The need for secured computer and internet storage has seen a rapid increase over time. To address this challenge, this project will develop a DNA nanotechnology-based cryptographic protocol for writing and reading digital data. It will be developed to enable both high-capacity and highly-secured information storage and high-speed information retrieval. DNA nanotechnology will be utilized to encrypt information in molecular patterns formed upon DNA folding, which is uniquely determined by a set of DNA information strands and a special folding route of DNA strands that function as the encryption keys. The programmability of DNA nanostructures creates a vast design space for the encryption keys, making it practically impossible to intercept and break the encryption. The molecular patterns on DNA nanostructures will be characterized by a super-resolution imaging method and a low-noise nanopore device. These methods can enable fast readout speed at 1 megahertz with a high spatial resolution of smaller than 10 nanometers. If successful, this DNA-based storage has a potential to be implemented on a portable platform, thus strongly supporting the development of next-generation DNA-based memories with significantly improved security and storage density at a low cost. Consequently, the secured DNA-based storage will benefit the U.S. economy and society. This research involves several disciplines including nanofabrication, materials science, biochemistry, electronics, photonics, and data science. The project will engage underrepresented groups in the research and positively impact STEM education.
DNA has emerged as a promising candidate to store information that can rival semiconductor memory, due to its high stability, high information density, and accompanying readout technologies. However, the potential of DNA as a material for highly-secured information storage has not been fully exploited. Additionally, the readout of conventional DNA-based memories has been limited by DNA sequencing, which requires special instruments and personnel training. This research is to fill the knowledge gap by creating a significantly improved and high-security DNA-based molecular cryptography and establishing a high-speed, high-resolution, and potentially portable readout platform for DNA memory. The research team will embed encrypted information in three-dimensional DNA origami nanostructures in the form of nanoscopic patterns. A pool of DNA scaffold strands decorated with specific information strands (i-strands) of different sequences, lengths, and binding positions will be designed on the basis of a chosen DNA folding scheme out of many possibilities, which will be used later in decryption of the pattern of i-strands. The high spatial resolution of DNA-PAINT (DNA-based point accumulation for imaging in nanoscopic topography) (<20 nm) and sapphire-supported nanopore sensors (<10 nm) will support high-density information decryption of intricate single-molecule patterns on the DNA origami, while enabling a fast readout speed of up to 1 MHz. The fast readout methods will employ deep-learning classification techniques for automated decryption and improved accuracy. The encryption scheme, single-molecule characterization methods, nanopore sensor designs, and data analysis algorithms will be synergistically improved in this project to enable robust and effective information storage and transmission.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
