| Abstrakt: |
Secondary RNA structures, such as hairpins and G-quadruplexes (G4s), play a crucial role in regulating viral life cycles, influencing replication, transcription, and translation of viral genomes. In the SARS-CoV-2 genome, guanine-rich sequences capable of forming G4s have been identified, which may modulate viral replication and gene expression [1]. The aim of this study was to evaluate the stability of hairpin and G4 structures in the SARS-CoV-2 genome through in silico molecular modeling at temperatures of 293 K and 310 K. This study applies a computational protocol combining molecular dynamics (MD) techniques similar to those discussed in recent studies on RNA structural dynamics, which have demonstrated the impact of structural motifs and environmental conditions on RNA stability [2]. Hairpin and G4s 3D structures were modeled using homology-based approaches and known experimental data, applying RNA-specific modeling services. MD simulations were conducted in GROMACS with the CHARMM36 force field. The results indicated that G4 structures with a uridine tetrad showed increased stability at 310 K, which aligns with physiological conditions and suggests that uridine may play a role in stabilizing G4s, potentially influencing viral replication and virulence. For hairpin structures, stability varied based on structural features: hairpins with long free ends and structures formed from roughly one-third of the nucleotide sequence exhibited more fluctuations during MD simulations, while those with longer complementary-paired or very short unpaired ends were more stable. This trend may be attributed to structural rigidity, as hairpins with longer free ends might require more time to stabilize, undergoing state transitions to achieve equilibrium. Temperature sensitivity analysis also showed that certain hairpin models demonstrated stability variations depending on specific modeling parameters, underscoring the importance of optimizing parameters for accurate RNA stability predictions. These findings highlight the importance of selecting appropriate modeling approaches and conducting detailed stability analyses, including long-term simulations and environmental factors, for accurate R NA behavior assessment. This study supports further in vivo research, such as in-cell NMR, to confirm their roles under physiological conditions, with implications for antiviral strategies. The funding is provided by the National Research Foundation of Ukraine, grant #2021.01/0087. [ABSTRACT FROM AUTHOR] |
