Solvent-Modulated Orthogonal Release from Covalent Organic Frameworks Enables Sequential Multiomics Enrichment

The efficient integration of genomics, transcriptomics, and proteomics in liquid biopsy is currently impeded by the lack of materials capable of simultaneous capture and stepwise separation of nucleic acids and proteins. To bridge this gap, we designed a series of covalent organic frameworks (COFs) with tunable pore characteristics, thereby identifying a specific pore size of 3.9 nm that maximizes the affinity for both single-stranded DNA and proteins. Mechanistic investigations, integrating isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations, revealed that whereas ssDNA adsorption is predominantly entropy-driven, protein binding is driven by entropy-enthalpy synergy. This distinct thermodynamic signature results in a substantial affinity difference between strongly bound proteins and weakly bound nucleic acids. Leveraging this mechanistic insight, we established a solvent-mediated strategy for orthogonal release: by precisely tuning solvent polarity and zeta potential, we achieved mild, sequential desorption of nucleic acids and proteins from a single interface. This mechanistically guided COF platform was successfully applied to urine samples, demonstrating superior performance in the high-fidelity enrichment of low-abundance cell-free DNA, cell-free RNA, and proteins, thus offering a versatile solution for comprehensive multiomics profiling.