Sprecher
Beschreibung
As global data storage demands surge, conventional technologies like magnetic tape, SSD and hard drive face critical limitations in scalability and sustainability. DNA offers a promising alternative due to its exceptional density and durability. Current sequence-based DNA storage methods, however, are hindered by the high cost of DNA synthesis, which requires unique sequences for each bit of data.
This work introduces a novel approach that encodes data using the geometry of DNA nanostructures, much like a compact disc, but at the nanoscale. We've developed two new combinatorial strand-displacement reactions—4-way/6-way strand displacement and associative handhold-mediated strand displacement (AHMSD)—that use two separate domains on different strands of DNA to generate unique N2 orthogonal species from just 2N strands. This dramatically reduces the synthesis cost per addressable location within the nanostructures.
Our preliminary results demonstrate successful, reversible data writing and deletion. In solution, the 4-way mechanism achieved ~60% completion in 3 minutes, while AHMSD reached ≈50% yield within 2 hours. Deletion using 6-way displacement was completed at ≈50% in 15 minutes, with AHMSD taking 2 hours. We further showed position-specific writing on a DNA nanostructure, visualized by AFM imaging as a ~4 nm bump with DNA dumbbell at a targeted location. To identify the set of orthogonal species that we can use, we have designed tested 9 orthogonal toehold pairs and 10 distinct handhold sequences. Both mechanisms showed variable kinetics and about 20% of the combinations showed leakage. Hidden energy drive has been incorporated into the reaction by mismatch repair scheme.
In conclusion, our research establishes fundamental design principles for a cost-effective generation of orthogonal DNA species with applications in geometry-based DNA storage system. These novel strand displacement mechanisms could be generalised in building a large set of DNA species using a small set of DNA strands.
