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.

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The transport of polymers across nanoscale pores underpins many biological processes, such as the ejection of bacteriophage DNA into a host cell and the transfer of genes between bacteria. The movement of polymers into and out of confinement is also the basis for a wide range of sensing technologies used for single-molecule detection and sequencing. Acquiring an accurate understanding of the translocation dynamics is an essential step in the quantitative analysis of polymer structure, including the localization of binding sites or sequences. Here, we use synthetic nanopores and nanostructured DNA molecules to directly measure the velocity profile of driven polymer translocation through synthetic nanopores. Our results reveal a two-stage behaviour in which the translocation initially slows with time before accelerating close to the end of the process. We also find distinct local velocity correlations as the DNA

and readout speed, [11][12][13][14] but it is almost helpless for DNA nanostructure-based storage. Even if the sequence is decoded, it is still difficult to reproduce the whole structure accurately, which indicates the higher security of this storage method from this perspective. Additionally, hardware encryption with physical keys can further improve the security of the information saved by this strategy. [10,15] Solid-state nanopore provides us with a versatile tool to investigate the biomole cules, such as DNA, ribonucleic acid (RNA), and proteins, at the singlemolecule level. [16,17] We recently introduced a solid-state nanopore sensing platform to read bits encoded by 56 DNA hairpins on a 7.2 kb DNA carrier. [18] Readout of the structures required glass nanopores with diameters of around 5 nm. Such a small diameter complicates the fabrication process and reduces the success rates compared to easily manufactured >10 nm glass nanopores. The smaller diameter also leads to more non-specific interaction and pore clogging. [19] In further work, we used a streptavidin-labelled DNA scaffold to build a secure data storage method with binary codes. [15] While protein labels can be used with larger diameter pores, they complicate the molecular assembly and set an upper bound on the data density through their defined size. Additionally, the number of usable protein labels is limited due to the high monovalent salt concentrations required for the readout. The presence of proteins also reduces the lifetime of solid-state nanopores and hence has a detrimental effect on the viability of the readout.In this work, we replace protein barcodes with multi-way DNA junctions to address the shortcoming and limitations of our prior approaches. Inspired by the work of Wang and Seaman [20] we designed a multi-level storage architecture. Building on our established DNA carrier-based rewritable storage system with 14 nm diameter nanopores, [19] we use three DNA junction structures of different sizes (4-way junction, 6-way junction, and 12-way junction) to generate a quaternary encoding system (0-3) on the long linear DNA carrier, which increases the data density compared to classic binary encoding. Through toehold-mediated strand displacement reaction (SDR), [21][22][23] the presence of nanostructures on the carrier can be precisely controlled, allowing data reading and writing. Based on this storage system, we successfully save a grayscale image into the DNA nanostructures on 16 different carriers and read out the information in the mixture. Furthermore, using SDR the image information can be easily encrypted and decrypted.Deoxyribonucleic acid (DNA) nanostructure-based data encoding is an emerging information storage mode, offering rewritable, editable, and secure data storage. Herein, a DNA nanostructure-based storage method established on a solid-state nanopore sensing platform to save and encrypt a 2D grayscale image is proposed. DNA multi-way junctions of different sizes are attached to a double strand of DNA carriers, resulting i...

The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change inverts from a current blockade to current enhancement. In this paper, we show that the crossover concentration for bundled DNA nanostructures composed of multiple connected DNA double-helices is lower than that of double-stranded DNA.Our measurements suggest that counterion mobility in the vicinity of DNA is reduced depending on the three-dimensional structure of the molecule. We further demonstrate that introducing neutral polymers such as polyethylene glycol into the measurement solution reduces electroosmotic outflow from the nanopore, allowing translocation of large DNA structures at low salt concentrations. Our experiments contribute to an improved understanding of ion transport in confined DNA environments, which is critical for the development of nanopore sensing techniques as well as synthetic membrane channels. Our salt-dependent measurements of model DNA nanostructures will guide the development of computational models of DNA translocation through nanopores.