Purchase this article with an account.
Jack M Sullivan, Mohammed Zuber, Tiffany A Kolniak, Dian Yu; Structure Activity Relationships for a Lead Hammerhead Ribozyme Therapeutic. Invest. Ophthalmol. Vis. Sci. 2014;55(13):3327.
Download citation file:
© ARVO (1962-2015); The Authors (2016-present)
Achievement of a potent catalytically active hammerhead ribozyme (hhRz) within human cells remains a challenge for gene-based therapeutics. We investigated structure-activity relationships of a proven successful hhRz (725 GUC↓) against human rod opsin mRNA (hRHO) in supportive RNA scaffolds. This hhRz is a candidate therapeutic for known RHO mutations causing autosomal dominant retinitis pigmentosa.
The 725 hhRz is embedded either in an engineered central domain between ultra-stable apical and basal stems of human adenoviral VAI scaffold RNA, or in the tRNA anticodon-like loop of a smaller and less stable chicken VAI scaffold. cDNAs for hhRzs or target hRHO fragment RNA (510 nt) were ligated in plasmids 3’ of T7 promoters. hRHO fragment RNA harbors an asymmetric 725 GUC↓ hhRz cleavage site. HhRz stem II stabilization elements or upstream tertiary accessory elements (TAE) were added to the basic structure. Controls are catalytic core hhRz mutations and scaffold only RNAs (no hhRz). In vitro hhRz cleavage reactions used T7 RNA polymerase for co-transcription of both hhRz and hRHO RNAs with analysis by PAGE. Computational folding of hhRz RNAs used MFold or RNAStructure (2D level) or RNA Composer (3D level).
Within the human VAI scaffold, 725 hhRz without an upstream TAE cleaved hRHO mRNA effectively, at the expected site, but not to completion. HhRz core mutation obviated cleavage, demonstrating hhRz mediated catalysis, and no cleavage occurred with scaffold alone. With 6-8% (w/v) PEG 8000 added to simulate cellular molecular crowding, the hhRz (4 bp stem II) in the human VAI scaffold cleaved more extensively. To stabilize hhRz folding we extended native stem II (4 bp) using two forms of stem II [8 bp (2.3 kCal/mol stabilized); 13 bp (8.2 kCal/mol stabilized)] from naturally occurring Chrysanthemum chlorotic mottle viroid hhRz, but in absence of its native TAE. hRHO cleavage was absent in both cases. HhRz in the small chicken VAI RNA cleaved hRHO minimally but an upstream TAE promoted substantial yet incomplete cleavage.
RNA scaffold structure and stability impact embedded hhRz function, an upstream TAE can enhance activity, and simple stabilization of Stem II can block activity. Close proximity to target and high hhRz concentrations are critical for 2nd order reaction mechanism in trans. These SAR findings establish direction to improve activity of candidate hhRz therapeutics.
This PDF is available to Subscribers Only