Optimizing the Toehold-Mediated Strand Displacement Reaction on the Nanoparticle Surface by Altering the Surface DNA Density for the Design of a microRNA NanoOptical Sensor

Abstract

We present a method for modulating the kinetics and thermodynamic properties of aggregation and disassembly processes of DNA-functionalized nanoparticles. Specifically, we examine factors influencing the toehold strand-displacement reaction on nanoparticle surfaces. Gold nanoparticles were functionalized with oligonucleotide sequences with varying surface density by incorporating diluent DNA strands. The hybridization of DNA yields aggregates which then disassemble via a strand-displacement reaction by the target sequence. Localized surface plasmon resonance of gold nanoparticles and fluorescently tagged DNA strands were employed to gain an understanding of the aggregation and disassembly steps. The surface density of DNA impacts the aggregation kinetics, the melting temperature and the target-induced disassembly of these nanoaggregates. It does so by modulating the cooperativity and attinebility of the oligonucleotides, the electrostatic repulsion between the nanoparticles and the accessibility of the linkers to the target nucleic acid. A dramatic decrease in the initiation time and increase in the rate of disassembly are achieved by optimizing the surface density. Our work provides insight into the strand-displacement reaction on nanoparticle surfaces that underpins various sensing and DNA-driven nanomachine applications. This fundamental understanding allowed the design of a label-free, low cost and miniaturized biosensing platform based on the disassembly of core-satellite nanoassemblies. We successfully manipulate the system for the rapid and selective detection of a nucleic acid biomarker microRNA-210, enabling diverse biological applicability