Versatile and Selective Biomolecule Pulldown with Combinatorial DNA‐Crosslinked Polymers

TL;DR

LASSO is a new method using smart polymers to efficiently and selectively capture biomolecules like DNA, RNA, and proteins with minimal background binding and low cost.

Contribution

LASSO introduces a programmable polymer system using combinatorial DNA crosslinking for sequence-selective biomolecule isolation with high efficiency and low off-target effects.

Findings

LASSO achieves >80% pulldown efficiency for DNA, RNA, and proteins with near-zero background binding.

LASSO outperforms commercial methods with 8–20x higher binding capacity and 7x fewer off-target outliers in RNA-seq.

Thrombin was captured with 90% efficiency and released with 98% enzymatic activity.

Abstract

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.

We present a programmable smart polymer system for universal, sequence‐selective bioseparation under native conditions. Polymer phase separation is achieved through combinatorial DNA crosslinking, enabling the capture of DNA, RNA, or proteins in a homogeneous solution with high pulldown efficiency and near‐zero background binding. This method reduces biases in ribosomal RNA depletion for RNA‐seq, while offering long‐term stability and cost‐efficiency.

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