Pan-Viral Conformational Landscapes of Frameshifting Elements Reveal Length-Dependent Plasticity and Antisense-Driven Structural Reprogramming

Programmed ribosomal frameshifting (PRF) is an essential strategy used by many RNA viruses to expand their coding capacity within compact genomes. This process is governed by frameshifting elements (FSEs), specialized RNA structures that regulate translation through dynamic secondary and tertiary conformations. While the structural adaptability of the SARS-CoV-2 FSE has been extensively characterized, the conformational landscapes of FSEs across other pathogenic viruses remain poorly understood. Here, we present a comparative structural analysis of FSEs from Japanese Encephalitis Virus (JEV), West Nile Virus (WNV), Hepatitis C Virus (HCV), and Human Immunodeficiency Virus (HIV) using integrative computational modeling and molecular simulations. Our analysis reveals previously uncharacterized, virus-specific conformational ensembles, alongside a conserved core architecture that exhibits pronounced length-dependent structural plasticity. Extension of flanking sequences induces substantial conformational rearrangements, highlighting the role of sequence context in shaping FSE topology and potentially modulating PRF efficiency. Importantly, we demonstrate that antisense oligonucleotide (ASO) binding can reprogram FSE architectures, disrupting native structural motifs and stabilizing alternative conformations with altered thermodynamic stability. Collectively, these findings establish viral FSEs as dynamic RNA ensembles governed by sequence context and external interactions, and position ASO-mediated structural perturbation as a promising strategy for modulating frameshifting and viral gene expression.