Structural Empowerment Sensing: Decoding the Structure–Activity Relationship and Detection Application of G-Quadruplex Aptamer

Abstract G-Quadruplex (G4) aptamers have emerged as versatile functional nucleic acid architectures for biosensing because of their unique conformational plasticity, programmable topologies, and intrinsic signal-regulation capabilities. Unlike conventional recognition elements that mainly function as passive binding scaffolds, G4 aptamers can actively regulate signal generation and transduction through topology-dependent structural dynamics. Increasing evidence indicates that biosensing performance is closely governed by conformational energetics, folding kinetics, loop organization, ion coordination, and nano-interfacial coupling. This review summarizes recent advances in structure-guided G4 aptamer biosensing from the perspective of “structural empowerment”, where conformational architectures directly determine sensing behavior and analytical output. We first discuss the structural fundamentals of G4 aptamers, including topology diversity, thermodynamic stability, folding pathways, and environmental responsiveness, emphasizing their influence on molecular recognition and signal accessibility. We then analyze the mechanistic relationship between G4 conformational transitions and multiple signal transduction modes, including fluorescence, electrochemical, colorimetric, surface-enhanced Raman scattering, photoelectrochemical, and catalytic sensing systems. Particular attention is given to the integration of G4 architectures with CRISPR platforms, nanozymes, DNA amplification circuits, metal–organic frameworks, and nanointerfacial engineering strategies. Importantly, this review establishes a structure–performance framework correlating G4 topological features and kinetic behaviors with analytical outcomes. Current limitations, including structural polymorphism, ionic dependence, reproducibility issues, and limited quantitative predictability, are critically discussed. Finally, future opportunities in adaptive biosensing, intelligent molecular interfaces, and AI-assisted structural design are highlighted. This review establishes a quantitative structure–performance framework by correlating G4 structural descriptors, conformational energetics, kinetic parameters, and analytical outputs, providing a basis for predictive design of G4-based sensing systems.