Abstract
DNA data storage has emerged as a promising route to managing the exponential growth in global data production. While sequence-based DNA data storage offers unprecedented storage densities, the high costs of DNA synthesis make it prohibitively expensive. As a more cost-efficient alternative, data can be stored in DNA origami nanostructures (DONs), which however comes with the disadvantage of dramatically reduced data densities. This work aims to increase the amount of data that can be stored in one DON sample by introducing topological barcodes to identify different data subsets by atomic force microscopy (AFM). Two barcoding approaches are compared based on either different DON shapes or a single shape with different notches that are generated by omitting groups of edge staples. Although the correct identification of barcodes is more difficult for the notch designs than for the DON shapes, the notch-based barcoding approach achieves more consistent and reliable data readout. At the same time, the notch-based barcoding approach is substantially more cost-efficient as it uses only a single set of staples, whereas the shape-based approach requires one staple set for each DON shape. Notch-based topographic barcodes thus represent a viable, low-cost approach for indexing data subsets in DON-based data storage.