Department of Chemistry, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada.
ACS Nano. 2014 Jul 22;8(7):6765-77. doi: 10.1021/nn500790m. Epub 2014 Jul 1.
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.
金纳米粒子（AuNPs）和核酸的组合已被用于生物传感应用。然而，对于金纳米粒子表面如何影响 DNA 杂交过程，我们的基本理解还很欠缺。在这里，我们测量了 DNA 在金纳米粒子表面上的杂交和解杂交的速率常数，以便使用过渡态理论来确定活化参数。我们表明，在套叠之前，靶碱基需要从金纳米粒子表面脱离。这导致杂交的限速步骤向错配敏感的套叠步骤转移。此外，我们的结果表明，金纳米粒子与双链 DNA 中的单链 DNA 片段（通常称为泡）的结合稳定了泡并加速了去杂交过程。我们利用所提出的 DNA 杂交/解杂交机制来解释在 NanoBioArray 芯片中，5nm 直径的金纳米粒子在帮助区分单碱基对错配 DNA 分子方面的能力。对 DNA-金纳米粒子杂交/解杂交过程的机理理解应导致新型生物传感器的发展。
