title: 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.
authors: Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada.
authors: Abootaleb
authors: A
authors: Sedighi
authors: Paul C H
authors: PC
authors: Li
authors: Idah C
authors: IC
authors: Pekcevik
authors: Byron D
authors: BD
authors: Gates
mesh_terms: D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D019277:Entropy; D006046:Gold / Q000737:chemistry* / Q000494:pharmacology*; D007700:Kinetics; D053768:Metal Nanoparticles; D009693:Nucleic Acid Hybridization / Q000187:drug effects; D015345:Oligonucleotide Probes / Q000737:chemistry; D010316:Particle Size; D020349:Surface Plasmon Resonance
chemical_list: D004277:DNA, Single-Stranded; D015345:Oligonucleotide Probes; D006046:Gold; D004247:DNA