Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing.

Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.

[1]  Jijun Tang,et al.  Robust data storage in DNA by de Bruijn graph-based de novo strand assembly , 2022, Nature Communications.

[2]  Kai Liu,et al.  In vivo processing of digital information molecularly with targeted specificity and robust reliability , 2022, Science advances.

[3]  Kai Liu,et al.  Preservation and Encryption in DNA Digital Data Storage. , 2022, ChemPlusChem.

[4]  Kai Liu,et al.  DNA‐Based Concatenated Encoding System for High‐Reliability and High‐Density Data Storage , 2022, Small methods.

[5]  Fan Wang,et al.  Biosynthetic structural proteins with super plasticity, extraordinary mechanical performance, biodegradability, biocompatibility and information storage ability. , 2022, Angewandte Chemie.

[6]  Bichlien H. Nguyen,et al.  Synthetic DNA applications in information technology , 2022, Nature Communications.

[7]  H. Sugiyama,et al.  Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity , 2022, Nucleic acids research.

[8]  Kai Liu,et al.  Highly Reliable and Efficient Encoding Systems for Hexadecimal Polypeptide-based Data Storage , 2021, Fundamental Research.

[9]  Jinsang Kim,et al.  Chaotic Organic Crystal Phosphorescent Patterns for Physical Unclonable Functions , 2021, Advanced materials.

[10]  Cheri M Ackerman,et al.  Random access DNA memory using Boolean search in an archival file storage system , 2021, Nature Materials.

[11]  Thomas E. Schaus,et al.  Three-dimensional nanolithography guided by DNA modular epitaxy , 2021, Nature Materials.

[12]  Luis Ceze,et al.  An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage. , 2021, Small methods.

[13]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[14]  Linda C Meiser,et al.  DNA synthesis for true random number generation , 2020, Nature Communications.

[15]  Reinhard Heckel,et al.  Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction , 2020, Nature Communications.

[16]  Dong Chen,et al.  Information stored in nanoscale: Encoding data in a single DNA strand with Base64 , 2020 .

[17]  Albert J. Keung,et al.  Dynamic and scalable DNA-based information storage , 2020, Nature Communications.

[18]  L. Cronin,et al.  A Crystallization Robot for Generating True Random Numbers Based on Stochastic Chemical Processes , 2020, Matter.

[19]  G. Church,et al.  Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage , 2020, Nature Communications.

[20]  Luis Ceze,et al.  Probing the physical limits of reliable DNA data retrieval , 2020, Nature Communications.

[21]  Hieu Bui,et al.  Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase , 2019, Nature Nanotechnology.

[22]  Reinhard Heckel,et al.  Reading and writing digital data in DNA , 2019, Nature Protocols.

[23]  Miklós Z. Rácz,et al.  DNA assembly for nanopore data storage readout , 2019, Nature Communications.

[24]  G. Church,et al.  Terminator-free template-independent enzymatic DNA synthesis for digital information storage , 2019, Nature communications.

[25]  L. Ceze,et al.  Molecular digital data storage using DNA , 2019, Nature Reviews Genetics.

[26]  V. Subramanian,et al.  Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements. , 2019, Langmuir : the ACS journal of surfaces and colloids.

[27]  Lulu Qian,et al.  Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks , 2018, Nature.

[28]  Nathan J Hillson,et al.  De novo DNA synthesis using polymerase-nucleotide conjugates , 2018, Nature Biotechnology.

[29]  M. A. Jensen,et al.  Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges. , 2018, Biochemistry.

[30]  Cyrus Rashtchian,et al.  Random access in large-scale DNA data storage , 2018, Nature Biotechnology.

[31]  Jocelyn Y. Kishi,et al.  Programmable autonomous synthesis of single-stranded DNA , 2017, Nature chemistry.

[32]  W. Wolkers,et al.  Freeze-drying of mammalian cells using trehalose: preservation of DNA integrity , 2017, Scientific Reports.

[33]  Yaniv Erlich,et al.  DNA Fountain enables a robust and efficient storage architecture , 2016, Science.

[34]  Andrew D Ellington,et al.  Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology. , 2017, Cold Spring Harbor perspectives in biology.

[35]  Andy Extance,et al.  How DNA could store all the world’s data , 2016, Nature.

[36]  Guillaume J. Filion,et al.  Starcode: sequence clustering based on all-pairs search , 2015, Bioinform..

[37]  Zhongze Gu,et al.  Photonic Crystal Microcapsules for Label‐free Multiplex Detection , 2014, Advanced materials.

[38]  Zhenda Lu,et al.  Colloidal nanoparticle clusters: functional materials by design. , 2012, Chemical Society reviews.

[39]  Hao Zhang,et al.  Hybridization of inorganic nanoparticles and polymers to create regular and reversible self-assembly architectures. , 2012, Chemical Society reviews.

[40]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[41]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[42]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[43]  Emily M. LeProust,et al.  Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process , 2010, Nucleic acids research.

[44]  Wael Mamdouh,et al.  Single-molecule chemical reactions on DNA origami. , 2010, Nature nanotechnology.

[45]  J. Bonnet,et al.  Chain and conformation stability of solid-state DNA: implications for room temperature storage , 2009, Nucleic acids research.

[46]  Orlin D. Velev,et al.  Materials Fabricated by Micro‐ and Nanoparticle Assembly – The Challenging Path from Science to Engineering , 2009 .

[47]  Jørgen Mollerup,et al.  A review of the thermodynamics of protein association to ligands, protein adsorption, and adsorption isotherms , 2008 .

[48]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

[49]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[50]  Edwin M. Southern,et al.  Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication , 2005, Nucleic acids research.

[51]  Benjamin G. Keselowsky,et al.  Adsorption-Induced Conformational Changes in Fibronectin Due to Interactions with Well-Defined Surface Chemistries , 2003 .

[52]  Michael J Sailor,et al.  Biomolecular screening with encoded porous-silicon photonic crystals , 2002, Nature Materials.

[53]  M. Sussman,et al.  Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array , 1999, Nature Biotechnology.

[54]  M. Caruthers,et al.  Synthesis of deoxyoligonucleotides on a polymer support , 1981 .