Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals

• DOI: 10.1021/jacs.3c07802
• Publication Date: 2023-11-21T14:43:50Z
• Authors: Chad R. Simmons; Alex Buchberger; Skylar J.W. Henry; Alexandra Novacek; Nour Eddine Fahmi; Tara MacCulloch; Nicholas Stephano...; Hao Yan
• Keywords: Netropsin; Antiparallel (mathematics); Dodecameric protein; A-DNA; Structural motif

The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven an elusive goal since its conception. Oligonucleotide frameworks provide especially attractive route toward studying DNA-binding by using three-dimensional lattices with defined sequence structure. In this work, we site-specifically position a suite minor groove binding molecules, solve their structures via X-ray crystallography as proof-of-principle scaffolding larger species. Two crystal motifs were used to precisely immobilize the DAPI, Hoechst, netropsin at positions lattice, allowing us control occupancy within crystal. We also solved structure three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs antiparallel dimeric arrangement groove. Finally, engineered both two distinct locations same lattice. Our work elucidates design principles for spatial functional guests opens new potential opportunities use display structurally characterize small peptides, ultimately proteins unknown