Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution

Eklund, AS; Comberlato, A; Parish, IA; Jungmann, R; Bastings, MMC

Author(s): Eklund, AS; Comberlato, A; Parish, IA; Jungmann, R; Bastings, MMC;
Details: Publication Year 2021-11,Volume 15,Issue #11,Page 17668-17677
Journal Title: ACS Nano
Publication Type: Research article
Abstract: DNA-based nanostructures are actively gaining interest as tools for biomedical and therapeutic applications following the recent development of protective coating strategies prolonging structural integrity in physiological conditions. For tailored biological action, these nanostructures are often functionalized with targeting or imaging labels using DNA base pairing. Only if these labels are accessible on the structure's surface will they be able to interact with their intended biological target. However, the accessibility of functional sites for different geometries and environments, specifically after the application of a protective coating, is currently not known. Here, we assay this accessibility on the level of single handle strands with two- and three-dimensional resolution using DNA-PAINT and show that the hybridization kinetics of top and bottom sides on the same nanostructure linked to a surface remain unaltered. We furthermore demonstrate that the functionality of the structures remains available after an oligolysine-PEG coating is applied, enabling bioassays where functionality and stability are imperative.
Keywords: Nucleic Acid Conformation; *DNA/chemistry; *Nanostructures/chemistry; Kinetics; Nanotechnology/methods; DNA origami; DNA-paint; handle accessibility; nanopatterns; nanotherapeutics; structure stability; super-resolution microscopy
Department(s): Laboratory Research
PubMed ID: 34613711
Publisher's Version: https://doi.org/10.1021/acsnano.1c05540
Open Access at Publisher's Site: https://doi.org/10.1021/acsnano.1c05540
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2026-09-24 05:52:43

Last Modified: 2026-09-24 05:53:56