Aptamer screening within sample matrices: Toward reliable applications

Nucleic acid aptamers are short oligonucleotide sequences selected in vitro by Systematic Evolution of Ligands by EXponential enrichment (SELEX). Often described as "chemical antibodies", they can recognize diverse targets with high affinity and specificity through structure-dependent interactions and offer multiple attractive features. Although riboswitches contain natural aptamer domains, SELEX has remained the dominant strategy for aptamer generation for over 35 years, with ongoing methodological development. These advances have expanded the application potential of aptamers in food safety, disease diagnosis, and drug delivery. Nevertheless, their reliable translation into practical applications remains challenging, largely due to complex matrix effects in real samples, which may interfere with aptamer folding, stability, and target recognition. In response to this challenge, increasing efforts have focused on matrix-integrated SELEX strategies that incorporate representative sample environments into the selection process. This review systematically summarizes recent progress in this developing field and discusses its potential as an upstream strategy for improving aptamer robustness and applicability. We first outline the biological basis of aptamers and the evolution of SELEX, followed by a brief overview of post-SELEX optimization approaches. We then provide an integrated analysis of matrix-integrated SELEX strategies, with emphasis on matrix-spiked selection, matrix-based negative selection, and holistic matrix selection, together with their underlying mechanisms, performance outcomes, and representative applications in environmental adaptation, interference suppression, and biomarker discovery. Finally, we discuss the remaining technical and conceptual challenges and highlight future directions for developing more robust, efficient, and application-oriented aptamer screening platforms.