Versatile and Selective Biomolecule Pulldown with Combinatorial DNA-Crosslinked Polymers

Current methods for sequence-selective biomolecule isolation suffer from high cost, off-target effects, and limited flexibility. Here, we introduce LASSO (crossLink-Assisted Sequence-Selective isOlation), a versatile platform using programmable polymer phase separation to capture biomolecules under native conditions. LASSO relies on combinatorial crosslinker libraries-diverse mixtures of DNA strands that collectively trigger the formation of highly swollen polymer agglomerates with near-zero background binding. We demonstrate >80% pulldown efficiency for diverse targets, including DNA, SARS-CoV-2 RNA, and human thrombin. LASSO provides 8-20x higher binding capacity (4 nmol mg^-1 polymer) than commercial microbeads. In RNA-seq workflows, LASSO depleted ribosomal RNA with 86% efficiency, while yielding up to 7x fewer off-target outliers versus state-of-the-art magnetic beads and enzyme-based methods. Thrombin was captured via switchable aptamers with 90% efficiency, and a gentle release mechanism allowed the subsequent isolation of 98% enzymatically active proteins from the polymer. LASSO's cost-effectiveness ($0.96/sample versus $46-$51 for commercial kits), long-term stability (7 + years), simple usage, and modularity position it to advance diagnostics, transcriptomics, and bionanotechnology workflows.