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

Area of Science:

• Materials Science
• Biochemistry
• Analytical Chemistry

Background:

• Efficient multiomics profiling from liquid biopsies requires simultaneous capture and separation of nucleic acids and proteins.
• Current methods are limited by the lack of suitable materials for this complex task.

Purpose of the Study:

• To design and characterize covalent organic frameworks (COFs) for the simultaneous capture and stepwise separation of nucleic acids and proteins.
• To elucidate the binding mechanisms and thermodynamic drivers for ssDNA and protein adsorption onto COFs.
• To develop a solvent-mediated strategy for orthogonal release of captured analytes.

Main Methods:

• Synthesis and characterization of covalent organic frameworks (COFs) with tunable pore sizes.
• Isothermal titration calorimetry (ITC) and molecular dynamics (MD) simulations to investigate binding thermodynamics.
• Solvent-mediated elution strategies to achieve sequential release of nucleic acids and proteins.
• Application of the COF platform for enrichment of cell-free DNA, cell-free RNA, and proteins from urine samples.

Main Results:

• A COF with a 3.9 nm pore size was identified, exhibiting maximal affinity for both single-stranded DNA (ssDNA) and proteins.
• ssDNA adsorption is primarily entropy-driven, while protein binding is driven by entropy-enthalpy synergy, creating distinct affinities.
• A solvent-mediated strategy enabled mild, sequential desorption of nucleic acids and proteins from the COF interface.
• The COF platform demonstrated superior performance in high-fidelity enrichment of low-abundance analytes from urine.

Conclusions:

• The developed COF platform offers a versatile solution for simultaneous capture and orthogonal release of nucleic acids and proteins.
• This approach significantly advances the field of liquid biopsy for comprehensive multiomics profiling.
• The mechanistic insights into binding thermodynamics guided the rational design of the COF material and elution strategy.