Nanostructured DNA Barcodes: Paving the Way for Digital Data Storage with Solid-State Nanopore Readout

Abstract

Humanity is creating information at speeds never seen before in human history. All this information needs to be stored and preserved for future generations. Modern electronic data storage is ideal for short-term storage and quick access but lacks longevity and requires huge amounts of energy. The production of storage capacity is also being outpaced by the rate of information generation. Alternatives for digital data storage solutions need to be found to provide a reliable, low-energy, and low-cost platform. Using DNA as a storage medium for data is one of the more promising technologies put forward to address this issue. DNA is stable for long times and requires minimal energy to keep the information contained within it. One of the ways proposed to store digital data on strands of DNA is the use of nanostructured DNA barcodes in the form of structured molecular attachments to a DNA carrier that encode sequences of binary pieces of information. An ideally suited readout mechanism for these nanostructured molecules is the solid-state nanopore. Nanopore blockage currents are proportional to the size of the molecule, and the presence of different sized attachments will generate distinguishable current spikes in the resulting nanopore current, which can then be interpreted as a binary sequence of bits, thus enabling readout of digital data stored in nanostructured molecules.

In this thesis I explore different strategies of building suitable nanostructured DNA barcode carriers that can be read using a solid-state nanopore. I first investigate the dynamics of DNA carrier translocations through solid-state nanopores to better understand the dynamics and kinetics involved with double-stranded DNA translocations to establish them as ideal carriers for these DNA data storage schemes.

Next, I investigate different designs of nanostructured DNA barcode carriers and bit attachments to find the optimal size, spacing, and attachment chemistry to generate molecules that can be read reliably by the solid-state nanopore. The key issues to solve to make DNA data storage with nanopore readout possible are ensuring each attachment generates a single peak, adjacent peaks are sufficiently far apart to not merge in the current trace, and different attachments generate distinguishable peaks that can be correctly identified based on their current signatures.

Finally, I show that nanostructured DNA barcoding with solid-state nanopore readout is possible and propose further steps to develop a full digital data storage scheme using this approach.