Nanoscale precise stamping of biomolecule patterns using DNA origami

Abstract

Understanding the importance of ligand patterning in biological processes requires precise control over molecular positioning and spacing. While DNA origami structures offer nanoscale precision in biomolecule arrangement, their biological applications are limited by challenges related to their structural stability, scalability, and surface area. Here, we present a straightforward and rapid DNA origami stamping technique for transferring nanoscale oligonucleotide patterns onto surfaces, visualized using DNA-PAINT super-resolution microscopy to quantitatively assess the stamping efficiency and precision across different stamp types. Unlike traditional top-down methods that require specialized equipment, our technique provides an accessible, self-assembled platform for surface patterning, with versatility across various substrates via modifiable pattern-transfer oligonucleotides. We demonstrate reliable, efficient, and precise pattern transfer at single-molecule resolution, enabling new opportunities to study distance-dependent biological processes, including receptor activation, multivalent binding, and enzymatic cascades across broader spatial scales and different detection techniques. The use of the passivated surface limits non-specific interactions with unpatterned areas and enables control over the interaction between the biological target and the patterned biomolecules. Our method advances surface patterning by combining DNA nanotechnology with single-molecule imaging techniques, expanding access to cost-effective analytical approaches and potentially enabling multiplexed detection and live measurements.