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Re-engineering 10–23 core DNA- and MNAzymes for applications at standard room temperature

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Abstract

DNA- and MNAzymes are nucleic acid-based enzymes (NAzymes), which infiltrated the otherwise protein-rich field of enzymology three decades ago. The 10–23 core NAzymes are one of the most widely used and well-characterized NAzymes, but often require elevated working temperatures or additional complex modifications for implementation at standard room temperatures. Here, we present a generally applicable method, based on thermodynamic principles governing hybridization, to re-engineer the existing 10–23 core NAzymes for use at 23 °C. To establish this, we first assessed the activity of conventional NAzymes in the presence of cleavable and non-cleavable substrate at 23 °C as well as over a temperature gradient. These tests pointed towards a non-catalytic mechanism of signal generation at 23 °C, suggesting that conventional NAzymes are not suited for use at this temperature. Following this, several novel NAzyme-substrate complexes were re-engineered from the conventional ones and screened for their performance at 23 °C. The complex with substrate and substrate-binding arms of the NAzymes shortened by four nucleotides on each terminus demonstrated efficient catalytic activity at 23 °C. This has been further validated over a dilution of enzymes or enzyme components, revealing their superior performance at 23 °C compared to the conventional 10–23 core NAzymes at their standard operating temperature of 55 °C. Finally, the proposed approach was applied to successfully re-engineer three other new MNAzymes for activity at 23 °C. As such, these re-engineered NAzymes present a remarkable addition to the field by further widening the diverse repertoire of NAzyme applications.

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Funding

This work has received funding from Research Foundation−Flanders (FWO SB/1S30116N, FWO G086114, FWO G084818N) and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 675412 (H2020-MSCA-ITN-ND4ID).

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  1. Karen Ven and Saba Safdar contributed equally to this work.

Authors and Affiliations

  1. Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem De Croylaan 42, 3001, Leuven, Belgium

    Karen Ven, Saba Safdar, Annelies Dillen, Jeroen Lammertyn & Dragana Spasic

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  1. Karen Ven
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Correspondence to Jeroen Lammertyn.

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Ven, K., Safdar, S., Dillen, A. et al. Re-engineering 10–23 core DNA- and MNAzymes for applications at standard room temperature. Anal Bioanal Chem 411, 205–215 (2019). https://doi.org/10.1007/s00216-018-1429-4

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