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

1 Citation (Scopus)

Abstract

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)1-7
JournalChemBioChem
DOIs
Publication statusE-pub ahead of print - 25 Mar 2019

Fingerprint

Adenosine Triphosphatases
Adenosine Triphosphate
Catalyst activity
Catalysts
Benzoic Acid
Molecular Dynamics Simulation
Thymidine
Nucleic Acids
Catalytic Domain
Binding Sites
Molecular dynamics
disalicylaldehyde ethylenediamine
Computer simulation
Substrates

Keywords

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

Cite this

Biniuri, Yonatan ; Shpilt, Zohar ; Albada, Bauke ; Vázquez-González, Margarita ; Wolff, Mariusz ; Hazan, Carina ; Golub, Eyal ; Gelman, Dimitri ; Willner, Itamar. / A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer : An ATPase-Mimicking Nucleoapzyme. In: ChemBioChem. 2019 ; pp. 1-7.
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abstract = "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.",
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author = "Yonatan Biniuri and Zohar Shpilt and Bauke Albada and Margarita V{\'a}zquez-Gonz{\'a}lez and Mariusz Wolff and Carina Hazan and Eyal Golub and Dimitri Gelman and Itamar Willner",
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Biniuri, Y, Shpilt, Z, Albada, B, Vázquez-González, M, Wolff, M, Hazan, C, Golub, E, Gelman, D & Willner, I 2019, 'A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer: An ATPase-Mimicking Nucleoapzyme', ChemBioChem, pp. 1-7. https://doi.org/10.1002/cbic.201900182

A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer : An ATPase-Mimicking Nucleoapzyme. / Biniuri, Yonatan; Shpilt, Zohar; Albada, Bauke; Vázquez-González, Margarita; Wolff, Mariusz; Hazan, Carina; Golub, Eyal; Gelman, Dimitri; Willner, Itamar.

In: ChemBioChem, 25.03.2019, p. 1-7.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - A Bis-Zn2+-Pyridyl-Salen-Type Complex Conjugated to the ATP Aptamer

T2 - An ATPase-Mimicking Nucleoapzyme

AU - Biniuri, Yonatan

AU - Shpilt, Zohar

AU - Albada, Bauke

AU - Vázquez-González, Margarita

AU - Wolff, Mariusz

AU - Hazan, Carina

AU - Golub, Eyal

AU - Gelman, Dimitri

AU - Willner, Itamar

PY - 2019/3/25

Y1 - 2019/3/25

N2 - 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.

AB - 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.

KW - catalytic DNA

KW - DNAzymes

KW - microscale thermophoresis

KW - molecular dynamics

KW - nucleic acids

U2 - 10.1002/cbic.201900182

DO - 10.1002/cbic.201900182

M3 - Article

SP - 1

EP - 7

JO - ChemBioChem

JF - ChemBioChem

SN - 1439-4227

ER -