Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds

High-precision nanomaterials to entrap DNA-binding moleculesaresought after for applications such as controlled drug delivery andscaffold-assisted structural biology. Here, we engineered protein-DNAcocrystals to serve as scaffolds for DNA-binding molecules. The designedcocrystals, isoreticular cocrystals, contain DNA-binding protein andcognate DNA blocks where the DNA-DNA junctions stack end-to-end.Furthermore, the crystal symmetry allows topology preserving (isoreticular)expansion of the DNA stack without breaking protein-proteincontacts, hence providing larger solvent channels for guest diffusion.Experimentally, the resulting designed isoreticular cocrystal adoptedan interpenetrating I222 lattice, a phenomenon previouslyobserved in metal-organic frameworks (MOFs). The interpenetratinglattice crystallized dependably in the same space group despite myriadmodifications at the DNA-DNA junctions. Assembly was modularwith respect to the DNA inserted for expansion, providing an interchangeableDNA sequence for guest-specified scaffolding. Also, the DNA-DNAjunctions were tunable, accommodating varied sticky base overhanglengths and terminal phosphorylation. As a proof of concept, we usedthe interpenetrating scaffold crystals to separately entrap threedistinct guest molecules during crystallization. Isoreticular cocrystaldesign offers a route to a programmable scaffold for DNA-binding molecules,and the design principles may be applied to existing cocrystals todevelop scaffolding materials.