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

Zhi Ping, Dongzhao Ma, Xiaoluo Huang, Shihong Chen, Longying Liu, Fei Guo, Sha Joe Zhu, Yue Shen
2019 GigaScience  
Therefore, data scientists are continually looking for better, more stable, and space-efficient alternatives to store these huge datasets.  ...  This review summarizes state-of-the-art methods, including digital-to-DNA coding schemes and the media types used in DNA-based data storage, and provides an overview of recent progress achieved in this  ...  These new nucleic acid candidates could help to increase the coding efficiency for DNA digital storage in the not-too-far future.  ... 
doi:10.1093/gigascience/giz075 pmid:31220251 pmcid:PMC6586197 fatcat:bn3bfpgaqneqzpge2iot6hmohe

Towards Practical and Robust DNA-based Data Archiving by Codec System Named 'Yin-Yang' [article]

Zhi Ping, Shihong Chen, Xiaoluo Huang, Sha Zhu, Chen Chai, Haoling Zhang, Henry H Lee, Guangyu Zhou, Tsan-Yu Chiu, Tai Chen, Huanming Yang, Xun Xu (+2 others)
2019 bioRxiv   pre-print
Motivation: DNA has been reported as a promising medium of data storage for its remarkable durability and space-efficient storage capacity.  ...  Compared to most DNA-based data storage coding schemes presented to date, this codec system can efficiently achieve a variety of user goals (e.g. reduce homopolymer length to 3 or 4 at most, maintain balanced  ...  Results High coding efficiency Coding efficiency is always one of the key features of DNA-based data storage coding scheme evaluation.  ... 
doi:10.1101/829721 fatcat:jhphe44ncrh5bij43ulgoiq5na

Efficient RNA synthesis by in vitro transcription of a triazole-modified DNA template

Afaf H. El-Sagheer, Tom Brown
2011 Chemical Communications  
A DNA strand containing a triazole phosphodiester mimic is an efficient template for in vitro transcription.  ...  This is the first demonstration of transcription through a heavily modified DNA backbone linkage and it suggests that click-ligated DNA could be useful for the direct synthesis of biologically active RNA  ...  T7-RNAP is an important enzyme for DNA-templated RNA synthesis; it is commonly used in biotechnology for the synthesis of small RNAs 7,8 and to direct the expression of cloned genes. 9 It does not require  ... 
doi:10.1039/c1cc14316f pmid:21961113 fatcat:b3aqhfprvjcjzgw6habyzrq454

Encoding movies and data in DNA storage

Naveen Goela, Jean Bolot
2016 2016 Information Theory and Applications Workshop (ITA)  
Focusing on error-correction methods and codes, a systems level design is presented for encoding movies and digital information in DNA storage.  ...  The goal is to decode the source from the DNA reliably even in the presence of diverse errors introduced by DNA synthesis, PCR amplification, and DNA sequencing processes.  ...  While accuracy in retrieval is paramount, such codes must be efficient to reduce overhead costs in DNA synthesis and sequencing. IV.  ... 
doi:10.1109/ita.2016.7888163 dblp:conf/ita/GoelaB16 fatcat:3u6njr65o5fgzj3rqidnauzw3a

Indel-correcting DNA barcodes for high-throughput sequencing

John A. Hawkins, Stephen K. Jones, Ilya J. Finkelstein, William H. Press
2018 Proceedings of the National Academy of Sciences of the United States of America  
Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions  ...  The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.  ...  We thank James Rybarski, Andrea Hawkins-Daarud, Jeffrey Hussmann, Prakash Mohan, Alexander Boulgakov, and Kevin Drew for useful feedback throughout the project.  ... 
doi:10.1073/pnas.1802640115 pmid:29925596 fatcat:sjc2vkafxndkvhelo7wgux7jkm

Identification of gene products programmed by restriction endonuclease DNA fragments using an E. coli in vitro system

Julie M. Pratt, Graham J. Boulnois, Valerie Darby, Elisha Orr, Elmar Wahle, I.Barry Holland
1981 Nucleic Acids Research  
The in vitro system can be used successfully with bacterial DNA from other species and efficient extracts can be prepared from any E. coli K-12 strain, which should greatly facilitate the purification  ...  DNA restriction enzyme fragments have been used to programme the synthesis of polypeptides in an in vitro system without apparent loss in fidelity compared with supercoiled templates.  ...  efficient as templates for these genes.  ... 
doi:10.1093/nar/9.18.4459 pmid:6272207 pmcid:PMC327450 fatcat:bv42zxj75vcdbdbiyxbybikkh4

Error-correcting DNA barcodes for high-throughput sequencing [article]

John A Hawkins, Stephen K Jones, Ilya J Finkelstein, William H Press
2018 bioRxiv   pre-print
Widely-used error-correcting codes borrowed from computer science (e.g., Hamming and Levenshtein codes) do not properly account for insertions and deletions in DNA barcodes, even though deletions are the  ...  The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.  ...  We thank James Rybarski, Andrea Hawkins-Daarud, Jeffrey Hussmann, Prakash Mohan, Alexander Boulgakov, and Kevin Drew for useful feedback throughout the project.  ... 
doi:10.1101/315002 fatcat:oftrbaxv3nfkjd4a6lhflcoy6q

Effects of partial silencing of genes coding for enzymes involved in glycolysis and tricarboxylic acid cycle on the enterance of human fibroblasts to the S phase

Aleksandra Konieczna, Aneta Szczepańska, Karolina Sawiuk, Grzegorz Węgrzyn, Robert Łyżeń
2015 BMC Cell Biology  
Decreased levels of expression of HK2, GADPH, CS1, ACO2, FH and MDH2 caused also a substantial impairment in DNA synthesis efficiency.  ...  Therefore, we asked if silencing of genes coding for glycolytic and/or Krebs cycle enzymes may affect the control of DNA replication in normal human fibroblasts.  ...  Decreased levels of expression of HK2, GADPH, CS1, ACO2, FH and MDH2 caused also a substantial impairment in DNA synthesis efficiency.  ... 
doi:10.1186/s12860-015-0062-8 pmid:26017754 pmcid:PMC4446904 fatcat:gtllxnyfgvfmtofdg35vcjlt7q

Methylation of single sites within the herpes simplex virus tk coding region and the simian virus 40 T-antigen intron causes gene inactivation

A Graessmann, G Sandberg, E Guhl, M Graessmann
1994 Molecular and Cellular Biology  
Using the HindIII-SphI HSV tk DNA fragment as a primer for in vitro DNA synthesis, all cytosine residues within the coding region, from +499 to +1309, were selectively methylated.  ...  We also methylated single HpaII sites within the HSV tk gene using a specific methylated primer for in vitro DNA synthesis.  ...  For DNA synthesis, 6 U of the Klenow fragment of E. coli polymerase (BRL) was used for 2 jig of DNA.  ... 
doi:10.1128/mcb.14.3.2004 pmid:7509450 pmcid:PMC358560 fatcat:4flrkitwmvbbzjacblidbedzzq

Mechanistic and Kinetic Differences between Reverse Transcriptases of Vpx Coding and Non-coding Lentiviruses

Gina M. Lenzi, Robert A. Domaoal, Dong-Hyun Kim, Raymond F. Schinazi, Baek Kim
2015 Journal of Biological Chemistry  
When we employed viral RNA templates that induce RT pausing by their secondary structures, the HIV-1 RTs showed more efficient DNA synthesis through pause sites than the HIV-2/SIV RTs, particularly at  ...  Here, we conducted the presteady-state kinetic analysis of reverse transcriptases (RTs) from two Vpx non-coding and two Vpx coding lentiviruses.  ...  Tatsuya Maehigashi for assistance with protein and RNA purification as well as comments on the paper. Additionally, we thank Russell Goetze for input on the manuscript.  ... 
doi:10.1074/jbc.m115.691576 pmid:26483545 pmcid:PMC4705996 fatcat:3ctiqov66rhnrbdlx5ucl6plu4

Mechanisms of synthesis of virion proteins from the functionally bigenic late mRNAs of simian virus 40

S A Sedman, J E Mertz
1988 Journal of Virology  
to that observed for VP3 in cells transfected with wild-type SV40 DNA.  ...  A leaky scanning model for the synthesis of VP3 was tested by the insertion of a strong initiation signal (CCAACATGG) upstream of the VP3-coding sequences.  ...  We also thank Gregory Gelembiuk and Robert Wisecup for technical assistance; Peter Good and Marilyn Kozak for discussions; and Jeff Ross, Roland Rueckert, Bill Sugden, Howard Temin, and Michael Young for  ... 
doi:10.1128/jvi.62.3.954-961.1988 fatcat:ae3ndou6x5ghpc7wt3owcpymla

Mechanisms of synthesis of virion proteins from the functionally bigenic late mRNAs of simian virus 40

S A Sedman, J E Mertz
1988 Journal of Virology  
to that observed for VP3 in cells transfected with wild-type SV40 DNA.  ...  A leaky scanning model for the synthesis of VP3 was tested by the insertion of a strong initiation signal (CCAACATGG) upstream of the VP3-coding sequences.  ...  We also thank Gregory Gelembiuk and Robert Wisecup for technical assistance; Peter Good and Marilyn Kozak for discussions; and Jeff Ross, Roland Rueckert, Bill Sugden, Howard Temin, and Michael Young for  ... 
pmid:2828690 pmcid:PMC253654 fatcat:qclgp4bfsvbrxajkpanx7xcuqa

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Li-Fu Song, Zheng-Hua Deng, Zi-Yi Gong, Lu-Lu Li, Bing-Zhi Li
2021 Frontiers in Bioengineering and Biotechnology  
Among them, de novo genome synthesis and DNA data storage are striking.  ...  Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.  ...  FUNDING We gratefully acknowledge the financial support from the National Key Research and Development Program of China (2018YFA0900100) and the Tianjin Fund for Distinguished Young Scholars (19JCJQJC63300  ... 
doi:10.3389/fbioe.2021.689797 fatcat:s6366gromfb2viwrtdouwvpyui

Molecular Chipper: Functional Mapping of the Non-Coding Genome with CRISPR

Jijun Cheng, Wen Pan, Christine Roden
2016 Journal of Next Generation Sequencing & Applications  
The functions of the vast majority of non-coding sequences, transcribed or non-transcribed, remain largely unknown.  ...  While these genome-scale biochemical data pave the way for deciphering the noncoding genome, high-throughput mapping technologies are required to assign functional roles to specific noncoding elements.  ...  Conventional array synthesis methods can generate coding sgRNA libraries (A) and tiling non-coding sgRNA libraries (B) Molecular Chipper method can generate near base-resolution tiling non-coding sgRNA  ... 
doi:10.4172/2469-9853.1000132 fatcat:uykfisokc5gttpeymoar4nign4

Uncertainties in synthetic DNA-based data storage

Chengtao Xu, Chao Zhao, Biao Ma, Hong Liu
2021 Nucleic Acids Research  
However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical  ...  Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties  ...  The choices of encoding framework and the ECC should be systematically considered for optimal error tolerance and coding efficiency.  ... 
doi:10.1093/nar/gkab230 pmid:33836076 fatcat:vy2anebyynb4llbqrchlynd46i
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