Capacity of DNA Data Embedding Under Substitution Mutations

A number of methods have been proposed over the last decade for encoding information using deoxyribonucleic acid (DNA), giving rise to the emerging area of DNA data embedding. Since a DNA sequence is conceptually equivalent to a sequence of quaternary symbols (bases), DNA data embedding (diversely called DNA watermarking or DNA steganography) can be seen as a digital communications problem where channel errors are tantamount to mutations of DNA bases. Depending on the use of coding or noncoding DNA hosts, which, respectively, denote DNA segments that can or cannot be translated into proteins, DNA data embedding is essentially a problem of communications with or without side information at the encoder. In this paper the Shannon capacity of DNA data embedding is obtained for the case in which DNA sequences are subject to substitution mutations modelled using the Kimura model from molecular evolution studies. Inferences are also drawn with respect to the biological implications of some of the results presented.Comment: 22 pages, 13 figures; preliminary versions of this work were presented at the SPIE Media Forensics and Security XII conference (January 2010) and at the IEEE ICASSP conference (March 2010

Digital Data Storage Using DNA Nanostructures and Solid-State Nanopores.

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 × 1033 (2112) 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

DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization.

DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations

Storing Digital Information in Long-Read DNA

There is urgent need for effective and cost-efficient data storage, as the worldwide requirement for data storage is rapidly growing. DNA has introduced a new tool for storing digital information. Recent studies have successfully stored digital information, such as text and gif animation. Previous studies tackled technical hurdles due to errors from DNA synthesis and sequencing. Studies also have focused on a strategy that makes use of 100‒150-bp read sizes in both synthesis and sequencing. In this paper, we a suggest novel data encoding/decoding scheme that makes use of long-read DNA (~1,000 bp). This enables accurate recovery of stored digital information with a smaller number of reads than the previous approach. Also, this approach reduces sequencing time

Coding for Optimized Writing Rate in DNA Storage

A method for encoding information in DNA sequences is described. The method is based on the precisionresolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis method. The suggested method optimizes the amount of information bits per synthesis time unit, namely, the writing rate. Additionally, the encoding scheme studied here takes into account the existence of multiple copies of the DNA sequence, which are independently distorted. Finally, quantizers for various run-length distributions are designed

On Optimal Family of Codes for Archival DNA Storage

DNA based storage systems received attention by many researchers. This includes archival and re-writable random access DNA based storage systems. In this work, we have developed an efficient technique to encode the data into DNA sequence by using non-linear families of ternary codes. In particular, we proposes an algorithm to encode data into DNA with high information storage density and better error correction using a sub code of Golay code. Theoretically, 115 exabytes (EB) data can be stored in one gram of DNA by our method.Comment: Supplementary file and the software DNA Cloud 2.0 is available at http://www.guptalab.org/dnacloud This is the preliminary version of the paper that appeared in Proceedings of IWSDA 2015, pp. 143--14