A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer: An ATPase-Mimicking Nucleoapzyme

Yonatan Biniuri, Zohar Shpilt, Bauke Albada, Margarita Vázquez-González, Mariusz Wolff, Carina Hazan, Eyal Golub, Dimitri Gelman, Itamar Willner*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)


Catalytic nucleic acids consisting of a bis-Zn2+-pyridyl-salen-type ([di-ZnII 3,5 bis(pyridinylimino) benzoic acid]) complex conjugated to the ATP aptamer act as ATPase-mimicking catalysts (nucleoapzymes). Direct linking of the Zn2+ complex to the 3′- or 5′-end of the aptamer (nucleoapzymes I and II) or its conjugation to the 3′- or 5′-end of the aptamer through bis-thymidine spacers (nucleoapzymes III and IV) provided a set of nucleoapzymes exhibiting variable catalytic activities. Whereas the separated bis-Zn2+-pyridyl-salen-type catalyst and the ATP aptamer do not show any noticeable catalytic activity, the 3′-catalyst-modified nucleoapzyme (nucleoapzyme IV) and, specifically, the nucleoapzyme consisting of the catalyst linked to the 3′-position through the spacer (nucleoapzyme III) reveal enhanced catalytic features in relation to the analogous nucleoapzyme substituted at the 5′-position (kcat=4.37 and 6.88 min−1, respectively). Evaluation of the binding properties of ATP to the different nucleoapzyme and complementary molecular dynamics simulations suggest that the distance separating the active site from the substrate linked to the aptamer binding site controls the catalytic activities of the different nucleoapzymes.

Original languageEnglish
Pages (from-to)53-58
Issue number1-2
Early online date25 Mar 2019
Publication statusPublished - 15 Jan 2020


  • catalytic DNA
  • DNAzymes
  • microscale thermophoresis
  • molecular dynamics
  • nucleic acids

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