Digital Data Storage Using DNA Nanostructures and Solid-State Nanopores

Abstract

Solid-state nanopores are powerful tools for reading the three-dimensional shape of molecules, allowing for the translation of molecular structure information into electric signals.Here, we show a high-resolution integrated nanopore system for identifying DNA nanostructures that has the capability of distinguishing attached short DNA hairpins with only a stem length difference of 8 bp along a DNA double strand named the DNA carrier. Using our platform, we can read up to 112 DNA hairpins with a separating distance of 114 bp attached on a DNA carrier that carries digital information. Our encoding strategy allows for the creation of a library of molecules with a size of up to 5 × 10 33 (2 112 ) that is only built from a few hundred types of base molecules for data storage and has the potential to be extended by linking multiple DNA carriers. Our platform provides a nanopore-and DNA nanostructure-based data storage method with convenient access and the potential for miniature-scale integration.

Flossing DNA in a Dual Nanopore Device

“…Recent research has showcased the potential of nanopores to detect molecular features along a DNA carrier strand, including proteins such as anti‐DNA antibodies and streptavidin, single‐stranded versus double‐stranded regions of a molecule, DNA‐hairpins, and aptamers . Potential applications range from digital information storage, multiplexed sensing, and genomic and/or functional genomic applications including genome mapping and epigenetics . Solid‐state pores in particular can target a more diverse analyte pool than protein pores (e.g., dsDNA, proteins, protein–DNA complexes, nucleosomes) and thereby give access to a broad range of single‐molecule applications.…”

“…Unwanted conformations/topologies and molecular fluctuations (both equilibrium and nonequilibrium in nature) create systematic and random distortions in the electrical signal pattern of motifs resolved by the sensor. For example, closely spaced features along DNA cannot always be resolved in a given single‐molecule read even with state‐of‐the‐art measurements performed with 5 nm diameter nanopores, requiring multiple independent reads from identical copies of different molecules to confidently resolve the features. In addition, the stochastic nature of the translocation process gives rise to broad distributions in tag spacings measured across a molecular ensemble; these broad distributions necessitate averaging over additional molecules to obtain precise spacing estimates.…”

Molecular Full Adder Based on DNA Strand Displacement

“…DNA, as the carrier of heredity information, can be used as a programmable computing nanomaterial [1]. Researchers have used synthetic DNA coding sequences for various applications, such as programmable DNA nanostructures [2][3][4][5], DNA information storage [6,7], and molecular logic calculations [8][9][10]. The DNA computing model was first proposed by Dr. Adleman in 1994 [11].…”

DNA Logic Circuits Based on Accurate Step Function Gate

“…Researchers have used DNA and fulfilled various applications. Such as, DNA nano architectures [2][3][4][5], information storage [6,7], logic computing [8][9][10], etc.…”