Conformational Transition of Viral Nucleic Acids in a Capsid-Like Confined Environment

Nucleic acid molecules within viral genomes can fold into noncanonical structures, such as G-quadruplexes (G4s), which play crucial roles in regulating viral gene expression. These genomes are confined within capsid environments that vary in dimensions and ionic compositions. Structural transitions in RNA or DNA within these confined environments are essential for modulating viral biological functions; however, these transitions remain poorly understood. In this study, we demonstrated that an RNA sequence derived from the human immunodeficiency virus (HIV-1) genome adopts a dynamic equilibrium between G4 and hairpin (Hp) structures modulated by ionic conditions. The equilibrium shifts toward the G4 conformation in the presence of potassium (K⁺) and magnesium (Mg²⁺) ions. Using reverse micelles (RMs) as mimetics of the intracapsid environment, we showed that the size of the RM water pool influences significantly this equilibrium: smaller water pools favor G4 formation, whereas larger pools prefer the Hp structure owing to variations in the dielectric constant. Notably, the addition of Mg²⁺ ions alters the size-dependent effects of RMs by stabilizing the G4 structure. These findings highlight the critical roles of environmental confinement and ionic conditions in regulating viral RNA structural dynamics, offering new insights into RNA-based regulatory mechanisms and their impact on viral gene expression.