Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition

Water molecules play a vital role in stabilizing ribonucleic acid (RNA) structures, not only as a solvent but as active participants in molecular recognition. Yet how hydration patterns encode binding specificity across RNA conformations remains poorly understood. The human immunodeficiency virus (HIV) Rev response element (RRE) provides a model system to address this question, as it adopts multiple conformations that engage distinct peptide partners. Here, the hydration landscapes of three RNA conformations are deciphered, and the role of water in RNA recognition is studied by mapping persistent water-binding sites and quantifying hydrogen-bond lifetime using all-atom molecular dynamics simulations. The apo state exhibits a diffuse hydration shell that uniformly stabilizes the backbone. By contrast, the Rev-binding conformation exhibits a reorganized and transient hydration environment, indicating that recognition involves the adaptive restructuring of the solvent network. In yet another manner, the RSG 1.2-binding conformation retains a highly ordered hydration scaffold that persists even without the peptide, consistent with a pre-organized recognition mechanism. Together, these results reveal that hydration encodes RNA adaptability, recognition readiness, and dictates whether recognition proceeds by induced-fit or pre-organized pathways. Importantly, these findings align with previous thermodynamic analyses reporting that RRE-Rev binding is driven by structural rearrangement and solvent displacement rather than direct enthalpic contacts, underscoring the central role of water in RNA adaptability and molecular recognition. • Decoded hydration landscapes across ribonucleic acid (RNA) conformations through mapping of persistent water-binding sites. • Hydration patterns differ remarkably between different rev-responsive element RNA conformations. • RNA can be recognized either by rearranging the hydration pattern or by exploiting pre-organized water networks as structural scaffolds.