Dynamic Assembly of Cascade Enzymes by the Shape Transformation of a DNA Scaffold

Abstract

Within cells, the close spatial arrangement of cascade enzymes facilitates the channeling of intermediates and enhances cascade reaction efficiency. Reconfigurable DNA nanostructures, owing to their structural controllability and precise spatial addressability, are promising tools for mimicking such processes. In this study, a 3D DNA origami scaffold, with a dynamic shape transformation from its open boat form to a closed hexagonal prism induced by toehold-mediated strand displacement, is designed to investigate the enzyme cascade reaction of xylose reductase and xylitol dehydrogenase from D-xylose metabolic pathway. Enzymes are assembled on the DNA scaffold in its open state, which is subsequently closed by the assistance of DNA sequence-specific closing keys. The enzyme cascade efficiency is much higher in the static encapsulated closed state than in the open state due not only to the enzyme proximity but also the environmental factors of 3D DNA structure. These results provide novel insights into controlling enzyme cascade reactions by inducing the shape transformation of DNA nanostructures and how environmental factors affect the action of multi-enzyme complexes in the cell.