Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics

Enhanced hammerhead ribozyme turnover rates: Reevaluating therapeutic space for small catalytic RNAs

We discovered enhanced hammerhead ribozyme (EhhRz) kinetic performance during therapeutic optimization of a lead agent against the human rhodopsin mRNA target. Turnover activity in trans was greater than 300 nMmin-1 under 10-fold substrate excess and physiological Mg2+ (1 mM). We validated a moderate-throughput fluorescence quantitative hhRz kinetic assay, which is linear with substrate and product moles. The EhhRz targets a CUC↓ cleavage site in a substrate with no predicted secondary/tertiary structure and demonstrates classical Michaelis-Menten turnover behavior with efficiency (V max/K m ) up to 3.2 × 106 min-1M-1. EhhRzs show cooperative Mg2+ titration (K Mg1/2  = 0.7 ± 0.02 mM; Hill = 1.7 ± 0.1). Structure-function assays showed that the upstream EhhRz antisense flank (substrate bound) interacts with stem-loop II. Tetraloop sequence variation reveals a marked effect on turnover rate. Downstream substrate U7 is not essential for enhanced activity. Single-turnover reaction rates show substantial improvements in hhRz rates at physiological Mg2+. Embedded within a target-reporter fusion mRNA, EhhRzs cleave regional target elements under intracellular conditions promoting strong knockdown at target mRNA and protein levels. EhhRzs have potential as druggable nucleic acid therapeutics against arbitrary targets, or in the design of improved aptazymes.

A Dual-Functioning 5'-PPP-NS1shRNA that Activates a RIG-I Antiviral Pathway and Suppresses Influenza NS1

Retinoic acid-inducible gene-I (RIG-I) is a cytosolic pathogen sensor that is crucial against a number of viral infections. Many viruses have evolved to inhibit pathogen sensors to suppress host innate immune responses. In the case of influenza, nonstructural protein 1 (NS1) suppresses RIG-I function, leading to viral replication, morbidity, and mortality. We show that silencing NS1 with in-vitro-transcribed 5'-triphosphate containing NS1 short hairpin RNA (shRNA) (5'-PPP-NS1shRNA), designed using the conserved region of a number of influenza viruses, not only prevented NS1 expression but also induced RIG-I activation and type I interferon (IFN) expression, resulting in an antiviral state leading to inhibition of influenza virus replication in vitro. In addition, administration of 5'-PPP-NS1shRNA in prophylactic and therapeutic settings resulted in significant inhibition of viral replication following viral challenge in vivo in mice with corresponding increases of RIG-I, IFN-β, and IFN-λ, as well as a decrease in NS1 expression.