Molecular understanding of Three-Way Junction Prohead RNA (3WJ-pRNA) stability

Abstract

Ribonucleic Acids (RNA) are one of the most pluri-potent chemical species. They play important roles of regulatory networks and catalyzing chemical reactions. With the advent of advanced molecular tools, RNA nanotechnology has gained attention. Its applications in biomedicine are noteworthy, offering fast, flexible and targeted drug delivery. They also have advantage of low immunogenicity compared to proteins. One promising RNA motif is the ϕ29 bacteriophage three-way junction motif from prohead RNA (3WJ pRNA). It is well-known for self-assembly and stability, making it suitable for biomedical applications. But little is understood about the specific mechanism responsible for its extraordinary thermodynamic stability. This study attempts to look into the dynamics of 3WJ-pRNA and its binding to fluorogenic ligands through molecular dynamics (MD) . Major factors affecting RNA stability are i) base pairing, ii) conformational entropy, iii) the effect of cations, and iv) hydration. Here, it was also observed that GFP-mimic fluorogen, HBC showing strong stacking interactions to the core of 3WJ RNA to form a stable complex. This can make way for experimental validation to use 3WJ pRNA to form RNA-fluorophore complexes, which have emerged as versatile tools for cellular imaging, surpassing traditional fluorescent proteins in brightness and application flexibility. Further study of 3WJ pRNA and its binding capabilities can pave way for the development of novel therapeutic, diagnostic, and imaging tools based on ribo nucleic acids .