Nanomaterial-Based Fluorescent DNA Analysis: A Comparative Study of the Quenching Effects of Graphene Oxide, Carbon Nanotubes, and Gold Nanoparticles

A variety of nanomaterials have shown extraordinarily high quenching ability toward a broad range of fluorophores. Recently, there has been intense interest in developing new tools for fluorescent DNA analysis in solution or inside the cell based on this property, and by exploiting interactions between these nanoscale superquenchers and DNA molecules in the single-stranded (ss-) or double-stranded (ds-) forms. Here, a comparative study on the nanoqueching effects is performed by using a series of nanomaterials with different dimensions, i.e., gold nanoparticles (AuNPs, 0D), carbon nanotubes (CNTs, 1D), and graphene oxide (GO, 2D). The quenching efficiency, kinetics, differentiation ability, and influencing factors such as concentration and ionic strength are studied. Interestingly, GO exhibits superior quenching abilities to the other two materials in both the quenching efficiency and kinetics. As a result, a GO-based fluorescent sensor, designed in a simple mix-and-detect format, can detect concentrations of DNA as low as 0.2 nM, which is better than either CNTs or AuNPs by an order of magnitude. This sensor can also differentiate single-base mismatches much better than either CNTs- or AuNPs- based sensors. This study paves the way to better choice of nanomaterials for bioanalysis and elaborate design of biosensors for both in vitro diagnosis and in vivo bioimaging.