Material-Selective Deposition of Reactive Group-Functionalized Poly‑l‑lysine for DNA Sensing at Optical Waveguides

Precise localization of biomarkers within the sensing area of biosensors is crucial for enhancing performance and minimizing analyte loss to nonsensing regions. Commercial material-selective coatings enable site-specific biofunctionalization but are typically constrained by limited reactive chemistries, reducing their versatility and controllability. We present a selective coating strategy based on a poly-l-lysine (PLL) scaffold that retains the material-selective properties of a commercial carboxylic acid (COOH)-based coating for a Si₃N₄ waveguide with a poly-(ethylene glycol) (PEG)-covered SiO₂ surrounding while enabling modular surface functionalization. The PLL scaffold was functionalized with controlled grafting densities of oligo-(ethylene glycol) (OEG) and cycloalkynes, facilitating the immobilization of azide-labeled DNA probes (pDNA) and enabling quantification of their hybridization. Using the hybridization of a dye-functionalized target DNA, we showed the selective deposition of the PLL onto the COOH-covered sensing areas. To understand the deposition behavior of PLL coatings, we varied the molar ratios of dibenzocyclooctyne (DBCO) and bicyclononyne (BCN) grafts. A higher DBCO content produced thicker layers, attributed to its hydrophobic-induced intramolecular interactions. Substitution with the less hydrophobic BCN yielded uniform coatings across all grafting densities, underscoring the role of hydrophobicity in scaffold deposition. pDNA immobilization on PLL coatings using a localized dispensing technique allowed for optimization of pDNA coupling conditions. This versatile and tunable approach offers enhanced control over surface biofunctionalization, paving the way for biosensors with improved spatial precision and probe density control.