Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins

Abstract

Inducing biomacromolecules to self-assemble into diffraction-quality crystals remains a major challenge, typically overcome by brute-force experimental screening. Inspired by Seemans vision of DNA-junction-based scaffolds organizing guest biomacromolecules, we developed a protein-DNA co-crystal combining modular DNA programmability with robust protein-lattice diffraction. Our engineered co-crystals are composed of stacked double-stranded DNA scaffolded by protein columns, surrounding solvent channels designed to enable guest protein diffusion. DNA strut variation allows positionally-controlled installation of diverse DNA binding guest proteins. Experimentally, we simply grow scaffold crystals under standardized conditions, ligate the scaffold, and soak guest proteins. Decoupling crystal growth from guest installation will enable high-throughput structure determination of diverse DNA-binding proteins and protein-macromolecule conjugates. Sub-nanometer position and orientation control of guest macromolecules will also enable functional applications beyond structural biology.