Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SDR. The kinetics of the blocker enzymatic degradation thus controls the time at which the SDR starts. By varying the concentration of the blocker strand and the concentration of the enzyme, we show that we can finely tune and modulate the delayed onset of SDR. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed SDRs using RNase H and two DNA repair enzymes (formamidopyrimidine DNA glycosylase and uracil-DNA glycosylase) and corresponding blockers. The achieved temporal delay can be programed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show three possible applications of the delayed SDRs to temporally control the ligand release from a DNA nanodevice, the inhibition of a target protein by a DNA aptamer, and the output signal generated by a DNA logic circuit.

Bucci, J., Irmisch, P., Del Grosso, E., Seidel, R., Ricci, F. (2022). Orthogonal enzyme-driven timers for DNA strand displacement reactions. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 144(43), 19791-19798 [10.1021/jacs.2c06599].

Orthogonal enzyme-driven timers for DNA strand displacement reactions

Del Grosso, Erica;Ricci, Francesco
2022-11-02

Abstract

Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SDR. The kinetics of the blocker enzymatic degradation thus controls the time at which the SDR starts. By varying the concentration of the blocker strand and the concentration of the enzyme, we show that we can finely tune and modulate the delayed onset of SDR. Additionally, we show that the strategy is versatile and can be orthogonally controlled by different enzymes each specifically targeting a different blocker strand. We designed and established three different delayed SDRs using RNase H and two DNA repair enzymes (formamidopyrimidine DNA glycosylase and uracil-DNA glycosylase) and corresponding blockers. The achieved temporal delay can be programed with high flexibility without undesired leak and can be conveniently predicted using kinetic modeling. Finally, we show three possible applications of the delayed SDRs to temporally control the ligand release from a DNA nanodevice, the inhibition of a target protein by a DNA aptamer, and the output signal generated by a DNA logic circuit.
2-nov-2022
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore CHIM/01 - CHIMICA ANALITICA
English
Bucci, J., Irmisch, P., Del Grosso, E., Seidel, R., Ricci, F. (2022). Orthogonal enzyme-driven timers for DNA strand displacement reactions. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 144(43), 19791-19798 [10.1021/jacs.2c06599].
Bucci, J; Irmisch, P; Del Grosso, E; Seidel, R; Ricci, F
Articolo su rivista
File in questo prodotto:
File Dimensione Formato  
Orthogonal Enzyme-Driven Timers for DNA Strand Displacement.pdf

accesso aperto

Tipologia: Versione Editoriale (PDF)
Licenza: Creative commons
Dimensione 3.1 MB
Formato Adobe PDF
3.1 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/313700
Citazioni
  • ???jsp.display-item.citation.pmc??? 0
  • Scopus 22
  • ???jsp.display-item.citation.isi??? 21
social impact