Sensing of Transcription Factor through Controlled-Assembly of Metal Nanoparticles Modified with Segmented DNA Elements

Abstract

We have developed a unique metal nanoparticle (mNPs)-based assay to detect sequence-specific interactions between transcription factor and its corresponding DNA-binding elements. This assay exploits the interparticle-distance dependent optical properties of noble mNPs as sensing element and utilizes specific protein-DNA interactions to control the dispersion status of the mNPs. The assay involves two sets of double-stranded (ds)DNA modified-mNPs, each carrying a half site segment of a functional DNA sequence for the protein of interest. Each of these half sites is designed to contain a short complementary sticky end that introduces base-pairing forces to facilitate particle aggregation and to form a transient full dsDNA sequence. The detection of specific protein-DNA binding is founded on the premise that the mixture of these two sets of dsDNA-mNPs experiences a remarkable particle aggregation under certain salt conditions; whereas the aggregation can be retarded in the presence of a specific protein that binds and stabilizes the transient full dsDNA structure and therefore introduces steric protection forces between particles. We have demonstrated the concept using estrogen receptor α and its response elements, with gold and silver NPs as the sensing platform. UV-vis spectroscopy, transmission electron spectroscopy, and dynamic light scattering measurements were conducted to provide full characterization of the particle aggregation/dispersion mechanism. Differing from most of the mNP-based colorimetric sensors that are designed based on the analyte-induced aggregation mechanism, current protein binding-stabilization sensing strategy reduces the false signals caused by unrelated particle destabilizing effects. It is expected that this assay principle can be directed toward other transcription factors by simply changing the recognition sequence to form different segmented dsDNA-mNP constructs.