A Proposed Mechanism of the Influence of Gold Nanoparticles on DNA Hybridization

Abstract

A combination of gold nanoparticles (AuNPs) and nucleic acids has been used in biosensing applications. However, there is a poor fundamental understanding of how gold nanoparticle surfaces influence the DNA hybridization process. Here, we measured the rate constants of the hybridization and dehybridization of DNA on gold nanoparticle surfaces to enable the determination of activation parameters using transition state theory. We show that the target bases need to be detached from the gold nanoparticle surfaces before zipping. This causes a shift of the rate-limiting step of hybridization to the mismatch-sensitive zipping step. Furthermore, our results propose that the binding of gold nanoparticles to the single-stranded DNA segments (commonly known as bubbles) in the duplex DNA stabilizes the bubbles and accelerates the dehybridization process. We employ the proposed mechanism of DNA hybridization/dehybridization to explain the ability of 5 nm diameter gold nanoparticles to help discriminate between single base-pair mismatched DNA molecules when performed in a NanoBioArray chip. The mechanistic insight into the DNA-gold nanoparticle hybridization/dehybridization process should lead to the development of new biosensors.

Selectivity enhancements in gel‐based DNA‐nanoparticle assays by membrane‐induced isotachophoresis: thermodynamics versus kinetics

“…In the case of an equilibrium assay, when dissociation constants are the determining factors, the PT and MM2a sequences are impossible to distinguish as shown by Table 2. The selectivity we report for our platform is superior to the values of two to six for previously reported assays which rely on probe-functionalized nanoparticles [28,29]. Importantly in our assay, we clearly demonstrate an improvement in selectivity beyond the equilibrium value.…”

“…Sedighi et al. measured ΔΔG ‡ d for their NanoBioArray chip which also uses DNA hybridization to DNA‐functionalized gold nanoparticles. They compared the dehybridization activation free energies for a perfectly matched target and one‐base mismatch with twenty‐base pairing sequences on 12 nm gold nanoparticles.…”

“…Therefore, unless the preexponential factors for the kinetic constants are very different for the two molecules, due perhaps to entropic effects introduced by the mismatches, the kinetically controlled selectivity is expected to be exponentially (geometrically) better than thermodynamic equilibrium selectivity for barrier differences much larger than RT. Sedighi et al [28] measured ⌬ ⌬ G ‡ d for their NanoBioArray chip which also uses DNA hybridization to DNA-functionalized gold nanoparticles. They compared the dehybridization activation free energies for a perfectly matched target and onebase mismatch with twenty-base pairing sequences on 12 nm gold nanoparticles.…”

“…Other types of biosensors attempting to address these issues have seen limited progress. Sedighi et al used targets conjugated to Au nanoparticles to achieve selectivity values of three to six for one-base mismatches [28] while Cao et al reported selectivity values of two to three for an assay based on molecular beacons and silver nanoclusters [29]. However, while these articles report selectivity values, they failed to report what extent their technique, if at all, improved over the free solution thermodynamic limit of selectivity [29][30][31][32][33][34][35].…”

Advances in the Experimental and Theoretical Understandings of Antibiotic Conjugated Gold Nanoparticles for Antibacterial Applications

“…The reason behind their colors is the coherent oscillations of conduction electrons upon irradiation with light of appropriate wavelength, also known as localized surface plasmon resonance (SPR) . The SPR can be adjusted by the change in the size, shape, and composition of AuNPs . AuNPs show strong absorption and elastic scattering of visible and near‐infrared light upon excitation of their SPR which is the basis of many biological sensing and imaging applications .…”