Modular Protein–DNA Cocrystals as Precise, Programmable Assembly Scaffolds

Abstract

High-precision nanomaterials to entrap DNAbinding molecules are sought after for applications such as controlled drug delivery and scaffold-assisted structural biology. Here, we engineered protein−DNA cocrystals to serve as scaffolds for DNA-binding molecules. The designed cocrystals, isoreticular cocrystals, contain DNA-binding protein and cognate 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−protein contacts, hence providing larger solvent channels for guest diffusion. Experimentally, the resulting designed isoreticular cocrystal adopted an interpenetrating I222 lattice, a phenomenon previously observed in metal−organic frameworks (MOFs). The interpenetrating lattice crystallized dependably in the same space group despite myriad modifications at the DNA−DNA junctions. Assembly was modular with respect to the DNA inserted for expansion, providing an interchangeable DNA sequence for guest-specified scaffolding. Also, the DNA−DNA junctions were tunable, accommodating varied sticky base overhang lengths and terminal phosphorylation. As a proof of concept, we used the interpenetrating scaffold crystals to separately entrap three distinct guest molecules during crystallization. Isoreticular cocrystal design offers a route to a programmable scaffold for DNA-binding molecules, and the design principles may be applied to existing cocrystals to develop scaffolding materials.

Synthesis of Zn(ii) coordination complexes, their molecular design and docking with SARS-CoV-2 RBD protein and Omicron spike protein

“…The modular protein–DNA (PDB ID: ) structure was obtained from the protein data bank and used as the receptor protein. 54 The initial structure of ivermectin and levosalbutamol were obtained from the PubChem database. The docking coordinates ( X , Y , Z ) and the grid size (and other parameters such as the grid spacing) of ivermectin and levosalbutamol were determined.…”

Porous protein crystals: synthesis and applications

“…A recent platform in the spirit of this approach was recently reported by Orun et al from our group in 2023. 177 In this platform, the porous crystal is a hybrid material consisting of replication factor E54 (RepE54) 178 and its 21-bp cognate DNA sequence, and contains protein complexes at the cell vertices. The resulting crystal scaffold was dubbed co-crystal 1 (CC1) (Fig.…”

“…Expansion of CC1 crystals from a single unit cell proceeds in a “Lincoln log” fashion, wherein two distinct protein–protein interfaces stabilize the crystal along the z -axis, while the crystal is further expanded in the xy -plane via the lengths of DNA running between the vertices; the resulting scaffolds were stabilized by chemical ligation of the 5′ and 3′ termini of the aligned DNA segments. 177 Critically, this topology theoretically allows the modular insertion of nearly any DNA sequence to support subsequent guest capture.…”

Tuning Chemical DNA Ligation within DNA Crystals and Protein–DNA Cocrystals

“…Recently, we designed an expanded, interpenetrating cocrystal lattice to serve as a molecular scaffold. 18 These cocrystals of RepE54 protein and cognate DNA duplex are the template cocrystals used in this study (Figure 1A). The expanded cocrystals were crystallized with RepE54 protein and 31mer cognate DNA duplex, 10 additional base pairs than the original cocrystal, called CC1 +10bp .…”

“…Crystals made from protein and DNA are versatile materials that precisely order molecules, self-assemble, and have tunable growth. − Porous crystals have been shown to act as molecular sieves − and to host molecules for structure determination, − enhance enzymatic activity, , and information storage via synthetic DNA sequences . Engineered crystals with DNA building blocks, from pure DNA crystals , to hybrid protein–DNA crystals, have been designed to serve as scaffolds for DNA-binding molecules. − However, the broad utility of crystals held together by DNA is restricted by their ability to survive in varied solution conditions. As grown, crystals made from biological units are held together by weak noncovalent bonds and are likely to dissolve when introduced to anything other than their growth solution.…”