The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study

Mechanical unfolding studies on Ribonucleic Acid (RNA) structures are a subject of tremendous interest as they shed light on the principles of higher order assembly of these structures. Pseudoknotting is one of the most elementary ways in which this higher order assembly is achieved as discrete secondary structural units in RNA are brought in close proximity to form a tertiary structure. Using steered molecular dynamics (SMD) simulations, we have studied the unfolding of five RNA pseudoknot structures that differ from each other either by base substitutions in helices or loops. Our SMD simulations reveal the manner in which a biologically functional RNA pseudoknot unfolds and the effect of changes in the primary structure on this unfolding pathway, providing necessary insights into the driving forces behind the functioning of these structures. We observed that an A → C mutation in the loop sequence makes the pseudoknot far more resistant against force induced disruption relative to its wild type structure. In contrast to this, a base-pair substitution GC → AU near the pseudoknot junction region renders it more vulnerable to this disruption. The quantitative estimation of differences in the unfolding paths was carried out using force extension curves, potential of mean force profiles, and the opening of different Watson-Crick and non-Watson-Crick interactions. The results provide a quantified view in which the unfolding paths of the small RNA structures can be used for investigating the programmability of RNA chains for designing RNA switches and aptamers as their biological folding and unfolding could be assessed and manipulated.