Stabilizing Functional Nucleic Acids for Real-Sample Diagnostics

Functional nucleic acids (FNAs), including aptamers and DNAzymes, offer programmable recognition and catalysis for biosensing, but their performance in real samples is often compromised by nuclease degradation, matrix effects, and interface-associated losses. For diagnostic translation, stability must, therefore, be defined not only as strand persistence, but as retained folding, binding, catalysis, and signal generation under assay-relevant conditions. This review examines strategies for stabilizing FNAs in complex biological matrices and organizes the field around four design levers: Chemical, topological, architectural, and microenvironment/interface engineering. Chemical modification of sugars, backbones, and bases can reduce nuclease susceptibility, but requires functional validation. Topological approaches, including terminus shielding, circularization, covalent locking, and mechanically interlocked structures, limit strand accessibility, and reinforce functional conformations. Architectural strategies use multivalency, scaffolded presentation, DNA nanostructures, and rolling circle amplification-derived concatemers to improve robustness and signal retention. Microenvironment engineering further stabilizes FNAs through controlled immobilization, antifouling interfaces, nanomaterial-assisted protection, hydrogel or microgel confinement, and sample processing. Case studies in saliva, serum, urine, and stool illustrate how these levers can be combined to enable reliable FNA-based real-sample diagnostics.