Decoding Atypical G‐Quadruplexes and Their Interactome in Liquid Biopsies via Integrated Electroanalytical–Proteomic Technologies

ABSTRACT

A multipurpose electroanalytical biotechnology to advance the role of atypical G‐quadruplex (G4) structures as emerging, multifunctional DNA biomarkers is reported. The technology presented enables determination, selective isolation, and in‐depth characterization of G4 motifs from liquid and solid biopsy samples obtained from oncology patients. The strategy relies on magnetic immunocaptors operating in a competitive assay between endogenous G4 targets and a homologous biotinylated G4 sequence labeled with an enzyme conjugate, coupled with amperometric transduction at screen‐printed electrodes. Beyond G4 determination and evaluation of the interaction of G4‐ligands using electroanalytical transduction, the strategy allows efficient G4 capture, facilitating their downstream structural and molecular characterization using complementary omics techniques. The analytical performance is validated in synthetic models and clinically relevant samples from colorectal cancer (CRC) patients, demonstrating the direct detection of G4 structures in plasma from oncology patients without prior nucleic acid extraction. Furthermore, by integrating magnetic immunocapture with PCR and DNA sequencing, and advanced proteomics, we confirm the selective isolation of endogenous G4‐forming DNA regions and show that CRC induces a stage‐dependent remodeling of the plasma G4 protein interactome beyond global G4 level changes, respectively. Notably, we identified a CRC‐associated G4‐binding protein linked to poor survival.