Rational design of gold nanoparticles functionalized with aptamers for improved West Nile virus detection

This study employs a multiscale approach to investigate the interaction dynamics between the West Nile virus (WNV) envelope (E) protein and gold nanoclusters functionalized with DNA aptamers. By integrating aptamer secondary and tertiary structure prediction, structural docking and atomistic molecular dynamics simulations, we reveal the structural, dynamic and electrostatic factors governing the aptamer-target WNV E protein recognition at the nanoscale. Two gold nanoclusters, Au₁₄₄(SR)₆₀ and Au₃₁₄(SR)₉₆ (SR = thiolate ligand), were examined to assess how nanoparticle size and surface functionalization influence aptamer anchoring and binding stability under physiological salt conditions. This approach enhances aptamer functionalization strategies for detecting West Nile virus and creates a flexible framework for aptamer-based diagnostics for other emerging pathogens, with implications for diagnostics across a range of viral and protein biomarkers.