Inhibition by polyamines of the hammerhead ribozyme from a Chrysanthemum chlorotic mottle viroid

Bulky cations greatly increase the turnover of a native hammerhead ribozyme

Methods to facilitate the catalytic turnover of ribozymes are required for advancing oligonucleotide-based technologies. This study examined tetraalkylammonium ions for their ability to increase the efficiency of catalytic turnover of a native hammerhead ribozyme. Kinetic analysis showed that large tetraalkylammonium ions significantly increased the turnover rate of the ribozyme and was much more effective than poly(ethylene glycol) (PEG) and urea. The magnitude of the rate increase depended on the concentrations of Mg²⁺ and tetrapentylammonium ions, and the rate was enhanced by more than 180-fold at the optimal concentrations of these salts. The results provide physical insights into interactions of ribozymes with large cationic molecules through electrostatic forces and steric hindrance.

Large tetraalkylammonium ions increase the turnover rate of the ribozyme derived from an intronic ribozyme in the human genome. The rate can be enhanced by more than a hundred-fold at the optimal concentrations of Mg²⁺ and TPeA ions.

Endogenous polyamine function--the RNA perspective

Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg²⁺) confirming their roles as independent molecular entities which help drive RNA-mediated processes.