Bulky cations greatly increase the turnover of a native hammerhead ribozyme

Yamashita, Hirofumi; Tanabe, Kazuya; Sugimoto, Naoki

doi:10.1039/c9ra06797c

Cited by 2 publications

(2 citation statements)

References 46 publications

(47 reference statements)

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“…[18] We previously reported that TPeA and TBA ions can increase the turnover rate of the native ribozyme HH10 derived from an intronic ribozyme in the human genome. [19] However, the mechanism for regulating the turnover rate is not understood. Here, several types of watersoluble organic cations are evaluated with truncated and extended hammerhead ribozymes derived from Schistosoma mansoni, which exhibit different kinetic behaviors.…”

Section: Introductionmentioning

confidence: 99%

Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations

Yamashita

Sugimoto

2021

ChemBioChem

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Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.

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Section: Introductionmentioning

confidence: 99%

Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations

Yamashita

Sugimoto

2021

ChemBioChem

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“…At physiological pH level, the activity of HHRz depends on metal ions, especially Mg 2+ [23], which supports cleavage in vitro for a minimal, but sub-optimal, HHRz sequence at 10 mM [24]. Other ions can also activate the self-cleavage of HHRz [25]: cations like ammonium (NH 4 + ) can support the activity of HHRz [26] and large tetraalkylammonium ions significantly increase the rate of HHRz in addition to Mg 2+ [27]. The cleavage rate of HHRz was tested with transition metals and depending on the conditions and ribozymes tested, cleavage with Mn 2+ showed three times [28] and up to seventy-six times [29] better cleavage than Mg 2+ .…”

Section: Introductionmentioning

confidence: 99%

Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium

Naghdi

Boutet

Mucha

et al. 2020

ncRNA

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Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg2+ is one of the most abundant divalent cations in the cell and therefore plays a major role in cleavage activity for most hammerhead ribozymes. Besides Mg2+, cleavage can also occur in the presence of other cations such as Mn2+. The catalytic core of hammerhead ribozymes is highly conserved, which could contribute to a preference of hammerhead ribozymes toward certain cations. Here, we show a naturally occurring variation in the catalytic core of hammerhead ribozymes, A6C, that can favor one metallic ion, Mn2+, over several other cations.

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Bulky cations greatly increase the turnover of a native hammerhead ribozyme

Abstract: 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.

Cited by 2 publications

References 46 publications

Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations

Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations

Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium

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