Photothermal nanocomposite hydrogels enable precise nucleic acid manipulation and separation

For nucleic acids and DNA nanotechnology, gel electrophoresis is a key technique requiring exact spatial and temporal control. Here, we report a light-driven gel electrophoresis platform based on hydrogels embedded with engineered photothermal nanoparticles, either carbon black (CB) or plasmonic gold bipyramids (AuBPs), whose silica encapsulation and zwitterionic surface chemistry ensure compatibility with biological samples and the gel matrix. Upon LED illumination, these embedded photothermal agents generate rapid, uniform, wavelength-specific heating from within the gel itself, enabling localized, reagent-free DNA strand separation without chaotropic agents or bulky external equipment. This internalized heating strategy allows precise resolution of DNA by length, sequence, conformation, and topology, including purification of complex DNA nanostructures, such as circular and knotted species, directly from crude mixtures. Overall, this high-precision platform for DNA strand separation eliminates the need for chemical additives, offering enhanced resolution, cleaner purification workflows, and a customizable framework for thermally controlled nucleic acid analysis.