Junction Topological Constraints in Hairpin Ribozyme Folding

Abstract

The hairpin ribozyme is an RNA enzyme found in plant viruses that catalyzes cleavage and ligation reactions in RNA replication. The active site is formed when two loop domains located on separate helical arms are in contact. We conduct coarse-grained molecular dynamics simulations of the hairpin ribozyme using the TOPRNA model. By modifying the topology of the junction between the two active arms we determine how topology, junction stress, and conformational entropy bias folding propensity. Modifications include using 2- through 5-way junctions, adding a small loop region at the junction, un-pairing one base pair at one or both arms, and shortening or lengthening one of the arms (changing the phase of helix-helix alignment). The TOPRNA model is ideal for answering these topological questions and, using only three beads per residue, it is efficient for throughput. This work is done in collaboration with the Walter group at the University of Michigan, who are conducting single molecule experiments on these hairpin ribozyme constructs, using FRET microscopy to determine their folding propensities. These measurements combined with our simulation data will allow us to isolate the contribution of topology in hairpin ribozyme folding.