For each sensor fabrication step, the samples were characterized by tapping mode AFM-IR. With this method, topographic and spectral information are obtained simultaneously, although in the following the topography is presented first (figure ). It is noted that granular features appeared in AFM topography at all sample conditions that are considered as substrate related features (figure S1, S2 a-c, and Supporting Discussion 1). Compared to the single crystalline Au(111) sc interface, Au(111) sc /C9t showed a slightly roughened surface after aptamer immobilization. The pure Au(111) sc interface shows atomically flat terraces that have a shallow root mean square (RMS) roughness value of 0.02 nm (figure a). In comparison, the RMS roughness in a selected region on Au(111) sc /C9t is increased, but still relatively low with a value of 0.11 nm (figure ). Line scans reveal typical height variations in the topography of Au(111) sc /C9t. While on the bare Au(111) sc substrate monoatomic steps of approx. 0.25 nm between terraces were found, Au(111) sc /C9t exhibits height variations up to 0.5 nm (figure ). The substrate employed here for the immobilization of C9t aptamer is atomically flat, hence the increase in roughness can be attributed to the formed DNA monolayer. The observed height differences on Au(111)/C9t are in the range expected for the diameter of an ss-DNA chain which is estimated to be between 0.5 nm to 0.7 nm. Spectroscopic ellipsometry was used to determine the thicknesses of the SAMs on Au(111).