Versatile and Selective Biomolecule Pulldown with Combinatorial DNA‐Crosslinked Polymers

Abstract

Abstract Current methods for sequence‐selective biomolecule isolation suffer from high cost, off‐target effects, and limited flexibility. Here, we introduce LASSO (cross L ink‐ A ssisted S equence‐ S elective is O lation), 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.