Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

Andreas Sprengel,Pierre Stegemann,Stephan Barcikowski,Christos Gatsogiannis,Pascal Lill,Lisa Gamrad,Kenny Bravo-Rodriguez,Daniel Gudnason,Melisa Merdanovic,Mikayel Aznauryan,Victoria Birkedal,Barbara Saccà,Elisa-C Schöneweiß,Michael Ehrmann,Elsa Sanchez-Garcia

doi:10.1038/ncomms14472

Abstract

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA–protein conjugation still limit true emulation of natural host–guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA–protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host–guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging.

Highlights

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation
Protein loading into DNA nanocontainers mostly relies on the chemical cross-linking of functionalized DNA strands to reactive cysteine or lysine side chains exposed on the protein surface and further hybridization of the resulting DNA–protein conjugate to complementary handles appended to the DNA–host surface
The high symmetry of the DegP oligomers ensures the equivalent display of several identical binding sites over the protein surface, allowing their targeting by a radial arrangement of convergent ligands anchored to the inner surface of the host

Summary

Introduction

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. Multienzyme complexes[4,5], protein cages[6,7] and bacterial microcompartments[8] are only few examples of host systems evolved by the cell to metabolize specific guest molecules Despite their diversity, host–guest complexes rely on non-covalent interactions between complementary shapes: a concave host surface, displaying convergent ligands, and a convex guest surface, exposing divergent binding sites[9]. Host–guest complexes rely on non-covalent interactions between complementary shapes: a concave host surface, displaying convergent ligands, and a convex guest surface, exposing divergent binding sites[9] Applying this basic principle, scientists succeeded in building synthetic hosts to stabilize reactive intermediates[10], catalyse reactions[11] and affect peptide conformations[12]. Inspired by natural strategies of molecular recognition, DNA shells can be engineered to identify the chemistry and geometry of a guest surface for its controlled caging with minimal human intervention

Methods

Results

Conclusion