What Controls the “Off/On Switch” in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles?

Abstract

In DNA dynamic nanotechnology, toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements displacing action is conjugated on gold nanoparticle. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, abrupt jump in behavior of an "off/on" switch, in reaction rate when invading toehold was prolonged to eight bases from seven bases. These phenomena are attributed to the effect of steric hinderance arising from high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.2

Investigating the dynamics of surface-immobilized DNA nanomachines

“…Despite these findings and the interest in surface-phase dynamic DNA machines, the effects of surface-immobilization on the kinetics of dynamic DNA processes such as strand displacement have not yet been fully investigated 37 38 39 . To address this, we undertook a detailed study of the mechanism and kinetics of strand displacement on-surface using quartz crystal microbalance with dissipation monitoring (QCM-D) 40 , a technique which involves the use of acoustic waves to probe surface-immobilized molecules, providing real-time information on their mass and conformation.…”

An Efficient Particle‐Based DNA Circuit System: Catalytic Disassembly of DNA/PEG‐Modified Gold Nanoparticle–Magnetic Bead Composites for Colorimetric Detection of miRNA

“…The extremely long waiting time is certain that DNA‐GNP‐based DNA circuit systems are slower than conventional DNA circuits that employ free DNA in solution. Indeed, the toehold‐mediated DNA displacement reactions at nanointerface of DNA‐GNPs differ greatly from that in solution phase . In particular, the toehold‐mediated DNA displacement reaction between DNA‐GNPs is quite slow, owing to steric hindrance and electrostatic repulsion between DNA‐GNPs.…”

“…Indeed, the toehold-mediated DNA displacement reactions at nanointerface of DNA-GNPs differ greatly from that in solution phase. [ 7 ] In particular, the toehold-mediated DNA displacement reaction between DNA-GNPs is quite slow, owing to steric hindrance and electrostatic repulsion between DNA-GNPs. In addition, the assembly of DNA-GNP has been reported to be an small 2016, 12, No.…”

Assembling Nanoparticle Clusters by Kinetic Control Using Weakly Interacting DNA

“…Manipulations to interparticle energies, achieved through changes in the DNA sequence and length, can set the scale of adhesion between the NPs and control both the hybridization kinetics and subsequent stability of the NP clusters. [37][38][39][40] Previous reports have shown that purification of discrete gold NP (AuNP)…”