Probing the Secondary Structure of the Monomeric Conformation in the HIV-1 5`-Leader RNA by NMR Spectroscopy

Human Immunodeficiency Virus (HIV), the AIDS pathogen, proliferates within infected human helper T cells, compromising an otherwise healthy and responsive immune system. Viral replication is mediated by the 5`Leader (5`L) element in viral genomic RNA. This 5`-L RNA exists in an equilibrium of two structural conformers – monomer and dimer, by which it directs and mediates viral assembly and replication. Here, we demonstrate an approach to probe for and characterize secondary structure in the 5`-L monomeric conformer by high-field nuclear magnetic resonance (NMR) spectroscopy, a technique used for high-resolution biomolecular structural studies. Signal assignment and validation of characteristic peaks in NMR experiments designed to explore the through-space interactions of base-paired residues provide evidence to support the formation of distinct secondary structures in our proposed model. Our study of the HIV-1 5`-L monomeric conformer structure and the processes that this highly conserved RNA sequence mediates in retroviral replication not only provide further insight into our current understanding of the functional and dynamic nature of three-dimensional RNA structure, but also highlight potential therapeutic value in the monomer as a drug target in clinical medicine.