Random access DNA memory using Boolean search in an archival file storage system
Open accessPublished version of a preprint
Abstract
DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets. Silica beads encapsulating DNA information and functionalized with DNA labels create an alternative DNA data storage system, where direct random access and data retrieval are enabled by complementary fluorescent strands that identify beads for separation in fluorescence-activated sorting.
AI snapshot
Written from the paper’s full text.
TL;DR
The paper demonstrates a random-access DNA archival file system that encapsulates DNA-encoded image files in silica capsules surface-labeled with ssDNA barcodes, enabling Boolean search and fluorescence-activated sorting without PCR amplification. It retrieves files from a 20-image proof-of-concept database with selection sensitivity of 1 in 10^6 files per channel and shows AND/OR/NOT queries.
Key findings
- Encapsulated 20 image files, each ~0.1 kB encoded in a 3,000-base-pair plasmid, within 6-µm silica particles labeled with up to three 25-mer ssDNA barcodes chosen from 240,000 orthogonal primers, allowing up to ~10^15 possible distinct files using three barcodes per file.
- Demonstrated direct random access by fluorescence-activated sorting without amplification: single-file selection sensitivity of 1 in 10^6 files, scaling to 1 in 10^6N with N optical channels; 60–95% of Airplane files sorted into the flying gate.
- Implemented Boolean AND, OR, and NOT queries, including president AND (NOT 18th century) and dog AND wild, with sequencing validation; selected single files could be transformed, amplified, and re-encapsulated for a write-store-access-read cycle.
- Estimated 10^6 plasmids per capsule and 10^8 barcodes per file; the data pool contained at least ~10^6 copies of each file; proof-of-concept search rate was ~1 kB per second, with a theoretical ~1 GB per second if data per capsule were increased, or ~15 days to search 1 PB.
Methods
- Proof-of-principle file system: 20 26 × 26-pixel black-and-white icon images were run-length encoded, converted to DNA, cloned into pUC19-based plasmids, amplified in bacteria, and validated by sequencing.
- Encapsulation and barcoding: plasmid DNA was condensed on fluorescein-core 5-µm silica particles, encapsulated with TMAPS/TEOS, surface-functionalized, and conjugated to 25-mer ssDNA barcodes representing metadata; files were pooled at ~2.0 mg/mL in 10 mL saline TAE buffer.
- Selection and readout: fluorescently labeled complementary probes hybridized to barcodes; FAS was performed on a BD FACSAria III with sorting gates; DNA was released using buffered oxide etch and sequenced with Illumina MiniSeq/MiSeq; sort probability/enrichment was calculated as the count for a file in a fraction divided by the sum of counts for that file across all fractions.
Limitations
- Stated: silica encapsulation lowers overall data storage density compared with bare DNA memory; encapsulation and barcoding latency is currently days and may limit archival use unless reduced to hours or less; FAS retrieval scales linearly with pool size, with proof-of-concept sorting rate ~1 kB per second; unprotected DNA barcodes and linkers are susceptible to hydrolysis and require periodic renewal or protection; sort probabilities were typically below 100%, with possible contamination or random FAS errors, though repeated selection cycles may mitigate this.
- Evident from the text: the demonstration is limited to 20 icon-resolution 26 × 26 black-and-white images and a small proof-of-concept pool, not exabyte- or yottabyte-scale storage; scalability depends on high-throughput silica encapsulation and surface DNA labeling that were not demonstrated here.
Model-written summary. Check it against the paper before relying on it.
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Cites
Statistics
Claims the paper makes
0 of 60 cited sources checked · 0 supported · 0 flagged
- Findingown data
The authors demonstrate Boolean AND, OR, NOT logic to select arbitrary subsets of files with combinations of distinct barcodes to query the data pool.
“We also demonstrate Boolean AND, OR, NOT logic to select arbitrary subsets of files with combinations of distinct barcodes to query the data pool, similar to conventional Boolean logic applied in text and file searches on solid-state silicon devices.”
Quote in the paperSubstantial claim - Findingown data
Using hybridization assays with fluorescently-labelled probes, the authors estimated the number of barcodes available for hybridization on each file to be on the order of 10^8.
“Using hybridization assays with fluorescently-labelled probes35–37, we estimated the number of barcodes available for hybridization on each file to be on the order of 108 (Supplementary Fig. 7).”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [35] Pillai, P. P., Reisewitz, S., Schroeder, H. & Niemeyer, C. M. Quantum-dot-encoded silica nanospheres for nucleic acid hybridization. Small 6, 2130–2134 (2010). source
Not checked in the free run.
- cites [36] Leidner, A. et al. Biopebbles: DNA-functionalized core–shell silica nanospheres for cellular uptake and cell guidance studies. Adv. Funct. Mater. 28, 1707572 (2018). source
Not checked in the free run.
- cites [37] Sun, P. et al. Biopebble containers: DNA-directed surface assembly of mesoporous silica nanoparticles for cell studies. Small 15, 1900083 (2019). source
Not checked in the free run.
- Findingown data
qPCR of the reaction supernatant after encapsulation showed full encapsulation of plasmids without residual DNA in solution.
“Quantitative PCR (qPCR) of the reaction supernatant after encapsulation (Supplementary Fig. 4) showed full encapsulation of plasmids without residual DNA in solution.”
Quote in the paperSubstantial claim - Findingown data
The authors were able to detect and select the desired Airplane file through FAS even at a relative abundance of 10^-6 compared with each other file.
“We were able to detect and select the desired Airplane file through FAS even at a relative abundance of 10−6 compared with each other file (Fig. 3c).”
Quote in the paperSubstantial claim - Findingown data
The sizes of bare, hydroxy-terminated silica particles representing capsules without barcodes were comparable with complete files consisting of capsules with barcodes attached, confirmed using scanning electron microscopy.
“Notably, the sizes of bare, hydroxy-terminated silica particles representing capsules without barcodes were comparable with complete files consisting of capsules with barcodes attached, confirmed using scanning electron microscopy (Fig. 2d and 2e, left).”
Quote in the paperNot a substantial claim
- Findingown data
Using qPCR to measure released DNA after de-encapsulation, the authors estimated 10^6 plasmids per capsule.
“Using qPCR to measure released DNA after de-encapsulation, we estimated 106 plasmids per capsule (Supplementary Fig. 5 and Supplementary Table 3).”
Quote in the paperNot a substantial claim - Findingown data
The data pool contains at least ~10^6 copies of each file based on the mass of silica used during encapsulation.
“The data pool contains at least ~106 copies of each file based on the mass of silica used during encapsulation (Supplementary Section 5).”
Quote in the paperNot a substantial claim - Findingown data
In cases where single images were selected, the authors were able to transform competent bacteria from each search query that resulted in a single file.
“In cases where single images were selected (Figs. 4c, 5a), we were able to transform competent bacteria from each search query that resulted in a single file (Supplementary Fig. 27).”
Quote in the paperSubstantial claim - Findingown data
Release of the encapsulated file sequence and subsequent sequencing of each gated population from the dog versus wild 2D plot validated sorting.
“Release of the encapsulated file sequence and subsequent sequencing of each gated population from the dog versus wild 2D plot validated sorting (Fig. 5b, right; Supplementary Fig. 26).”
Quote in the paperSubstantial claim - Findingnone given
The authors introduced a direct random access molecular file system for the retrieval of arbitrary files and file-subsets from an archival DNA data store.
“We introduced a direct random access molecular file system for the retrieval of arbitrary files and file-subsets from an archival DNA data store.”
Quote in the paperSubstantial claim - Findingown data
The simultaneous addition of the 18th century ssDNA probe, fluorescently labeled with AFDye 647, discriminated Washington, which contained the 18th century barcode, from the Lincoln file.
“The simultaneous addition of the 18th century ssDNA probe, fluorescently labeled with AFDye 647 (Fig. 5a, left), discriminated Washington, which contained the 18th century barcode, from the Lincoln file (Fig. 5a, middle, Supplementary Fig. 15a).”
Quote in the paperSubstantial claim - Findingown data
The president ssDNA probe, fluorescently labeled with TAMRA, selected both Lincoln and Washington files from the data pool.
“The president ssDNA probe, fluorescently labeled with TAMRA, selected both Lincoln and Washington files from the data pool.”
Quote in the paperSubstantial claim - Findingown data
The system offers the ability to apply Boolean logic to select random file subsets from the data pool.
“Beyond direct selection of 1 in 106N individual random files, without thermal cycling or loss of fidelity due to primer crosstalk, our system offers the ability to apply Boolean logic to select random file subsets from the data pool.”
Quote in the paperSubstantial claim - Findingown data
In an OR gate, all files that showed TAMRA signal were sorted into the dog OR building subset by the FAS.
“An example of an OR gate was applied to the data pool by simultaneously adding dog and building probes that both had the TAMRA label (Fig. 4b, Supplementary Fig. 14b). All files that showed TAMRA signal were sorted into the dog OR building subset by the FAS.”
Quote in the paperSubstantial claim - Findingown data
In an AND gate, files showing signal for both AFDye 647 and TAMRA were sorted into the fruit AND yellow subset in the FAS.
“Finally, an example of an AND gate was achieved by adding fruit and yellow probes that were labelled with AFDye 647 and TAMRA, respectively. Files showing signal for both AFDye 647 and TAMRA were sorted into the fruit AND yellow subset in the FAS (Fig. 4c, Supplementary Fig. 14c).”
Quote in the paperSubstantial claim - Findingreasoning
The combination of the president and 18th century probes permitted the complex search query president AND (NOT 18th century).
“The combination of these two ssDNA probes permitted the complex search query president AND (NOT 18th century).”
Quote in the paperSubstantial claim - Findingown data
Sequencing analysis of the gated populations after reverse encapsulation validated that the sorted populations matched search queries for president AND (NOT 18th century), president AND 18th century, and NOT president.
“Sequencing analysis of the gated populations after reverse encapsulation validated that the sorted populations matched search queries for president AND (NOT 18th century), president AND 18th century, and NOT president (Fig. 5a, right; Supplementary Fig. 25).”
Quote in the paperSubstantial claim - Premisecitation
The barcode library allows for individual selection of up to ~10^15 possible distinct files using only three unique barcodes per file.
“which allows for individual selection of up to ~1015 possible distinct files using only three unique barcodes per file20”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [20] Xu, Q., Schlabach, M. R., Hannon, G. J. & Elledge, S. J. Design of 240,000 orthogonal 25mer DNA barcode probes. Proc. Natl Acad. Sci. USA 106, 2289–2294 (2009). source
Not checked in the free run.
- Premisecitation
Each PCR amplification may introduce stochastic variation in copy number of the file sequences, leading to up to 2% data loss per amplification if using ten-fold physical redundancy.
“In this case, each PCR amplification may introduce stochastic variation in copy number of the file sequences, leading to up to 2% data loss per amplification19 if using ten-fold physical redundancy, as recently suggested18.”
Quote in the paperSubstantial claim0 of 2 sources checked - Interpretationreasoning
Any sort probability above 50% indicates enrichment of Airplane within the correct population subset (flying) relative to the incorrect subset (NOT flying).
“where we note that any sort probability above 50% indicates enrichment of Airplane within the correct population subset (flying) relative to the incorrect subset (NOT flying).”
Quote in the paperNot a substantial claim - Interpretationown data
The use of plasmids as a substrate for encoding information offered the ability to restore selected files back into the data pool after retrieval.
“Our use of plasmids as a substrate for encoding information offered the ability to restore selected files back into the data pool after retrieval.”
Quote in the paperSubstantial claim - Interpretationown data
FAS can be used to create multiple gating conditions simultaneously, thereby increasing the complexity of target file selection operations.
“FAS can also be used to create multiple gating conditions simultaneously, thereby increasing the complexity of target file selection operations, as noted above.”
Quote in the paperSubstantial claim - Interpretationown data
The preceding demonstrations of Boolean logic gates enable file sorting with varying specificity of selection criteria for the retrieval of different subsets of the data pool.
“The preceding demonstrations of Boolean logic gates enable file sorting with varying specificity of selection criteria for the retrieval of different subsets of the data pool.”
Quote in the paperSubstantial claim - Interpretationreasoning
Retrieval time is currently limiting for the file system in an exabyte-scale data pool because FAS scales linearly with the size of the pool.
“Third, retrieval time is currently limiting for our system in an exabyte-scale data pool because FAS scales linearly with the size of the pool.”
Quote in the paperSubstantial claim- Rests on an assumption: FAS scales linearly with the size of the data pool.
- Interpretationreasoning
Latency associated with DNA-based barcoding of silica capsules may limit its application to archival data storage and retrieval applications for the foreseeable future.
“Second, latency associated with DNA-based barcoding of silica capsules may limit its application to archival data storage and retrieval applications for the foreseeable future.”
Quote in the paperSubstantial claim
- May combine two claims. 25
- Classified as probably not a substantial claim. 22
May combine two claims.
FindingcitationDNA-based files are encapsulated physically within discrete, impervious silica capsules, which are subsequently surface-labeled with unique single-stranded DNA barcodes that offer Boolean logic based selection on the entire data pool via simple hybridization.
“To realize this file system, we first encapsulate DNA-based files physically within discrete, impervious silica capsules9,23,24, which we subsequently surface-label with unique single-stranded DNA barcodes that offer Boolean logic based selection on the entire data pool via simple hybridization.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [9] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. & Stark, W. J. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). source
Not checked in the free run.
- cites [23] Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R. & Grass, R. N. Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA ‘fossils’. Nat. Protoc. 8, 2440–2448 (2013). source
Not checked in the free run.
- cites [24] Paunescu, D., Fuhrer, R. & Grass, R. N. Protection and deprotection of DNA—high-temperature stability of nucleic acid barcodes for polymer labeling. Angew. Chem. Int. Ed. 52, 4269–4272 (2013). source
Not checked in the free run.
May combine two claims.
Findingnone givenThe authors introduce a direct random access memory approach that retrieves specific files, or arbitrary subsets of files, directly using physical sorting, without a need for amplification, and without any potential for barcode-memory crosstalk, while preserving non-selected files intact by recycling them into the original memory pool.
“As an alternative to PCR-based approaches, here we introduce a direct random access memory approach that retrieves specific files, or arbitrary subsets of files, directly using physical sorting, without a need for amplification, and without any potential for barcode-memory crosstalk, while also preserving non-selected files intact by recycling them into the original memory pool.”
Quote in the paperNot a substantial claim- The authors state this as an assumption: DNA synthesis costs will decline sufficiently for DNA storage to meet exponentially growing worldwide demand for archival data storage.
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataSystematic shifts in the surface charge of the silica particles were observed as different functional groups were introduced onto their surfaces.
“We also observed systematic shifts in the surface charge of the silica particles as different functional groups were introduced onto their surfaces (Fig. 2e).”
Quote in the paperNot a substantial claimMay combine two claims.
Findingnone givenDigital information in the form of 20 icon-resolution images was stored in a data pool, with each image encoded into DNA and synthesized on a plasmid.
“Digital information in the form of 20 icon-resolution images was stored in a data pool, with each image encoded into DNA and synthesized on a plasmid.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataAll capsules synthesized in the presence of both DNA and TO-PRO showed a distinct fluorescence signal, consistent with the presence of plasmid DNA in the majority of capsules, compared with a silica particle negative control that contained no DNA.
“All capsules synthesized in the presence of both DNA and TO-PRO showed a distinct fluorescence signal, consistent with the presence of plasmid DNA in the majority of capsules, compared with a silica particle negative control that contained no DNA.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Findingown dataThe authors selected the Wolf file from the data pool using the query dog AND wild, and used the black & white probe to validate the selected file.
“To demonstrate the feasibility of performing Boolean search using more than three fluorescence channels for sorting, we also selected the Wolf file from the data pool using the query dog AND wild, and used the black & white probe to validate the selected file (Fig. 5b, left).”
Quote in the paperSubstantial claimMay combine two claims.
Findingnone givenThe authors' approach allows for repeated rounds of FAS selection, as well as Boolean logic.
“Besides single file selection, our approach allows for repeated rounds of FAS selection, as well as Boolean logic, described below.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Findingown dataIn a NOT query, files that did not show AFDye 647 signal were sorted into the NOT cat subset.
“To demonstrate a NOT query, we added to the data pool an AFDye 647-labelled ssDNA probe that hybridized to files that contained the cat barcode. Files that did not show AFDye 647 signal were sorted into the NOT cat subset (Fig. 4a, Supplementary Fig. 14a).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn the proof-of-concept system, data reconstruction was successful with 100 copies of a file, so that the file size of 0.1 kB and search rate of 1,000 files per second yield a final sorting rate of only ~1 kB per second.
“For example, in our proof-of-concept system, data reconstruction was successful with 100 copies of a file (Figure 3 and Supplementary Figure 13), so that our file size of 0.1 kB and search rate of 1,000 files per second yield a final sorting rate of only ~1 kB per second.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataThe internal agitator in the flow cytometer at 300 rpm was not sufficient to prevent the silica particles from sedimenting over time.
“We note that the internal agitator in the flow cytometer with a 300 rpm agitation speed was not sufficient to prevent the silica particles from sedimenting over time”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataPerforming fluorescence-activated sorting at a flow rate that exceeds 1,200 events per second intermittently clogged the FAS instrument.
“We found that performing sorting at a flow rate that exceeds this events rate clogged the FAS instrument intermittently.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataPeriodically agitating the sample tube every 5 minutes with a vortex mixer was more effective than the internal agitator at preventing silica particles from sedimenting.
“we found that periodically agitating the sample tube every 5 minutes with a vortex mixer was more effective.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationRecent progress in nucleic acid synthesis and sequencing continues to reduce the cost of writing and reading DNA, foreshadowing future commercially competitive DNA-based information storage.
“Recent progress in nucleic acid synthesis and sequencing technologies continue to reduce the cost of writing and reading DNA, foreshadowing future commercially competitive DNA-based information storage1,3–5.”
Quote in the paperNot a substantial claim0 of 4 sources checked- cites [1] Zhirnov, V., Zadegan, R. M., Sandhu, G. S., Church, G. M. & Hughes, W. L. Nucleic acid memory. Nat. Mater. 15, 366–370 (2016). source
Not checked in the free run.
- cites [3] Kosuri, S. & Church, G. M. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11, 499–507 (2014). source
Not checked in the free run.
- cites [4] Palluk, S. et al. De novo DNA synthesis using polymerase-nucleotide conjugates. Nat. Biotechnol. 36, 645–650 (2018). source
Not checked in the free run.
- cites [5] Lee, H. H., Kalhor, R., Goela, N., Bolot, J. & Church, G. M. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat. Commun. 10, 2383 (2019). source
Not checked in the free run.
May combine two claims.
PremisecitationDNA can be used for the storage of arbitrary digital information at densities far exceeding conventional data storage technologies such as flash and tape memory, at scales well beyond the capacity of the largest existing data centers.
“While DNA is the polymer selected by evolution for the storage and transmission of genetic information in biology, it can also be used for the storage of arbitrary digital information at densities far exceeding conventional data storage technologies such as flash and tape memory, at scales well beyond the capacity of the largest existing data centers1,2.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [1] Zhirnov, V., Zadegan, R. M., Sandhu, G. S., Church, G. M. & Hughes, W. L. Nucleic acid memory. Nat. Mater. 15, 366–370 (2016). source
Not checked in the free run.
- cites [2] Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. Nat. Rev. Genet. 20, 456–466 (2019). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationDemonstrations of DNA storage viability include the storage and retrieval of books, images, computer programs, audio clips, works of art, and Shakespeare's sonnets using a variety of encoding schemes, with data size limited primarily by the cost of DNA synthesis.
“Demonstrations of its viability as a general information storage medium include the storage and retrieval of books, images, computer programs, audio clips, works of art, and Shakespeare’s sonnets using a variety of encoding schemes6–12, with data size limited primarily by the cost of DNA synthesis.”
Quote in the paperNot a substantial claim0 of 7 sources checked- cites [6] Church, G. M., Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 337, 1628–1628 (2012). source
Not checked in the free run.
- cites [7] Goldman, N. et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013). source
Not checked in the free run.
- cites [8] Yazdi, S. M. H. T., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O. A rewritable, random-access DNA-based storage system. Sci. Rep. 5, 14138 (2015). source
Not checked in the free run.
- cites [9] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. & Stark, W. J. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). source
Not checked in the free run.
- cites [10] Yazdi, S. M. H. T., Gabrys, R. & Milenkovic, O. Portable and error-free DNA-based data storage. Sci. Rep. 7, 5011 (2017). source
Not checked in the free run.
- cites [11] Erlich, Y. & Zielinski, D. DNA Fountain enables a robust and efficient storage architecture. Science 355, 950–954 (2017). source
Not checked in the free run.
- cites [12] Organick, L. et al. Random access in large-scale DNA data storage. Nat. Biotechnol. 36, 242–248 (2018). source
Not checked in the free run.
Classified as probably not a substantial claim.
PremisecitationMolecular random access has largely relied on PCR, which uses up to ~20-30 heating and cooling cycles with DNA polymerase to selectively amplify specific DNA sequences from a DNA data pool using primers.
“To date, molecular random access has largely relied on conventional polymerase chain reaction (PCR)8,10,12,13, which uses up to ~20–30 heating and cooling cycles with DNA polymerase to selectively amplify specific DNA sequences from a DNA data pool using primers.”
Quote in the paperSubstantial claim0 of 4 sources checked- cites [8] Yazdi, S. M. H. T., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O. A rewritable, random-access DNA-based storage system. Sci. Rep. 5, 14138 (2015). source
Not checked in the free run.
- cites [10] Yazdi, S. M. H. T., Gabrys, R. & Milenkovic, O. Portable and error-free DNA-based data storage. Sci. Rep. 7, 5011 (2017). source
Not checked in the free run.
- cites [12] Organick, L. et al. Random access in large-scale DNA data storage. Nat. Biotechnol. 36, 242–248 (2018). source
Not checked in the free run.
- cites [13] Ranu, N., Villani, A.-C., Hacohen, N. & Blainey, P. C. Targeting individual cells by barcode in pooled sequence libraries. Nucleic Acids Res. 47, e4 (2018). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationNested addressing barcodes have been used to uniquely identify a greater number of files, and biochemical affinity tags have been used to selectively pull down oligos for targeted amplification.
“Nested addressing barcodes14–16 have also been used to uniquely identify a greater number of files, as well as biochemical affinity tags to selectively pull down oligos for targeted amplification17.”
Quote in the paperNot a substantial claim0 of 4 sources checked- cites [14] Kashiwamura, S., Yamamoto, M., Kameda, A., Shiba, T. & Ohuchi, A. Hierarchical DNA memory based on nested PCR. In 8th International Workshop on DNA-Based Computers (DNA8) (eds Hagiya, M. & Ohuchi, A.) 112–123 (Springer, 2003). source
Not checked in the free run.
- cites [15] Yamamoto, M., Kashiwamura, S., Ohuchi, A. & Furukawa, M. Large-scale DNA memory based on the nested PCR. Nat. Comput. 7, 335–346 (2008). source
Not checked in the free run.
- cites [16] Yamamoto, M., Kashiwamura, S. & Ohuchi, A. DNA memory with 16.8M addresses. In 13th International Meeting on DNA Computing (DNA13) (eds Garzon, M. H. & Yan, H.) 99–108 (Springer, 2008). source
Not checked in the free run.
- cites [17] Tomek, K. J. et al. Driving the scalability of DNA-based information storage systems. ACS Synth. Biol. 8, 1241–1248 (2019). source
Not checked in the free run.
May combine two claims.
PremisecitationFor an exabyte-scale data pool, each file requires at least three barcodes, or up to sixty nucleotides in total barcode sequence length, thereby reducing the number of nucleotides that can be used for data encoding.
“For example, for an exabyte-scale data pool, each file requires at least three barcodes17, or up to sixty nucleotides in total barcode sequence length, thereby reducing the number of nucleotides that can be used for data encoding.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [17] Tomek, K. J. et al. Driving the scalability of DNA-based information storage systems. ACS Synth. Biol. 8, 1241–1248 (2019). source
Not checked in the free run.
May combine two claims.
InterpretationreasoningBecause physical encapsulation separates file sequences from external barcodes, the file system offers long-term environmental protection of encoded file sequences via silica encapsulation for permanent archival storage, where external barcodes may be renewed periodically, further protected with secondary encapsulation, or data pools may be stored using methods implemented in PCR-based random
“Because physical encapsulation separates file sequences from external barcodes that are used to describe the encapsulated information, our file system offers long-term environmental protection of encoded file sequences via silica encapsulation for permanent archival storage9,23,24, where external barcodes may be renewed periodically, further protected with secondary encapsulation, or data pools”
Quote in the paperSubstantial claim0 of 4 sources checked- cites [9] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. & Stark, W. J. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). source
Not checked in the free run.
- cites [23] Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R. & Grass, R. N. Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA ‘fossils’. Nat. Protoc. 8, 2440–2448 (2013). source
Not checked in the free run.
- cites [24] Paunescu, D., Fuhrer, R. & Grass, R. N. Protection and deprotection of DNA—high-temperature stability of nucleic acid barcodes for polymer labeling. Angew. Chem. Int. Ed. 52, 4269–4272 (2013). source
Not checked in the free run.
- cites [21] Newman, S. et al. High density DNA data storage library via dehydration with digital microfluidic retrieval. Nat. Commun. 10, 1706 (2019). source
Not checked in the free run.
May combine two claims.
Premisenone givenPCR-based retrieval requires an aliquot of the entire data pool to be irreversibly consumed for random access, and therefore additional PCR amplification of the entire data pool may periodically be needed to restore this loss of data.
“Second, PCR-based retrieval requires an aliquot of the entire data pool to be irreversibly consumed for random access, and therefore additional PCR amplification of the entire data pool may periodically be needed to restore this loss of data.”
Quote in the paperSubstantial claimMay combine two claims.
Premisenone givenStrategies to circumvent PCR limitations generally reduce data density and might not be easily scalable to exabyte and larger file-systems.
“While strategies exist to circumvent these preceding challenges, they generally reduce data density and might not be easily scalable to exabyte and larger file-systems.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAvoiding spurious amplification of off-target files due to crosstalk of PCR primers with incorrect barcodes or main file sequences requires careful primer design.
“Finally, avoiding spurious amplification of off-target files due to crosstalk of PCR primers with incorrect barcodes or main file sequences requires careful primer design20.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [20] Xu, Q., Schlabach, M. R., Hannon, G. J. & Elledge, S. J. Design of 240,000 orthogonal 25mer DNA barcode probes. Proc. Natl Acad. Sci. USA 106, 2289–2294 (2009). source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningThe file system may in principle be scaled to considerably larger sets of images, limited primarily by the cost of DNA synthesis and the need to develop strategies for high-throughput silica encapsulation of distinct file sequences and surface-based DNA labeling for barcoding.
“While only twenty icon-resolution images were chosen as our image database, representing diverse subject matter including animals, plants, transportation, and buildings (Supplementary Fig. 1), our file system may in principle be scaled to considerably larger sets of images, limited primarily by the cost of DNA synthesis and the need to develop strategies for high-throughput silica encapsulation of”
Quote in the paperNot a substantial claim- The authors state this as an assumption: DNA synthesis costs will decline sufficiently for DNA storage to meet exponentially growing worldwide demand for archival data storage.
May combine two claims.
Interpretationown dataUnlike PCR that requires 20-30 rounds of heating and cooling to selectively amplify the selected sequence, the authors' approach selects files directly without need for thermal cycling and amplification.
“While comparable in sensitivity to a nested PCR barcoding data indexing approach17, unlike PCR that requires 20–30 of rounds of heating and cooling to selectively amplify the selected sequence, our approach selects files directly without need for thermal cycling and amplification.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [17] Tomek, K. J. et al. Driving the scalability of DNA-based information storage systems. ACS Synth. Biol. 8, 1241–1248 (2019). source
Not checked in the free run.
May combine two claims.
InterpretationreasoningBecause encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, the approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, and is compatible with alternative DNA file compositions such as 100-200-mer oligonucleotides or multiple layers of encapsulated
“Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, our approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes, as demonstrated previously23, and is compatible with alternative DNA file compositions such as 100–200-mer oligonucleotides that”
Quote in the paperNot a substantial claim0 of 8 sources checked- cites [23] Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R. & Grass, R. N. Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA ‘fossils’. Nat. Protoc. 8, 2440–2448 (2013). source
Not checked in the free run.
- cites [2] Ceze, L., Nivala, J. & Strauss, K. Molecular digital data storage using DNA. Nat. Rev. Genet. 20, 456–466 (2019). source
Not checked in the free run.
- cites [6] Church, G. M., Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 337, 1628–1628 (2012). source
Not checked in the free run.
- cites [7] Goldman, N. et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013). source
Not checked in the free run.
- cites [11] Erlich, Y. & Zielinski, D. DNA Fountain enables a robust and efficient storage architecture. Science 355, 950–954 (2017). source
Not checked in the free run.
- cites [12] Organick, L. et al. Random access in large-scale DNA data storage. Nat. Biotechnol. 36, 242–248 (2018). source
Not checked in the free run.
- cites [17] Tomek, K. J. et al. Driving the scalability of DNA-based information storage systems. ACS Synth. Biol. 8, 1241–1248 (2019). source
Not checked in the free run.
- cites [34] Chen, W. D. et al. Combining data longevity with high storage capacity—layer-by-layer DNA encapsulated in magnetic nanoparticles. Adv. Funct. Mater. 29, 1901672 (2019). source
Not checked in the free run.
- Rests on an assumption: Encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA.
May combine two claims.
InterpretationcitationGating of N barcodes simultaneously in parallel optical channels offers file selection sensitivity of 1 in 10^6N total files, where common commercial FAS systems offer up to N = 17 channels.
“This strategy also applies to gating of N barcodes simultaneously in parallel optical channels, which offers file selection sensitivity of 1 in 106N total files, where common commercial FAS systems offer up to N = 17 channels38,39.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [38] Perfetto, S. P., Chattopadhyay, P. K. & Roederer, M. Seventeen-colour flow cytometry: unravelling the immune system. Nat. Rev. Immunol. 4, 648–655 (2004). source
Not checked in the free run.
- cites [39] Chattopadhyay, P. K. et al. Quantum dot semiconductor nanocrystals for immunophenotyping by polychromatic flow cytometry. Nat. Med. 12, 972–977 (2006). source
Not checked in the free run.
May combine two claims.
Interpretationown dataAmplified material was pure and ready for re-encapsulation into silica particles, which could be re-introduced directly back into the data pool and thereby represents a complete write-store-access-read cycle that in principle may be applied to larger-scale datasets, with periodic renewal of single-stranded DNA barcodes and bacterial replication of DNA data following reading.
“Amplified material was pure and ready for re-encapsulation into silica particles, which could be re-introduced directly back into the data pool and thereby represents a complete write-store-access-read cycle that in principle may be applied larger-scale datasets, with periodic renewal of single-stranded DNA barcodes and bacterial replication of DNA data following reading25–27.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [25] Farzadfard, F. et al. Single-nucleotide-resolution computing and memory in living cells. Mol. Cell 75, 769–780.E4 (2019). source
Not checked in the free run.
- cites [26] Farzadfard, F. & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 1256272 (2014). source
Not checked in the free run.
- cites [27] Farzadfard, F. & Lu, T. K. Emerging applications for DNA writers and molecular recorders. Science 361, 870–875 (2018). source
Not checked in the free run.
May combine two claims.
InterpretationreasoningIn a practical implementation of the file system, only the selected files must be restored via amplification, encapsulation, and barcoding, because files that are not selected can be returned to the data pool immediately following FAS.
“Notably, in a practical implementation of our file system, only the selected files must be restored via amplification, encapsulation, and barcoding, because files that are not selected can be returned to the data pool immediately following FAS.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationcitationThe file system overcomes several challenges associated with pre-existing PCR-based file systems, including obviating the need for numerous heating and cooling cycles and enzymatic synthesis, and eliminating non-specific crosstalk between file sequences and barcodes, while enabling arbitrary Boolean logical search queries.
“Our file system overcomes several challenges associated with pre-existing PCR-based file systems, including obviating the need for numerous heating and cooling cycles and enzymatic synthesis, and eliminating non-specific crosstalk between file sequences and barcodes17,19,21, while enabling arbitrary Boolean logical search queries.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [17] Tomek, K. J. et al. Driving the scalability of DNA-based information storage systems. ACS Synth. Biol. 8, 1241–1248 (2019). source
Not checked in the free run.
- cites [19] Chen, Y.-J. et al. Quantifying molecular bias in DNA data storage. Nat. Commun. 11, 3264 (2020). source
Not checked in the free run.
- cites [21] Newman, S. et al. High density DNA data storage library via dehydration with digital microfluidic retrieval. Nat. Commun. 10, 1706 (2019). source
Not checked in the free run.
May combine two claims.
Interpretationown dataWhile the file system supports theoretical storage densities orders of magnitude higher than archival file storage systems based on hard disk, magnetic tape, or similar archival media, silica encapsulation of DNA file sequences lowers overall data storage density compared with bare DNA memory.
“First, while our file system supports theoretical storage densities that are orders of magnitude higher than archival file storage systems based on hard disk, magnetic tape, or similar archival media1,40 commonly used today, silica encapsulation of DNA file sequences lowers overall data storage density compared with bare DNA memory (Supplementary Section 6).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [1] Zhirnov, V., Zadegan, R. M., Sandhu, G. S., Church, G. M. & Hughes, W. L. Nucleic acid memory. Nat. Mater. 15, 366–370 (2016). source
Not checked in the free run.
- cites [40] Fontana, R. E.Jr & Decad, G. M. Moore’s law realities for recording systems and memory storage components: HDD, tape, NAND, and optical. AIP Adv. 8, 056506 (2018). source
Not checked in the free run.
May combine two claims.
InterpretationreasoningBecause the proof-of-concept system did not make use of the vast majority of DNA stored in each capsule, the data stored in each capsule can in theory be significantly increased to yield a search rate of ~1 GB per second, or ~15 days to search through 1 PB of data.
“However, because our proof-of-concept system did not make use of the vast majority of DNA stored in each capsule, the data stored in each capsule can in theory be significantly increased to yield a search rate of ~1 GB per second, or ~15 days to search through 1 PB of data (Supplementary Section 10).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Interpretationnone givenBecause the system is not limited to synthetic DNA, it also applies to compact and energy-efficient long-term archival storage of bacterial, human, and other genomes for archival sample preservation and retrieval.
“Finally, because our system is not limited to synthetic DNA, it also applies to compact and energy-efficient long-term archival storage of bacterial, human, and other genomes for archival sample preservation and retrieval.”
Quote in the paperNot a substantial claim- Rests on an assumption: The file system is not limited to synthetic DNA.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataPCR bias was checked by qPCR.
“PCR bias was checked by qPCR (Supplementary Fig. 3).”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataEach master primer and hash barcode pair was verified by PCR and agarose gel analysis.
“Each master primer and hash barcode pairs were verified by PCR and agarose gel analysis”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationcitationWhile DNA file protection by silica encapsulation offers millennium-scale protection and storage of the encapsulated file, unprotected DNA barcodes and their covalent linkers are susceptible to hydrolysis and will therefore require either periodic renewal or additional protection.
“Finally, while DNA file protection by silica encapsulation offers millennium-scale protection and storage9 of the encapsulated file, unprotected DNA barcodes and their covalent linkers are susceptible to hydrolysis and will therefore require either periodic renewal or additional protection, as noted at the outset of this article.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [9] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. & Stark, W. J. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). source
Not checked in the free run.
- Rests on an assumption: Unprotected DNA barcodes and their covalent linkers are susceptible to hydrolysis.
Classified as probably not a substantial claim. May combine two claims.
Study design and conductnone givenGenerated DNA sequences were synthesized, cloned, sequenced, and validated by Integrated DNA Technologies into a pUC19-based vector.
“Generated DNA sequences were ordered as custom genes synthesized, cloned, sequenced, and validated by Integrated DNA Technologies into pUC19-based vector.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe final sequence was checked for problematic subsequences (GGGG, CCCC, AAAAA, TTTTT, GAATTC, CTGCAG) and regenerated with a new random seed if any were found outside expected constant flanking regions.
“The final sequence was checked for problematic subsequences, specifically, GGGG, CCCC, AAAAA, TTTTT, and the restriction enzyme recognition sites GAATTC and CTGCAG. If any of these subsequences were found outside of expected occurrences in the constant flanking regions, the entire sequence was regenerated with a new random seed until no such subsequences appeared.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataPlasmid preparations were verified by PCR, Sanger sequencing, and short-read sequencing using Illumina MiniSeq for quality control.
“Plasmid preparations were verified by PCR, Sanger sequencing, and short-read sequencing using Illumina MiniSeq for quality control (Supplementary Fig. 3).”
Quote in the paperNot a substantial claimMay combine two claims.
InterpretationreasoningThe latency times associated with file selection and recovery of DNA from files renders the file system ideally suited to archival data storage in which data are written once, stored for decades or longer, and accessed rarely, and file protection by silica encapsulation offers millennium-scale storage of immutable data, such as astronomical image databases, high-energy physics datasets, or high
“The latency times associated with file selection and recovery of DNA from files renders our file system ideally suited to archival data storage in which data are written once, stored for decades or longer, and accessed rarely, file protection by silica encapsulation offers millennium-scale storage9 of immutable data, such as astronomical image databases48, high-energy physics datasets49, or high”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [9] Grass, R. N., Heckel, R., Puddu, M., Paunescu, D. & Stark, W. J. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Angew. Chem. Int. Ed. 54, 2552–2555 (2015). source
Not checked in the free run.
- cites [48] Broekema, P. C., van Nieuwpoort, R. V. & Bal, H. E. In Proceedings of the 2012 Workshop on High-Performance Computing for Astronomy Date 9–16 (Association for Computing Machinery, 2012).
Not checked in the free run.
- cites [49] Gaillard, M. & Pandolfi, S. CERN Data Centre passes the 200-petabyte milestone. CERN https://cds.cern.ch/record/2276551 (2017).
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningAll particles were gated by FITC and standard FSC/SSC gates to minimize sorting of doublets.
“all particles were gated by default using the ‘FITC’ laser and detector settings, which is defined by gating the majority population in the ‘FITC-A’ channel histogram, in addition to standard FSC and SSC gates to minimize sorting of doublets”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationSimilar to PCR-based approaches, barcodes can be protected by dehydrating the data pool or immersing files in hydrophobic liquids.
“As also noted there, similar to PCR-based approaches, barcodes can be protected by dehydrating the data pool or immersing files in hydrophobic liquids21.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [21] Newman, S. et al. High density DNA data storage library via dehydration with digital microfluidic retrieval. Nat. Commun. 10, 1706 (2019). source
Not checked in the free run.
Classified as probably not a substantial claim.
Study design and conductown dataThe sequence containing image hash, seed, and image encoding was flanked by sequences that allow amplification from a master primer pair that would amplify every sequence in the molecular plasmid database.
“The sequence containing image hash, seed, and image encoding, was additionally flanked on the 5’ and 3’ ends by sequences (5′-CGTCGTCGTCCCCTCAAACT-3′ and 5′-GCTGAAAAGGTGGCATCAAT-3′, respectively) that allow amplification from a “master primer” pair that would amplify every sequence in the molecular plasmid database”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenSamples were filtered through a 70-μm cell strainer prior to particle sorts.
“Samples were filtered through a Corning® 70-µm cell strainer (Fisher Scientific; catalog number: 07–201-431) prior to particle sorts.”
Quote in the paperNot a substantial claim
The authors state this as an assumption.
DNA synthesis costs will decline sufficiently for DNA storage to meet exponentially growing worldwide demand for archival data storage.
“DNA is an ultra-high-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible.”
The paper relies on this without support.
FAS scales linearly with the size of the data pool.
“Third, retrieval time is currently limiting for our system in an exabyte-scale data pool because FAS scales linearly with the size of the pool.”
The paper relies on this without support.
Unprotected DNA barcodes and their covalent linkers are susceptible to hydrolysis.
“unprotected DNA barcodes and their covalent linkers are susceptible to hydrolysis and will therefore require either periodic renewal or additional protection”
The paper relies on this without support.
Encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA.
“Because encapsulation of the DNA file sequence relies only on electrostatic interactions between positively-charged silica and the phosphate backbone of DNA, our approach can equally encapsulate any molecular weight of DNA molecule applicable to MB and larger file sizes”
The paper relies on this without support.
The file system is not limited to synthetic DNA.
“Finally, because our system is not limited to synthetic DNA, it also applies to compact and energy-efficient long-term archival storage of bacterial, human, and other genomes for archival sample preservation and retrieval.”
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?
PCR-based random access irreversibly removes oligos from the pool, which necessitates potentially lossy reamplification of the entire pool after repeated data retrieval.
“Second, PCR-based random access irreversibly removes oligos from the pool, which necessitates potentially lossy reamplification of the entire pool after repeated data retrieval.75,76”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [75]
Incorporation of random-access priming regions into each oligo decreases the available space for data-encoding bases, thereby decreasing storage density, currently by about 15% per address region.
“First, the incorporation of random-access priming regions into each oligo decreases the available space for data-encoding bases, thereby also decreasing the storage density (currently by about 15% per address region).71,75”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [75]
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.
Surface-functionalization reagent has two different names
MinorThe File Synthesis section identifies the reagent as 3-aminopropyltriethoxysilane, whereas the corresponding Methods step identifies it as 2-aminopropyltriethoxysilane.
“Condensation of 3-aminopropyltriethoxysilane with the hydroxy-terminated surface of the encapsulated plasmid DNA provided a primary amine chemical handle”
“A volume of 20 µL of 2-aminopropyltriethoxysilane (Millipore Sigma; catalog number: 440140), was then added”
The 1:1 mixture contains no background-file stock
MinorThe table labels this condition as a 1:1 ratio of Airplane to the other 19 files, but specifies 500 μL of Airplane stock and 0 μL of the other-file stock. As prepared, it contains only Airplane stock.
“| 1:1 | 500 [a] | 0 |”
“| Ratio of Airplane:19other files | Volume of Airplane stocksolution [µL] | Volume of stock solution of 19 other files[µL] [a] |”
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- Authors
- Banal, J. L., Shepherd, T. R., Berleant, J., Huang, H., Reyes, M., Ackerman, C. M., Blainey, P. C., & Bathe, M.
- Affiliations
- Massachusetts Institute of Technology (US)
- Broad Institute (US)
- Corresponding author
- Bathe, Mark
- ORCID
- Venue
- Nature Materials
- Published
- 2021-06-10
- Volume
- 20
- Issue
- 9
- Pages
- 1272-1280
- ISSN
- 1476-1122 (ISSN-L)
- 1476-4660
- PMC
- PMC8564878
- OpenAlex
- W3168942844
- Semantic Scholar
- 083dd616930e4422e552abc9463db66be0db32df
- Cited by
- 143
- References
- 60
- Citations by year
- 2026: 18 · 2025: 34 · 2024: 32 · 2023: 31 · 2022: 20 · 2021: 6 · 2020: 2
- FWCI
- 6.99
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Materials (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- United States Department of Defense | United States Navy | Office of Naval Research (N00014-17-1-2609, N00014-12-1-0621, N00014-18-1-2290)
- National Science Foundation (CCF-1564025, CCF-1956054, CBET-1729397, Grant # 1122374)
- United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (W911NF-19-2-0026)
- U.S. Department of Health & Human Services | National Institutes of Health (F32CA236425)
- Burroughs Wellcome Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Keywords
- DNA data storage, Boolean search, DNA barcodes, data archiving, DNA synthesis, molecular databases
- MeSH terms
- Archives, DNA, Fluorescence, Plasmids, Silicon Dioxide, Polymerase Chain Reaction, Information Storage and Retrieval, Synthetic Biology
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