Effects of flanking regions on HDV cotranscriptional folding kinetics

Hepatitis delta virus (HDV) ribozyme performs the self-cleavage activity through folding to a double pseudoknot structure. The folding of functional RNA structures is often coupled with the transcription process. In this work, we developed a new approach for predicting the cotranscriptional folding kinetics of RNA secondary structures with pseudoknots. We theoretically studied the cotranscriptional folding behavior of the 99-nucleotide (nt) HDV sequence, two upstream flanking sequences, and one downstream flanking sequence. During transcription, the 99-nt HDV can effectively avoid the trap intermediates and quickly fold to the cleavage-active state. It is different from its refolding kinetics, which folds into an intermediate trap state. For all the sequences, the ribozyme regions (from 1 to 73) all fold to the same structure during transcription. However, the existence of the 30-nt upstream flanking sequence can inhibit the ribozyme region folding into the active native state through forming an alternative helix Alt1 with the segments 70-90. The longer upstream flanking sequence of 54 nt itself forms a stable hairpin structure, which sequesters the formation of the Alt1 helix and leads to rapid formation of the cleavage-active structure. Although the 55-nt downstream flanking sequence could invade the already folded active structure during transcription by forming a more stable helix with the ribozyme region, the slow transition rate could keep the structure in the cleavage-active structure to perform the activity.