Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities
Open accessAbstract
Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications. Among them, de novo genome synthesis and DNA data storage are striking. However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements, which is a challenge to be met by the phosphoramidite chemistry. Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge. In this review, we first summarize the status of large-scale oligonucleotide synthesis technologies including the basic methodology and large-scale synthesis approaches, with special focus on the emerging enzymatic methods. Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.
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TL;DR
This review summarizes large-scale de novo oligonucleotide synthesis, contrasting phosphoramidite chemistry with emerging enzymatic methods and discussing applications in whole-genome synthesis and DNA data storage. It argues that enzymatic synthesis and automation integration could enable cheaper, faster, longer, higher-throughput oligo synthesis, but current enzymatic methods remain proof-of-concept with lower stepwise yields and shorter lengths than phosphoramidite chemistry.
Key findings
- Phosphoramidite chemistry dominates commercial synthesis: column-based synthesis produces 100 nt at $0.05–$0.15 per nt with an error rate of 1/600 or less, while microchip-based synthesis costs $0.00001–0.001 per nt, 2–4 orders of magnitude cheaper; oligo length is generally limited to within 200 nt and cannot exceed 300 nt theoretically.
- Reported enzymatic methods have faster coupling but lower performance than phosphoramidite chemistry: TdT–dNTP conjugates show 10–20 s coupling, 97.7% stepwise yield, and 10-mer max length; transient hybridization shows ~1 min coupling, 98.4% stepwise yield, and 20-mer max length; reversible terminator shows 60 min coupling, unavailable stepwise yield, and 4-mer max length; phosphoramidite chemistry shows ~4–10 min coupling, 99.5% stepwise yield, and 300-mer max length.
- DNA data storage has advanced from 0.66 MB in 2012 to 200 MB in 2018, with storage density increasing from 2.2 PB/g to 17,000 PB/g and coding efficiency from 1 to 4.29 bits per base.
- For practical DNA data storage, the paper states a 7–8 orders-of-magnitude decrease in synthesis cost is needed to outpace magnetic tape, and there is a six orders-of-magnitude gap for DNA synthesis to catch up with mainstream cloud archival storage bandwidth.
Methods
- Design: narrative mini-review of large-scale de novo oligonucleotide synthesis technologies, with special focus on emerging enzymatic methods and two applications: whole-genome synthesis and DNA data storage.
- Data/sample: peer-reviewed literature and public media reports from enzymatic synthesis start-up companies; includes a comparison table of coupling time, stepwise yield, maximal length, substrates, enzymes, and template requirements.
- Main analysis: qualitative synthesis and tabular comparison of chemical versus enzymatic oligo synthesis methods, plus discussion of historical and recent progress in genome synthesis and DNA data storage; no primary experiments are reported.
Limitations
- Stated: enzymatic oligo synthesis methods are still in their methodology developing stage; their stepwise yield and maximal length remain below the phosphoramidite method, and no microchip-based enzymatic de novo oligo synthesis has been reported in peer-reviewed articles or public media.
- Stated: some high-performance claims, such as 99.7% stepwise yield and 280-mer synthesis by DNA Script, or 300-mer synthesis with >99.9% stepwise yield by Camena, come from start-up companies in public media rather than peer-reviewed articles.
- Evident from the text: as a narrative review, it does not conduct a systematic search, meta-analysis, or independent experimental validation, and the company-reported performance figures and future projections are not verified within the paper.
Model-written summary. Check it against the paper before relying on it.
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Claims the paper makes
0 of 88 cited sources checked · 0 supported · 0 flagged
- Premisecitation
The cost per nucleotide for microchip-based oligo synthesis is between $0.00001 and 0.001.
“The cost per nucleotide is between $0.00001 and 0.001”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Kosuri and Church, 2014 source
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- Premisecitation
For construction of long DNAs, DNA assembly is required to assemble short oligos into long DNAs.
“For construction of long DNAs, DNA assembly is required to assemble the short oligos into long DNAs”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Casini et al., 2015 source
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- Premisecitation
The solid-phase phosphoramidite method has been the primary choice for most commercial oligo synthesizers in the past few decades.
“In the past few decades, the solid-phase phosphoramidite method has been the primary choice for most commercial oligo synthesizers”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Roy and Caruthers, 2013
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- cites Kosuri and Church, 2014 source
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- Premisecitation
The predominant activity of TdT is addition of deoxynucleotide triphosphates to the 3′ end of DNA.
“The predominant activity of TdT is addition of deoxynucleotide triphosphates to the 3′ end of DNA.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites Motea and Berdis, 2010
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- cites Palluk et al., 2018 source
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- Interpretationcitation
Column-based oligonucleotide synthesis cannot satisfy the requirements of large-scale DNA synthesis in the era of synthetic biology, due to limitations of low throughput and high cost.
“However, column-based oligonucleotide synthesis cannot satisfy the requirements of large-scale DNA synthesis in the era of synthetic biology, due to the limitations of low throughput and high cost”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Ma et al., 2012
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- Interpretationreasoning
The phosphoramidite chemistry faces a challenge in meeting the required improvements in synthesis length, speed, cost, and throughput.
“which is a challenge to be met by the phosphoramidite chemistry”
Quote in the paperSubstantial claim - Premisecitation
No concrete method using TdT for enzymatic oligo synthesis was established until 2017.
“Although the natural features of TdT are favorable for the implementation of the enzymatic oligo synthesis method, no concrete method using TdT was established until 2017”
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- Premisecitation
Enzymatic oligo synthesis can start from natural DNA (i.e., DNA without protecting groups).
“Synthesis can start from natural DNA (i.e., DNA without protecting groups)”
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Recently emerged enzymatic methods provide a competitive route to overcome the challenge of improving large-scale oligonucleotide synthesis.
“Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge.”
Quote in the paperNot a substantial claim - Premisecitation
The costs of microchip-based oligo synthesis are 2-4 orders of magnitude cheaper than column-based oligo synthesis.
“In general, the costs of microchip-based oligo synthesis are 2–4 orders of magnitude cheaper than the column-based oligo synthesis.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Kosuri and Church, 2014 source
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- Premisecitation
Mathews et al. demonstrated the feasibility of light-mediated deprotection for enzymatic oligo synthesis using TdT.
“By developing the methods for synthesis and purification of 3′-O-caged 2′-deoxyribonucleoside triphosphates, Mathews et al. (2016, 2017) demonstrated the feasibility of light-mediated deprotection for enzymatic oligo synthesis using TdT.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Mathews et al., 2016, 2017
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- Premisecitation
Microchip-based oligo synthesis has enabled high-fidelity synthesis of oligo pools ∼300-mer after procedure optimization.
“Although microchip-based oligo synthesis is more prone to errors due to the heterogeneity and edge effects of the microchip, it has enabled high-fidelity synthesis of oligo pools ∼300-mer after procedure optimization”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Ma et al., 2012
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- cites Kosuri and Church, 2014 source
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- Premisecitation
Protein engineering (such as directed evolution or rational protein design) can be used to optimize enzymatic oligo synthesis, which cannot be achieved using organic chemistry alone.
“Protein engineering (such as directed evolution or rational protein design) can be used to optimize the system, which cannot be achieved using organic chemistry alone”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
Microchip-based oligo synthesis provides an inexpensive source of oligo building blocks for various applications.
“This microchip-based (also called ‘microarray-based’) large-scale oligo synthesis technologies, provides an inexpensive source of oligo building blocks for various applications”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites Ma et al., 2012
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- cites Kosuri and Church, 2014 source
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- Interpretationcitation
The TdT and 3′-blocked dNTP method suffers from the obstacle that 3′-O-modified nucleotides cannot be efficiently incorporated by TdT because there is almost no room for 3′-OH modifications in the nucleotide position of TdT structure.
“This method suffers from the obstacle that 3′-O-modified nucleotides cannot be efficiently incorporated by TdT since there is almost no room for 3′-OH modifications in the nucleotide position of TdT structure”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Palluk et al., 2018 source
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- Premisecitation
The time and labor-intensive DNA assembly and testing process consumes a major part of the costs of whole-genome synthesis.
“Meanwhile, the time and labor-intensive DNA assembly and testing process consumes a major part of the costs”
Quote in the paperSubstantial claim0 of 3 sources checked - Premisecitation
Palluk et al. established a novel strategy using TdT-dNTP conjugates for suspending oligo elongation in each synthesis cycle.
“To overcome the limitations of TdT with 3′-blocked dNTPs, Palluk et al. (2018) established a novel strategy by using TdT–dNTP conjugates for suspending of oligo elongation in each synthesis cycle.”
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- Interpretationreasoning
Currently, enzymatic oligo synthesis methods are still in their methodology developing stage.
“Currently, enzymatic oligo synthesis methods are still in their methodology developing stage.”
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The rapid developing CRISPR/Cas9 base editing tools have promise in fixing the bugs in whole genome synthesis.
“The rapid developing CRISPR/Cas9 base editing tools, which has been widely used for correction of disease associated mutations, have promise in fixing the bugs”
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- Premisecitation
A pioneering study shows dramatically reduced cost and time required to synthesize a genome by integrating functions into one platform.
“A pioneering study toward this direction shows dramatically reduced cost and time required to synthesize a genome”
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- Premisecitation
After optimization, the coupling time of the TdT-dNTP conjugate method was around 10-20 s.
“After optimization, the coupling time of this method was around 10–20 s.”
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- Interpretationreasoning
'Bug fixation', i.e., correction of errors, is crucial for whole genome synthesis.
“It is worth to emphasize that ‘bug fixation’, i.e., correction of the errors, is crucial for whole genome synthesis.”
Quote in the paperSubstantial claim - Premisecitation
Hoff et al. achieved single-base extension using oligo that can instantaneously hybridize to adjacent strands using as few as two binding bases.
“They achieved the single-base extension using oligo that can instantaneously hybridizes to adjacent strands using as few as two binding bases.”
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- Interpretationown data
The coupling time of enzymatic oligo synthesis methods is much shorter than that of chemical methods.
“Despite preliminary results from proof-of-concept studies, the coupling time of enzymatic methods was shown to be much shorter than the chemical methods.”
Quote in the paperNot a substantial claim - Premisecitation
In early studies of de novo genome synthesis, route B (PCR amplification using primers produced by traditional column-based oligo synthesizer) was preferred.
“In early studies of de novo genome synthesis, route B is preferred”
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- cites Gibson et al., 2008, 2010
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- Premisecitation
There is a general trend that the cost and efforts required rises exponentially with the increased size of the genome to be synthesized.
“There is a general trend that the cost and efforts required rises exponentially with the increased size of the genome to be synthesized”
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Nowadays, all the techniques required to synthesize a whole-genome are already available, especially those with small genome size such as bacteria genomes.
“Nowadays, all the techniques required to synthesize a whole-genome are already available as shown in Figure 3, especially those with small genome size such as bacteria genomes.”
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Hoff et al. reported a novel enzymatic oligo synthesis method using template-dependent polymerase including DNA polymerases and reverse transcriptase.
“Until very recently, Hoff et al. (2019) reported a novel enzymatic oligo synthesis method using template-dependent polymerase including DNA polymerases and reverse transcriptase.”
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- Premisecitation
Due to the low efficiency of in vitro assembly of long DNA fragments, in vivo assembly is the general choice in most previous studies.
“Due to the low efficiency of in vitro assembly of long DNA fragments, in vivo assembly is the general choice in most previous studies”
Quote in the paperNot a substantial claim0 of 3 sources checked - Premisecitation
The storage density of DNA data storage increased from 2.2 PB/g to 17,000 PB/g.
“The storage density has increased from 2.2 PB/g (petabytes per gram DNA) to 17,000 PB/g (Erlich and Zielinski, 2017; Organick et al., 2020).”
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Storing data-encoding DNA strands in silica beads achieved reliable DNA data storage estimated to be stable for more than 2000 years.
“In 2015, by storing data-encoding DNA strands in silica beads, Grass et al. (2015) achieved reliable data storage in DNA, which was estimated be stable for more than 2000 years.”
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- Premisecitation
The coding efficiency of DNA data storage increased from 1 to 4.29 bits per base.
“The coding efficiency has increased from 1 to 4.29 bits per base (Anavy et al., 2019).”
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- Premisecitation
A random access approach was constructed that can work on large data sets of more than 200M.
“Organick et al. (2018) constructed a random access approach which can work on large data sets of more than 200M.”
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- Premisecitation
A DNA-based storage architecture enabling random access of data blocks was established for the first time.
“Also in 2015, Yazdi et al. (2015) established a DNA-based storage architecture that enables random access of data blocks for the first time.”
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An in vivo coding system enabling ultra-long-term short message storage in the DNA of living cells was established.
“Song and Zeng (2018) established an in vivo coding system which enables ultra-long-term short message storage in the DNA of living cells.”
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- Premisecitation
The data scale of DNA data storage increased from 0.66 MB in 2012 to 200 MB in 2018.
“The data scale has increased from the 0.66 MB (megabytes) in 2012 to 200 MB in 2018 (Church et al., 2012; Organick et al., 2018).”
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A base-3 Huffman code system developed by researchers at the European Bioinformatics Institute significantly increased the scale, density, and reliability of data storage in DNA.
“researchers of European Bioinformatics Institute developed a base-3 Huffman code system that significantly increased the scale, density, and reliability of data storage in DNA (Goldman et al., 2013).”
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- Premisecitation
Applying a Nanopore sequencer for reading DNA-encoded data proved the concept of portable DNA data storage.
“The next year (2016), Tabatabaei Yazdi et al. (2016) applied Nanopore sequencer for reading of DNA encoded data and considering its low-cost and pocket-size advantages, proving the concept of portable DNA data storage.”
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- Interpretationreasoning
DNA data storage requires much lower accuracy of synthesized DNA strands than life science because error-correcting codes can be incorporated.
“Unlike life science, with the incorporation of error-correcting codes, DNA data storage requires much lower accuracy of synthesized DNA strands.”
Quote in the paperSubstantial claim- Rests on an assumption: Error-correcting codes can correct errors that emerge in DNA data storage.
- Premisecitation
Assembling a large oligo pool into vector plasmids based on homology and introducing them into bacterial cells for mixed culture achieved high-fidelity replication of DNA molecules at low cost.
“Hao et al. (2020) assembled a large oligo pool into vector plasmids based on homology and introduced them into bacterial cells for mixed culture, then combining the advantages of in vivo cell systems and in vitro data storage mediated by oligo pools to achieve high-fidelity replication of DNA molecules at low cost.”
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- Interpretationreasoning
There is a trade-off between accuracy and cost-throughput.
“Thus, there is a trade-off between the accuracy and the cost-throughput.”
Quote in the paperSubstantial claim - Interpretationnone given
Bandwidth (throughput of data writing and reading) is another obstacle to current DNA data storage technology.
“And, another obstacle to current data storage technology is bandwidth (throughput of data writing and reading).”
Quote in the paperSubstantial claim - Premisecitation
Smaller spot size can save reagent consumption proportionally.
“The smaller spot size can also save the reagent consumption proportionally as discussed previously (Ceze et al., 2019).”
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- Premisecitation
TdT-based enzymatic DNA synthesis has already been applied to data storage applications.
“Indeed, two groups of Jensen et al. (2018) and Lee et al. (2018) have already applied TdT-based enzymatic DNA synthesis method to data storage applications.”
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Enzymatic DNA synthesis methods using template-independent TdT or template-dependent DNA polymerase can provide a route for development of high-throughput and low-cost oligo synthesis technology for data storage purposes.
“Otherwise, the newly emerged enzymatic DNA synthesis methods using template-independent TdT or using template-dependent DNA polymerase can provide another route for development of high-throughput and low-cost oligo synthesis technology for data storage purposes (Palluk et al., 2018; Hoff et al., 2019).”
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- cites Hoff et al., 2019
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- Interpretationreasoning
Many aspects can be optimized to reduce the cost of oligo synthesis technology for data storage purposes.
“Although the throughput and cost gap seem immense, there are many aspects that can be optimized to reduce the cost of oligo synthesis technology for data storage purposes.”
Quote in the paperSubstantial claim - Interpretationreasoning
Our capacity to write DNA sequences still lags far behind our ability to read them.
“Despite the astonishing achievements on large-scale oligo synthesis that have been made in the past decades, our capacity to write DNA sequences still lags far behind our ability to read them.”
Quote in the paperNot a substantial claim - Premisecitation
Cost, especially synthesis cost, is one of the key obstacles for practical data storage in DNA.
“While previous studies achieved substantial progress on data scale, stability, random access and copy free, etc., the cost, especially the synthesis cost, emerged as one of the key obstacles for practical data storage in DNA (Ceze et al., 2019; Ping et al., 2019).”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
The development of cheaper, longer, and higher throughput oligo synthesis technologies is necessary for DNA-based storage.
“The development of cheaper, longer, and higher throughput oligo synthesis technologies would be necessary for DNA-based storage.”
Quote in the paperSubstantial claim - Interpretationreasoning
For DNA-based data storage, the accuracy requirement is much lower compared to genome synthesis because error correction codes could be integrated to correct errors.
“Differently, for the DNA-based data storage, the accuracy requirement is much lower compared to the genome synthesis application since the error correction codes could be integrated to correct the errors that emerge.”
Quote in the paperSubstantial claim- Rests on an assumption: Error-correcting codes can correct errors that emerge in DNA data storage.
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Findingnone givenCurrently, no microchip-based enzymatic de novo oligo synthesis has been reported either in peer-reviewed articles or in public media.
“Currently, no microchip-based enzymatic de novo oligo synthesis has been reported either in peer-reviewed articles or in public media.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Premisenone givenOver the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications.
“Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone givenTo make de novo genome synthesis and DNA data storage more practical, synthesis length, speed, cost, and throughput require vast improvements.
“However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationEnzymatic oligo synthesis methods are carried out under hydrated and mild conditions, and coupled with enzyme specificity, can reduce formation of by-products and depurination of DNA and other damages, so longer oligonucleotides can be synthesized directly.
“The enzymatic synthesis reaction is carried out under hydrated and mild conditions, coupled with the specificity of the enzyme, the enzymatic synthesis can reduce the formation of by-products and the depurination of DNA and other damages, so that longer oligonucleotides can be synthesized directly”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
PremisecitationColumn-based oligo synthesis can synthesize 100 nt at cost of $0.05 to $0.15 per nt, with an error rate of 1/600 or less.
“Over the past decades, advances in materials, automation, procedure, and purification have led to the synthesis of 100 nt at cost of $0.05 to $0.15 per nt, with an error rate of 1/600 or less”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Kosuri and Church, 2014
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PremisecitationThe length of oligos synthesized by phosphoramidite chemistry-based methods is limited within 200 nucleotides in general and cannot exceed 300 nucleotides theoretically.
“Currently, the length of oligos synthesized by the phosphoramidite chemistry-based methods is limited within 200 nucleotides in general and cannot exceed 300 nucleotides theoretically”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Palluk et al., 2018 source
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PremisecitationThe TdT and 3′-blocked dNTP method has a coupling time of around 60 min and synthesized a 4 mer oligonucleotide, with stepwise yields not reported.
“The coupling time was indicated to be around 60 min and a 4 mer oligonucleotide was synthesized using this method (stepwise yields not reported)”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Mathews et al., 2016, 2017
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PremisecitationDNA has outstanding features of long-term, high-density, and low maintenance cost for data storage.
“with outstanding features of long-term, high-density, and low maintain cost”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
InterpretationreasoningThe stepwise yield and maximal length of enzymatic oligo synthesis methods are still below the phosphoramidite method.
“As preliminary results of proof-of-concept studies, the stepwise yield and maximal length of enzymatic methods are still below the phosphoramidite method.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
Interpretationnone givenThe knowledge obtained during optimization of chemical methods can be very helpful to speed up the development process of microchip-based enzymatic synthesis.
“Nevertheless, the knowledge obtained during optimization of the chemical methods can be very helpful to speed up the development process of microchip-based enzymatic synthesis.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationA 20-base oligonucleotide was successfully synthesized using the transient hybridization approach with stepwise efficiency more than 98% and coupling time around 1 min.
“A 20-base oligonucleotide was successfully synthesized utilizing this approach with stepwise efficiency more than 98% and coupling time around 1 min.”
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InterpretationcitationOwe to fast developments in large-scale oligo synthesis, route A became more advanced in terms of cost and labor intensity and has been applied widely in recent studies.
“Owe to the fast developments in large-scale oligo synthesis, route A became more advanced in terms of cost and labor intensity and has been applied widely in recent studies”
Quote in the paperNot a substantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationA complete end-to-end DNA data storage device was developed.
“Takahashi et al. (2018) developed a complete end-to-end DNA data storage device.”
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PremisecitationElectrical signals were used to regulate redox reactions in cells, causing changes in plasmid copy number, and used to control trapping frequency of different sequences by Cas proteins to achieve one-step storage of data in cells.
“Yim et al. (2021) used electrical signals to regulate redox reactions in cells, thus causing changes in plasmid copy number, and then used it to control the trapping frequency of different sequences by Cas proteins and to achieve one-step storage of data in cells.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Yim et al., 2021 source
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PremisecitationA DNA assembly strategy was established to overcome the problem in reading short DNA strands by Nanopore sequencer.
“Lopez et al. (2019) established a DNA assembly strategy to overcome the problem in reading short DNA strands by Nanopore sequencer.”
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PremisecitationA DNA-of-things storage architecture was proposed to create materials with embedded memory.
“Koch et al. (2020) proposed a DNA-of-things storage architecture to create materials with embedded memory.”
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PremisecitationA high coding efficiency of 4.29 bits per base was implemented using composite DNA letters.
“Anavy et al. (2019) implemented a high coding efficiency of 4.29 bits per base by using composite DNA letters.”
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PremisecitationDigital microfluidic was applied to automatically retrieve data from a high-density DNA data storage library.
“Newman et al. (2019) applied digital microfluidic to automatically retrieve data from high-density DNA data storage library.”
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PremisereasoningThere are three key technologies required for data storage in DNA: codec system, DNA synthesis technology, and DNA sequencing technology.
“There are three key technologies required for data storage in DNA: (A) codec system, (B) DNA synthesis technology, (C) DNA sequencing technology as shown in Figure 4.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningDNA and its derivatives have significant advantages over other types of polymers for data storage purposes, at least for now, due to the tremendous availability of enzymes that can synthesize, replicate and repair DNA molecules.
“With tremendous availability in enzymes that can synthesize, replicate and even repair DNA molecules, DNA and its derivatives have significant advantages over other types of polymers for data storage purposes, at least for now.”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationApplying fountain codes established an architecture achieving ultra-high coding efficiency and enabling PCR-based copy-free DNA data storage.
“Later in 2017, by applying fountain codes, Erlich and Zielinski (2017) established an architecture which achieves ultra-high coding efficiency (bits per base) and enables PCR-based copy free DNA data storage.”
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PremisecitationA DNA micro-disks concept was proposed for efficient management of DNA-based data storage by QR-coded micro-sized disks carrying data-encoded DNA molecules.
“Choi et al. (2020) proposed DNA micro-disks concept for the efficient management of DNA-based data storage by QR-coded micro-sized disks carrying data-encoded DNA molecules.”
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PremisecitationA unique way of using Nanopore sequencer by encoding information in different DNA hairpins instead of nucleic acid bases was developed.
“Chen K. et al. (2019) developed a unique way of using Nanopore sequencer by encoding information in different DNA hairpins instead of nucleic acid bases.”
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May combine two claims.
PremisecitationInformation was encoded in a synthetic yeast artificial chromosome with four autonomously replicating sequences and maintained good stability during yeast replication.
“Chen et al. (2021) encoded the information in a synthetic yeast artificial chromosome with four autonomously replicating sequences and maintained good stability during yeast replication.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Chen et al., 2021 source
Not checked in the free run.
May combine two claims.
InterpretationreasoningDNA is a viable and compelling alternative to traditional storage media and has the potential to solve the world crisis of digital data explosion.
“DNA is believed to be a viable and compelling alternative to traditional storage media and to be potential to solve the world crisis of digital data explosion”
Quote in the paperNot a substantial claim0 of 3 sources checkedMay combine two claims.
InterpretationreasoningMolecular data storage can distribute encoded information in a three-dimensional space, allowing it to be an ultra-high-density storage technology outpacing traditional planar media which are only two-dimensional.
“This extra dimension allows the molecular data storage to be an ultra-high-density storage technology outpacing the traditional planner media which are only two-dimensional (2D)”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites Boukis and Meier, 2018
Not checked in the free run.
- cites Martens et al., 2018 source
Not checked in the free run.
- cites Song and Zeng, 2018
Not checked in the free run.
Classified as probably not a substantial claim.
Premisenone givenDNA sequencing technology development has heavily relied on the sequencing by synthesis method, which can utilize naturally formed polymerase.
“While the rapid development of DNA sequencing technology has heavily relied on the “sequencing by synthesis” method which can utilize the power of naturally formed polymerase for sequencing purpose, the oligo synthesis is dominated by chemical synthesis method with several limitations like limited synthesis length and environmentally hazardous, etc.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationFour new synthetic nucleic acids-6-Amino-5-nitropyridin-2-one (Z), 5-Aza-7-deazaguanine (P), Isocytosine (S), and Isoguanine (B)-are reported.
“Finally, four new synthetic nucleic acids: 6-Amino-5-nitropyridin-2-one (Z), 5-Aza-7-deazaguanine (P), Isocytosine (S), and Isoguanine (B) are reported (Hoshika et al., 2019).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Hoshika et al., 2019 source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
InterpretationreasoningRemoving the capping step may increase synthesis speed, length limitation, and reduce cost in principle.
“For example, the capping step is applied to reduce the deletion errors and can be removed which may increase the synthesis speed, length limitation and reduce the cost in principle.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningWithout accordant writing and reading bandwidth, the storage capacity of DNA is not feasible and cannot be utilized to solve the world crisis of digital data explosion.
“Without an accordant writing and reading bandwidth, the storage capacity of DNA is not feasible and cannot be utilized to solve the world crisis of digital data explosion.”
Quote in the paperSubstantial claim- Rests on an assumption: There is a world crisis of digital data explosion.
May combine two claims.
Premisenone givenOligo synthesis is dominated by chemical synthesis method with limitations like limited synthesis length and environmentally hazardous.
“While the rapid development of DNA sequencing technology has heavily relied on the “sequencing by synthesis” method which can utilize the power of naturally formed polymerase for sequencing purpose, the oligo synthesis is dominated by chemical synthesis method with several limitations like limited synthesis length and environmentally hazardous, etc.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S4 (based).
Interpretationnone givenFor oligo synthesis, accuracy and cost are two contradictory factors; increasing one factor will bring down another when using the same technique.
“For oligo synthesis, accuracy and cost are two contradictory factors which means increasing one factor will bring down another one when using the same technique.”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningFor data storage purposes, dNTP reagents with 99% purity or even lower may be acceptable and may greatly reduce cost.
“For data storage purposes, the dNTP reagents with 99% purity or even lower may be acceptable which may greatly reduce the cost.”
Quote in the paperSubstantial claim- Rests on an assumption: High purity reagents are much more expensive than low purity ones.
- Rests on an assumption: State-of-the-art large-scale oligo synthesis platforms use super high purity (>99.99%) dNTP reagents.
May combine two claims.
PremisecitationTerminator-free TdT-based DNA synthesis was proved to be a superior combination with Nanopore sequencer, which is optimal for sequencing long DNA strands with high error rate.
“It is worth mentioning that, in the study by Lee et al. (2019), the terminator free TdT-based DNA synthesis was proved to be a superior combination with Nanopore sequencer which is optimal for sequencing of long DNA strands with high error rate.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Lee et al., 2019 source
Not checked in the free run.
May combine two claims.
InterpretationreasoningData storage application requires much higher throughput and lower costs.
“Instead, data storage application requires much higher throughput and lower costs.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S2 (checkable). May combine two claims.
InterpretationreasoningFor de novo whole-genome synthesis, accuracy is always the priority focus because the debugging cost is much higher than the benefits from an inaccurate synthesis process.
“For de novo whole-genome synthesis, accuracy is always the priority focus. This is because the debugging cost is much higher than the benefits that we can get from an inaccurate synthesis process.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
InterpretationreasoningThe emerging enzymatic methods uncover a route for pushing large-scale oligo synthesis technology into next-generation by harnessing the power of naturally formed polymerases.
“The emerging enzymatic methods uncovers an exciting route for pushing large-scale oligo synthesis technology into next-generation by harnessing the power of naturally formed polymerases.”
Quote in the paperSubstantial claim
The paper relies on this without support.
The cost to synthesize a whole-genome is still very high due to chemical reagent consumption during oligo synthesis, as well as sequencing validation and error correction steps during oligo assembly.
“However, the cost to synthesize a whole-genome is still very high due to the chemical reagent consumption during oligo synthesis, as well as sequencing validation and error correction steps during oligo assemble steps.”
The paper relies on this without support.
There is a world crisis of digital data explosion.
“Without an accordant writing and reading bandwidth, the storage capacity of DNA is not feasible and cannot be utilized to solve the world crisis of digital data explosion.”
The paper relies on this without support.
A 7–8 orders of magnitude decrease in synthesis cost is essential for DNA data storage to outpace magnetic tape storage.
“It was estimated that 7–8 orders magnitude decrease of the synthesis cost is essential for DNA data storage to outpace the currently used magnetic tape based on storage technology.”
The paper relies on this without support.
There is a six orders-of-magnitude gap for DNA synthesis to catch up with mainstream cloud archival storage system.
“There is a six orders-of-magnitude gap for DNA synthesis to catch up with mainstream cloud archival storage system.”
The paper relies on this without support.
State-of-the-art oligo synthesis technologies are designed for life science, where the accuracy of synthesized DNA molecules is highly desired.
“The-state-of-the-art oligo synthesis technologies are designed for life science, where the accuracy of synthesized DNA molecules is highly desired.”
The paper relies on this without support.
High purity reagents are much more expensive than low purity ones.
“High purity reagents are much more expensive than the low purity ones.”
The paper relies on this without support.
State-of-the-art large-scale oligo synthesis platforms use super high purity (>99.99%) dNTP reagents.
“The state-of-the-art large-scale oligo synthesis platforms use super high purity (>99.99%) dNTP reagents.”
The paper relies on this without support.
Magnetic tape is the currently used storage technology.
“It was estimated that 7–8 orders magnitude decrease of the synthesis cost is essential for DNA data storage to outpace the currently used magnetic tape based on storage technology.”
The paper relies on this without support.
Error-correcting codes can correct errors that emerge in DNA data storage.
“with the incorporation of error-correcting codes, DNA data storage requires much lower accuracy of synthesized DNA strands”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Microarrays have enabled high-fidelity synthesis of oligo pools of about 300 nucleotides in length.
“Microarrays have enabled the high-fidelity synthesis of oligo pools of about 300 nucleotides in length [30].”
From DNA Data Storage. (2023) · cites this paper as [30]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Not all enzymatic methods have shorter coupling times
MinorThe table lists a 60-minute coupling time for the enzymatic reversible-terminator method, compared with approximately 4-10 minutes for phosphoramidite chemistry. Thus the stated comparison does not hold for all the enzymatic methods presented.
“the coupling time of enzymatic methods was shown to be much shorter than the chemical methods.”
“| Reversible terminator | 60 min | Not available | 4 mer | Purified 3′-blocked dNTP | TdT | No | | TdT-dNTP conjugator | 10∼20 s | 97.7% | 10 mer | Purified TdT-dNTP complex | TdT | No | | Transient hybridization | 1 min | 98.4% | 20 mer | Purified 3′-blocked dNTP | Template dependent DNA polymerase | Yes | | Phosphoramidite chemistry | ∼4∼10 min | 99.5% | 300 mer | Purified 5′-blocked dNTP | NA | NA |”
Protecting-group claim conflicts with described enzymatic methods
MinorThe conclusion lists no requirement for protecting groups as an advantage of enzymatic methods, yet the paper describes enzymatic synthesis cycles that require 3′-blocking groups and a deprotection step.
“Given that the numerous advances of mild conditions, no generation of hazardous waste, no requirements of protecting groups, etc., we believe that the further optimization of enzymatic methods and its microchip-based parallelization will potentially drive the large-scale oligo synthesis technology into next-generation”
“Step 2 – Deprotection: the 3′-blocking groups of surface-bound oligonucleotide is removed for next base extension;”
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- Authors
- Song, L.-F., Deng, Z.-H., Gong, Z.-Y., Li, L.-L., & Li, B.-Z.
- Affiliations
- Tianjin University (CN)
- ORCID
- Gong, Zi-Yi
- Venue
- Frontiers in Bioengineering and Biotechnology
- Publisher
- Frontiers Media SA
- Published
- 2021-06-22
- Volume
- 9
- Pages
- 689797-689797
- ISSN
- 2296-4185 (ISSN-L)
- PMC
- PMC8258115
- OpenAlex
- W3177141277
- Semantic Scholar
- 4e58100b319d74f97ed550a4e5fa32dea8c06fe1
- Cited by
- 74
- References
- 86
- Citations by year
- 2026: 15 · 2025: 19 · 2024: 8 · 2023: 19 · 2022: 11 · 2021: 1 · 2020: 1
- FWCI
- 1.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Bioengineering and Biotechnology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Key Research and Development Program of China (2018YFA0900100)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- phosphoramidite chemistry, enzymatic oligonucleotide synthesis, DNA data storage
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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