A Gold Nanoparticle–Based Approach for Screening Triplex DNA Binders*
Regulating gene expression by controlling nucleic acid transcription is a potential strategy for the treatment of genetic-based diseases. A promising approach involves the use of triplex-forming oligonucleotides. This chapter describes a colorimetric assay which can screen for potential triple helix specific DNA binders and simultaneously determine their relative binding affinities using DNA-functionalized gold nanoparticles. Gold nanoparticle probes are ideal for this purpose due to their intense optical properties, enhanced binding properties, and sharp melting transitions. The assay consists of two sets of gold nanoparticles (NPs), NP-1 and NP-2, and a free strand of DNA, DNA-3. The colorimetric assay allows dramatically improved discrimination between stabilizing and nonstabilizing triplex binders. The simplicity of this assay makes it more convenient than other methods, such as competitive dialysis, mass spectroscopy, electrophoresis, and UV-vis melting experiments.