Developing Three-Dimensional Models of Putative-Folding Intermediates of the HDV Ribozyme

Abstract

Both the role and the interacting partners of an RNA molecule can change depending on its tertiary structure. Consequently, it is important to be able to accurately predict the complete folding pathway of an RNA molecule. The hepatitis delta virus (HDV) ribozyme is a small catalytic RNA with the greatest number of folding intermediates making it the model of choice with which to address this problem. The tertiary structures of the known putative intermediates along the folding pathway of the HDV ribozyme were predicted using the Macromolecular Conformations Symbolic programming (MC-Sym) software. The structures obtained by this method received physical support from Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE). The analysis of these structures elucidated several features of the HDV ribozyme. In addition, this report represents an application for MC-Sym that permits progression one step further toward the computer prediction of an RNA molecule-folding pathway.

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

“…Most notably, it is now becoming apparent that secondary structure encoded topological constraints play a prominent role specifying the geometric positioning of groups involved in key tertiary contacts. For example, simulations by Reymond et al [21] show that constraining the HCV ribozyme to its secondary structure results in a global fold that places distant loops, which participate in a tertiary pseudoknot motif, in close proximity to one another. This suggests that the topology of the RNA secondary structure is optimized to stabilize specific tertiary interactions.…”

“…Another particularly interesting application of topological constraints, which involves the use of secondary and tertiary structure constraints to produce 3D RNA structures was demonstrated by the Perreault group [21] and the Herschlag group [31••]. Using prior experimental data on the tertiary contacts present in different intermediates along the folding pathway of the HDV ribozyme Reymond et al were able to use the MC-Sym software to make predictions about the 3D conformation of these intermediates and infer the 3D structural changes that occur during folding.…”

Selection of the Most Potent Specific On/Off Adaptor-Hepatitis Delta Virus Ribozymes for Use in Gene Targeting

“…2). Initially, during the folding pathway of the HDV ribozyme, the stem-loop III is located outside the catalytic core (Reymond et al, 2010), and, therefore, was shown to be relatively available for interaction with an oligonucleotide (Ananvoranich and Perreault, 2000). This is in agreement with the observation that the inactive structure of an allosteric HDV ribozyme was caused by the presence of a sequence located at the top of the stem II that interacts with the stem-loop III region (Beaudoin and Perreault, 2008).…”

“…Conversely, when the biosensor sequence was complementary to junction IV/II, the other mainly single-stranded region of the catalytic core, the cleavage activity was not impaired. The biosensor and the junction IV/II are most likely located in opposite orientations, at least according to the tridimensional structure of the HDV ribozyme (Reymond et al, 2010). The second situation investigated that can result in the production of an inactive ribozyme was the extension of the blocker stem.…”

Determining RNA three-dimensional structures using low-resolution data

“…the stable nucleotides are considered involved in stacked Watson-Crick base pairs. For instance, using SHAPE data the Miller group has modelled the cap-binding translation initiation factor eIF4E bound to a pseudo-knotted element [20], and the Perreault’s group modelled putative folding intermediates of the HDV ribozyme [21]. However, it is not clear how SHAPE data can be interpreted and used in the context of 3-D structure.…”