Molecular dynamics analysis of 3’ dangling-end stabilization at an AU-rich RNA helix terminus

Single unpaired nucleotides adjacent to RNA helix termini, commonly termed dangling ends, can measurably modulate local helix stability through sequence-dependent stacking interactions. Here, we use all-atom molecular dynamics simulations to investigate the contribution of single-nucleotide 3' dangling ends to the stability of an RNA helix terminus containing an AAUU terminal motif. By monitoring reversible transitions between closed and open terminal states over a temperature series, we estimate apparent free-energy, enthalpic, and entropic signatures associated with a 3' dangling Guanine. We further compare the effects of 3'-terminal A, G, C, and U dangling nucleotides at 410 K to assess sequence dependence within the same structural framework. The simulations indicate that 3' dangling ends stabilize the terminal base pair in a strongly sequence-dependent manner, with purines producing substantially larger stabilization than pyrimidines. Within the present model, the stabilizing contribution is predominantly enthalpic and is consistent with stronger terminal stacking accompanied by reduced conformational freedom. Because the analysis concerns local terminal opening rather than global duplex melting, the extracted thermodynamic quantities are interpreted as apparent parameters of the modeled closed/open equilibrium. Together, these results provide a molecularly resolved view of dangling-end stabilization in an AU-rich helix and support the idea that end effects should be treated explicitly and sequence specifically in RNA thermodynamic models.