Literature DB >> 29457795

Random access in large-scale DNA data storage.

Lee Organick1, Siena Dumas Ang2, Yuan-Jyue Chen2, Randolph Lopez3, Sergey Yekhanin2, Konstantin Makarychev2, Miklos Z Racz2, Govinda Kamath2, Parikshit Gopalan2, Bichlien Nguyen2, Christopher N Takahashi1, Sharon Newman1, Hsing-Yeh Parker2, Cyrus Rashtchian2, Kendall Stewart1, Gagan Gupta2, Robert Carlson2, John Mulligan2, Douglas Carmean2, Georg Seelig1,4, Luis Ceze1, Karin Strauss2.   

Abstract

Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA. We also develop an algorithm that greatly reduces the sequencing read coverage required for error-free decoding by maximizing information from all sequence reads. These advances demonstrate a viable, large-scale system for DNA data storage and retrieval.

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Year:  2018        PMID: 29457795     DOI: 10.1038/nbt.4079

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  10 in total

1.  Long-term data storage in DNA.

Authors:  J P Cox
Journal:  Trends Biotechnol       Date:  2001-07       Impact factor: 19.536

2.  NUPACK: Analysis and design of nucleic acid systems.

Authors:  Joseph N Zadeh; Conrad D Steenberg; Justin S Bois; Brian R Wolfe; Marshall B Pierce; Asif R Khan; Robert M Dirks; Niles A Pierce
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

3.  Design of 240,000 orthogonal 25mer DNA barcode probes.

Authors:  Qikai Xu; Michael R Schlabach; Gregory J Hannon; Stephen J Elledge
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-26       Impact factor: 11.205

4.  Robust chemical preservation of digital information on DNA in silica with error-correcting codes.

Authors:  Robert N Grass; Reinhard Heckel; Michela Puddu; Daniela Paunescu; Wendelin J Stark
Journal:  Angew Chem Int Ed Engl       Date:  2015-02-04       Impact factor: 15.336

5.  DNA Fountain enables a robust and efficient storage architecture.

Authors:  Yaniv Erlich; Dina Zielinski
Journal:  Science       Date:  2017-03-03       Impact factor: 47.728

6.  Next-generation digital information storage in DNA.

Authors:  George M Church; Yuan Gao; Sriram Kosuri
Journal:  Science       Date:  2012-08-16       Impact factor: 47.728

7.  Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.

Authors:  Nick Goldman; Paul Bertone; Siyuan Chen; Christophe Dessimoz; Emily M LeProust; Botond Sipos; Ewan Birney
Journal:  Nature       Date:  2013-01-23       Impact factor: 49.962

8.  A Rewritable, Random-Access DNA-Based Storage System.

Authors:  S M Hossein Tabatabaei Yazdi; Yongbo Yuan; Jian Ma; Huimin Zhao; Olgica Milenkovic
Journal:  Sci Rep       Date:  2015-09-18       Impact factor: 4.379

9.  Portable and Error-Free DNA-Based Data Storage.

Authors:  S M Hossein Tabatabaei Yazdi; Ryan Gabrys; Olgica Milenkovic
Journal:  Sci Rep       Date:  2017-07-10       Impact factor: 4.379

Review 10.  Large-scale de novo DNA synthesis: technologies and applications.

Authors:  Sriram Kosuri; George M Church
Journal:  Nat Methods       Date:  2014-05       Impact factor: 28.547

  10 in total
  50 in total

Review 1.  Carbon-based archiving: current progress and future prospects of DNA-based data storage.

Authors:  Zhi Ping; Dongzhao Ma; Xiaoluo Huang; Shihong Chen; Longying Liu; Fei Guo; Sha Joe Zhu; Yue Shen
Journal:  Gigascience       Date:  2019-06-01       Impact factor: 6.524

2.  Erratum: Random access in large-scale DNA data storage.

Authors:  Lee Organick; Siena Dumas Ang; Yuan-Jyue Chen; Randolph Lopez; Sergey Yekhanin; Konstantin Makarychev; Miklos Z Racz; Govinda Kamath; Parikshit Gopalan; Bichlien Nguyen; Christopher N Takahashi; Sharon Newman; Hsing-Yeh Parker; Cyrus Rashtchian; Kendall Stewart; Gagan Gupta; Robert Carlson; John Mulligan; Douglas Carmean; Georg Seelig; Luis Ceze; Karin Strauss
Journal:  Nat Biotechnol       Date:  2018-07-06       Impact factor: 54.908

3.  An archive written in DNA.

Authors:  Reinhard Heckel
Journal:  Nat Biotechnol       Date:  2018-03-06       Impact factor: 54.908

4.  Specificity from nonspecific interaction: regulation of tumor necrosis factor-α activity by DNA.

Authors:  Helena Andrade; Weilin Lin; Yixin Zhang
Journal:  J Biol Chem       Date:  2019-02-27       Impact factor: 5.157

5.  Fractal construction of constrained code words for DNA storage systems.

Authors:  Hannah F Löchel; Marius Welzel; Georges Hattab; Anne-Christin Hauschild; Dominik Heider
Journal:  Nucleic Acids Res       Date:  2022-03-21       Impact factor: 16.971

6.  An Intelligent Optimization Algorithm for Constructing a DNA Storage Code: NOL-HHO.

Authors:  Qiang Yin; Ben Cao; Xue Li; Bin Wang; Qiang Zhang; Xiaopeng Wei
Journal:  Int J Mol Sci       Date:  2020-03-22       Impact factor: 5.923

7.  Random access DNA memory using Boolean search in an archival file storage system.

Authors:  James L Banal; Tyson R Shepherd; Joseph Berleant; Hellen Huang; Miguel Reyes; Cheri M Ackerman; Paul C Blainey; Mark Bathe
Journal:  Nat Mater       Date:  2021-06-10       Impact factor: 43.841

Review 8.  Uncertainties in synthetic DNA-based data storage.

Authors:  Chengtao Xu; Chao Zhao; Biao Ma; Hong Liu
Journal:  Nucleic Acids Res       Date:  2021-06-04       Impact factor: 16.971

9.  Purification of multiplex oligonucleotide libraries by synthesis and selection.

Authors:  Hansol Choi; Yeongjae Choi; Jaewon Choi; Amos Chungwon Lee; Huiran Yeom; Jinwoo Hyun; Taehoon Ryu; Sunghoon Kwon
Journal:  Nat Biotechnol       Date:  2021-07-29       Impact factor: 54.908

10.  Promiscuous molecules for smarter file operations in DNA-based data storage.

Authors:  Kyle J Tomek; Kevin Volkel; Elaine W Indermaur; James M Tuck; Albert J Keung
Journal:  Nat Commun       Date:  2021-06-10       Impact factor: 14.919

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