1712.