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

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

Tunable Loading of Single-Stranded DNA on Gold Nanorods through the Displacement of Polyvinylpyrrolidone

A quantitative and tunable loading of single-stranded (ss-DNA) molecules onto gold nanorods was achieved through a new method of surfactant exchange. This new method involves the exchange of cetyltrimethyl­ammonium bromide surfactants for an intermediate stabilizing layer of polyvinyl­pyrrolidone and sodium dodecylsulfate. The intermediate layer of surfactants on the anisotropic gold particles was easily displaced by thiolated ss-DNA, forming a tunable density of single-stranded DNA molecules on the surfaces of the gold nanorods. The success of this ligand exchange process was monitored in part through the combination of extinction, X-ray photoelectron, and infrared absorption spectroscopies. The number of ss-DNA molecules per nanorod for nanorods with a high density of ss-DNA molecules was quantified through a combination of fluorescence measurements and elemental analysis, and the functionality of the nanorods capped with dense monolayers of DNA was assessed using a hybridization assay. Core–satellite assemblies were successfully prepared from spherical particles containing a probe DNA molecule and a nanorod core capped with complementary ss-DNA molecules. The methods demonstrated herein for quantitatively fine tuning and maximizing, or otherwise optimizing, the loading of ss-DNA in monolayers on gold nanorods could be a useful methodology for decorating gold nanoparticles with multiple types of biofunctional molecules