Spectroscopic Ellipsometry Investigation of a Sensing Functional Interface: DNA SAMs Hybridization

Abstract

Here, a comprehensive study of a label-free detection platform for the recognition of oligonucleotide sequences based on hybridization of thiol-tethered DNA strands self-assembled on flat gold films is presented. The study exploits in-buffer spectroscopic ellipsometry (SE) measurements, a noninvasive method sensitive to monolayer films, supported by surface mass density change measurements (Quartz Crystal Microbalance with Dissipation, QCM-D) obtained under comparable experimental conditions. SE and QCM-D allow monitoring deposition of molecular precursors and DNA chain hybridization. Combining SE measurements with QCM-D data paves the way for quantification of the assay through the possible calibration of SE data. Optical measurements also demonstrate the selectivity and recovery properties of the sensing platform. Broadband SE measurements are interpreted by means of an effective optical model. The model, complemented by information on film thickness (scanning probe nanolithography), and surface composition (monochromatic X-ray Photoemission Spectroscopy, XPS), enables a clear spectral identification of UV DNA resonances and the formation of the thiolate interface with gold. Spectroscopic validation of the hybridization is complemented by employing labeled target strands. The influence of hybridization on UV resonances and optical thickness of the DNA film is discussed in the light of hypochromism, through comparison with QCM-D data.