Capturing transient antibody conformations with DNA origami epitopes

Ping Zhang,Xiaoguo Liu,Lihua Wang,Pi Liu,Fei Wang,Hirotaka Ariyama,Chunhai Fan,Jianping Lin,Jun Hu,Bin Li,Toshio Ando

doi:10.1038/s41467-020-16949-4

Abstract

Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. However, structural determination under crystal or cryogenic conditions does not provide temporal resolution for resolving transient, physiologically or pathologically relevant functional antibody-antigen complexes. Here, we develop a triangular DNA origami framework with site-specifically anchored and spatially organized artificial epitopes to capture transient conformations of immunoglobulin Gs (IgGs) at room temperature. The DNA origami epitopes (DOEs) allows programmed spatial distribution of epitope spikes, which enables direct imaging of functional complexes with atomic force microscopy (AFM). We establish the critical dependence of the IgG avidity on the lateral distance of epitopes within 3–20 nm at the single-molecule level. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy.

Highlights

Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology
Having established the DNA origami epitopes (DOEs) platform, we performed immunoglobulin Gs (IgGs) capture which was imaged with atomic force microscopy (AFM)
DOEs were deposited onto a freshly cleaved mica substrate, which was incubated with IgGs

Summary

Introduction

Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy. High-speed (HS) AFM offers up to video-rate temporal resolution, revealing certain types of dynamic processes of IgGs, e.g., walking on the viral surface, oligomerization, and complement activation upon antigen recognition[24,30,31]. These exciting advances in unveiling distinctive molecular events of Abs reveal its compelling implications in resolving heterogeneous conformations of Ab–Ag complexes. Using AFM, HS-AFM and single-molecule FRET (smFRET), we interrogate the structure, avidity, and dynamic binding processes of IgGs at the single-molecule level

Methods

Results

Conclusion