Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA
Open accessAbstract
Using DNA as a durable, high‐density storage medium with eternal format relevance can address a future data storage deficiency. The proposed storage format incorporates dehydrated particle spots on glass, at a theoretical capacity of more than 20 TB per spot, which can be efficiently retrieved without significant loss of DNA. The authors measure the rapid decay of dried DNA at room temperature and present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution. In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation. A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude: A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH) corresponding to 116 years at room temperature and the stored information is successfully recovered.
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Written from the paper’s full text.
TL;DR
The paper integrates silica-encapsulated DNA with digital microfluidics (DMF) to automate storage and retrieval, showing that encapsulated DNA survives accelerated aging and can be decoded. A DNA library of 7373 unique sequences encoding a 115,394-byte image was recovered after 4 days at 70 °C, 50% RH, corresponding to 116 years at room temperature.
Key findings
- Dried, unprotected DNA stored at room temperature degraded to less than 10% of its original concentration over one year, whereas encapsulated DNA did not degrade for at least 200 days at 40 °C, 50% RH.
- Engineered silica particles (PD particles) were DMF-compatible: zeta potential changed from 56 ± 12 mV after core ammonization to 4.5 ± 0.4 mV after DNA encapsulation and 33 ± 10 mV after functionalization; particle diameter increased by 15–20 nm.
- Retrieval required high driving voltage for complete recovery; 5 µL BOE retrieved all DNA, and 20 wt% NaHCO₃ gave the most consistent recoveries, while HCl and citric acid did not retrieve all deposited DNA particles.
- The 7373-sequence DNA library encoding 115,394 bytes was perfectly decoded after accelerated aging (4 days at 70 °C, 50% RH), while the unprotected DNA library degraded almost completely; the authors calculate a conservative 23.5 TB per spot, up to 280 TB per spot potentially, and 6144× denser storage than LTO-9 tape.
Methods
- DNA was encapsulated in silica nanoparticles using an adapted Paunescu et al. sol-gel synthesis with TMAPS and TEOS, dilute condensation, annealing buffer and 2-propanol, and a final TMAPS ammonization; particles were characterized by zeta potential and size.
- DMF experiments used a Microsoft PurpleDrop Rev 6 board and version 3 electrode board with a Raspberry Pi, ITO-coated glass top plate, and mylar film; droplets were moved at 155–275 V, dried, and retrieved with BOE and NaHCO₃, with DNA quantified by qPCR.
- Stability and sequencing tests included one-year decay measurements at room temperature, 4, −25, and −80 °C; accelerated aging at 70 °C, 50% RH for 4 or 9 days; and Illumina iSeq 100 sequencing of a 7373-oligonucleotide, 150 nt DNA library encoding 115 kB.
Limitations
- The paper states that the current prohibitive cost of synthesizing large DNA databases means the work extrapolates from a small example file, and that the specific configuration and required volume of synthesis, PCR, and sequencing are hard to estimate and were neglected in the density calculation.
- The paper states that DNA loading was relatively low (≈0.5 wt% in retrieval experiments; ≈1 wt% in accelerated aging), and that formulations stabilizing significantly more than 10 wt% DNA have not yet been reported.
- Evident from the text: accelerated aging is a proxy rather than real-time multi-year storage; only one image file/library was tested; DMF handled deposition and retrieval but synthesis and sequencing remained external; and high driving voltage was needed for complete retrieval even though low voltages would be preferred for coating longevity.
Model-written summary. Check it against the paper before relying on it.
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Cites
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Claims the paper makes
0 of 39 cited sources checked · 0 supported · 0 flagged
- Findingown data
The stored information from the encapsulated DNA library is successfully recovered.
“and the stored information is successfully recovered.”
Quote in the paperSubstantial claim - Findingown data
Dried DNA at room temperature decays rapidly.
“The authors measure the rapid decay of dried DNA at room temperature”
Quote in the paperSubstantial claim - Findingnone given
The proposed storage format can be efficiently retrieved without significant loss of DNA.
“which can be efficiently retrieved without significant loss of DNA.”
Quote in the paperNot a substantial claim - Findingown data
A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH).
“A DNA library containing 7373 unique sequences is encapsulated and stored under accelerated aging conditions (4 days at 70 °C, 50% RH)”
Quote in the paperSubstantial claim- Rests on an assumption: The accelerated aging conditions (4 days at 70 °C, 50% RH) correspond to 116 years at room temperature.
- Findingown data
The tailored solvent by addition of annealing buffer and 2-propanol ensured obtaining single particles after the silica growth phase.
“We also tailored the solvent to the need of well-dispersed reactants by the addition of annealing buffer and 2-propanol, which ensured obtaining single particles after the silica growth phase (Figure 3c).”
Quote in the paperSubstantial claim
- Findingreasoning
The authors adapted the synthesis conditions such that no agglomeration of particles occurred.
“In this step, we adapted the synthesis conditions such that no agglomeration of particles occurred.”
Quote in the paperSubstantial claim - Findingnone given
The authors have developed silica nanoparticles encapsulating DNA in a near-to water-free environment to protect it from degradation.
“We have developed silica nanoparticles encapsulating DNA in a near-to water-free environment to protect it from degradation.”
Quote in the paperSubstantial claim - Findingown data
Additional ammonization with TMAPS in the last synthesis step significantly improved the handling and persistence of nonagitated droplets, also at high concentrations with the use of the DMF device.
“This significantly improved the handling and persistence of nonagitated droplets, also at high concentrations with the use of the DMF device.”
Quote in the paperSubstantial claim - Findingown data
Successful storage and decoding of DNA files under accelerated aging conditions was achieved.
“We present successful storage and decoding of DNA files under accelerated aging conditions”
Quote in the paperSubstantial claim- Rests on an assumption: The accelerated aging conditions (4 days at 70 °C, 50% RH) correspond to 116 years at room temperature.
- Findingreasoning
For untailored particles, this behavior leads to agglomeration of particles upon movement on the DMF device.
“For untailored particles, this behavior leads to agglomeration of particles upon movement on the DMF device as shown in Figure 2a.”
Quote in the paperSubstantial claim - Findingcitation
Storage in TE buffer was the only other method to successfully stabilize DNA at room temperature.
“We also investigated storage in TE buffer (Figure S3, Supporting Information), which was the only other method to successfully stabilize DNA at room temperature.[34,35]”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [34] source
Not checked in the free run.
- cites [35]
Not checked in the free run.
- Findingown data
Also 5 μL BOE could retrieve all DNA.
“Last, also 5 µL BOE could retrieve all DNA, which reduces retrieval droplet size and could enable better access through more densely spotted particles on a glass plate.”
Quote in the paperNot a substantial claim - Findingown data
Only a high driving voltage ensured the complete retrieval of encapsulated DNA.
“However, only a high driving voltage ensured the complete retrieval of encapsulated DNA (Figure 5a).”
Quote in the paperSubstantial claim - Findingreasoning
Due to the dispersion stability of the particles, the concentration did not interfere with DMF operations, namely droplet movement before and after retrieval.
“Due to the dispersion stability of the particles, the concentration did not interfere with DMF operations, namely droplet movement before and after retrieval.”
Quote in the paperNot a substantial claim - Findingown data
Over the course of a year, dried, unprotected DNA, stored in a plastic vial at room temperature, degraded to less than 10% of its original concentration.
“Over the course of a year, dried, unprotected DNA, stored in a plastic vial at room temperature, degraded to less than 10% of its original concentration (Figure 4a).”
Quote in the paperSubstantial claim - Findingown data
The procedure increased the core particle diameter by 15-20 nm.
“The procedure increased the core particle diameter by 15-20 nm (Figure 3b).”
Quote in the paperNot a substantial claim - Findingown data
Conventionally encapsulated DNA did not degrade for at least 200 days, even at an elevated temperature and ambient humidity (40 °C, 50% RH), exhibiting exceptional stability.
“Conventionally encapsulated DNA on the other hand, did not degrade for at least 200 days, even at an elevated temperature and ambient humidity (40 °C, 50% RH), exhibiting exceptional stability.”
Quote in the paperSubstantial claim - Findingown data
The second retrieval did not recover more DNA.
“As shown in Figure 5a, also the second retrieval did not recover more DNA”
Quote in the paperNot a substantial claim - Findingown data
Other retrieval solutions such as hydrochloric acid (HCl) and citric acid did not retrieve all of the deposited DNA particles.
“Second, the results showed, that other retrieval solutions such as hydrochloric acid (HCl) and citric acid did not retrieve all of the deposited DNA particles.”
Quote in the paperSubstantial claim - Findingown data
Decay experiments with model DNA in an aqueous solution or dry showed stable conditions for all actively cooled samples stored at 4, -25, and -80 °C.
“Decay experiments with model DNA in an aqueous solution or dry showed stable conditions for all actively cooled samples stored at 4, -25, and -80 °C (Figures S1 and S2, Supporting Information).”
Quote in the paperSubstantial claim - Findingown data
The silica core and protection layer could be quickly dissolved with buffered oxide etch (BOE), containing fluoride ions, to access the encapsulated DNA after storage.
“To access the encapsulated DNA after storage, the silica core and protection layer could be quickly dissolved with buffered oxide etch (BOE), containing fluoride ions.”
Quote in the paperSubstantial claim - Findingreasoning
A conservative estimate of data storage capacity is 23.5 TB per spot.
“From these numbers, we could calculate a conservative 23.5 TB of data per spot (see details in Supporting Information).”
Quote in the paperSubstantial claim- Rests on an assumption: The smallest informational unit in DNA is one base pair, with an average molecular weight of 650 g/mol.
- Findingown data
20 wt% NaHCO3 gave the most consistent recoveries.
“As a result, we settled with 20 wt% NaHCO 3 which gave the most consistent recoveries.”
Quote in the paperSubstantial claim - Findingown data
The indicated occurrences relative to their total number showed no increase in specific error frequencies due to synthesis or aging.
“The indicated occurrences relative to their total number showed no increase in specific error frequencies due to synthesis or aging.”
Quote in the paperSubstantial claim - Findingown data
Dried DNA is prone to degradation at room temperature.
“Our data shows that dried DNA is prone to degradation at room temperature and should therefore be protected against hydrolysis and oxidation.”
Quote in the paperSubstantial claim - Findingnone given
The engineered DNA nanoparticles allow for room temperature storage.
“Moreover, they allow for room temperature storage.”
Quote in the paperSubstantial claim - Findingnone given
The authors developed a synthesis that encapsulates DNA between silica layers.
“As a possible solution, we report the development of a synthesis that encapsulates DNA between silica layers.”
Quote in the paperSubstantial claim - Interpretationreasoning
Protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation.
“In this form, the protected DNA can be readily applied to digital microfluidics (DMF) used to handle retrieval operations amenable to full automation.”
Quote in the paperSubstantial claim - Interpretationown data
A storage architecture is demonstrated that can increase the storage capacity of today's archival storage systems by more than three orders of magnitude.
“A storage architecture is demonstrated, which can increase the storage capacity of today's archival storage systems by more than three orders of magnitude:”
Quote in the paperSubstantial claim - Interpretationnone given
The proposed storage format incorporates dehydrated particle spots on glass.
“The proposed storage format incorporates dehydrated particle spots on glass”
Quote in the paperSubstantial claim- Rests on an assumption: The proposed storage format has a theoretical capacity of more than 20 TB per spot.
- Premisecitation
An automated write-read cycle for DNA data storage is feasible.
“Recent work on the automation of a synthesisto-sequencing process has shown, that an automated writeread-cycle is feasible”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [13] source
Not checked in the free run.
- Interpretationreasoning
Synthesis of encapsulated DNA in silica nanoparticles is a possible solution to the rapid decay of dried DNA at room temperature.
“present the synthesis of encapsulated DNA in silica nanoparticles as a possible solution.”
Quote in the paperSubstantial claim - Premisecitation
DNA has improbable format obsolescence due to its importance in medicine and bioscience.
“With a storage density in the Exabyte/gram range and improbable format obsolescence due to its importance in medicine and bioscience, DNA encoded data gains more relevance in today's information technology.[1,6]”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [1] source
Not checked in the free run.
- cites [6]
Not checked in the free run.
- Premisecitation
The force acting on the particles is proportional to r^3 of a spherical particle and its polarizability.
“The force acting on the particles is proportional to r 3 of a spherical particle and its polarizability.[30]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [30] source
Not checked in the free run.
- Interpretationreasoning
With the combination of encapsulation of DNA in silica nanoparticles and DMF, the authors offer a working solution for the automated, stable storage of digital data encoded in DNA.
“With the combination of two established technologies, the encapsulation of DNA in silica nanoparticles and DMF for the use of DNA data storage, we offer a working solution for the automated, stable storage of digital data encoded in DNA.”
Quote in the paperSubstantial claim - Interpretationown data
The storage and decoding under accelerated aging conditions builds the basis for reliable archival storage.
“building the basis for reliable archival storage”
Quote in the paperSubstantial claim - Premisereasoning
Protecting DNA through a protective layer of silica has proven to be an efficient method to conserve the molecule's integrity.
“Protecting the DNA through a protective layer of silica has proven to be an efficient method to conserve the molecule's integrity.”
Quote in the paperSubstantial claim - Premisenone given
Water and its local concentration is one of the main drivers for damage to the DNA molecule.
“Water and its local concentration has been identified as one of the main drivers for damage to the DNA molecule.”
Quote in the paperNot a substantial claim - Premisecitation
Common storage media for archival storage, such as hard disk drives, have a failure rate of more than 1% per year.
“Common storage media for archival storage, such as hard disk drives have a failure rate of more than 1% per year.[23]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [23]
Not checked in the free run.
- Premisecitation
Magnetic tape, currently used for many archival storage services, only lasts between one to three decades under regular conditions.
“Also magnetic tape, currently used for many archival storage services, only lasts between one to three decades under regular conditions.[24,25]”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [24] source
Not checked in the free run.
- cites [25]
Not checked in the free run.
- Interpretationown data
The storage and decoding under accelerated aging conditions surpasses current solutions more than three orders of magnitude.
“surpassing current solutions more than three orders of magnitude (Figure 1).”
Quote in the paperNot a substantial claim - Premisenone given
The dielectrophoretic mobility in the nonuniform electric field created by electrodes and glass top plate causes particles to move inside the droplet.
“The dielectrophoretic mobility in the nonuniform electric field created by electrodes and glass top plate causes particles to move inside the droplet.”
Quote in the paperSubstantial claim - Interpretationreasoning
Similar to aqueous storage formats, storage in TE buffer would be subject to the same inadequacies.
“Similar to aqueous storage formats, storage in TE buffer would be subject to the same inadequacies.”
Quote in the paperSubstantial claim - Interpretationown data
To achieve stable storage, dried, unprotected DNA has to be chilled well below room temperature.
“In order to achieve stable storage, dried, unprotected DNA has to be chilled well below room temperature.”
Quote in the paperSubstantial claim - Interpretationreasoning
Encapsulation in silica could offer strong protection in case of longer ventilation failures.
“Encapsulation in silica could therefore also offer strong protection in case of longer ventilation failures.”
Quote in the paperNot a substantial claim - Interpretationreasoning
The gaseous CO2 bubbles assisted the redispersion process by providing agitation.
“The gaseous CO 2 bubbles assisted the redispersion process by providing agitation.”
Quote in the paperSubstantial claim - Premisecitation
During PCR, the imine form of A is misinterpreted as a G, which in the next PCR cycle results in a G-C base pair instead of the original A-T.
“During PCR this imine form of A is misinterpreted as a G, which is the next PCR cycle results in a G-C base pair instead of the original A-T.”
Quote in the paperNot a substantial claim - Premisecitation
From previous work it is known that the net information density including primer regions for the DNA library is 0.81 bit nt-1.
“From previous work it is known, that the net information density including primer regions for the DNA library is 0.81 bit nt -1 .[4]”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [4] source
Not checked in the free run.
- Interpretationreasoning
Consequently, the observed substitution errors must have been introduced in steps preceding the aging process, which include DNA synthesis and PCR amplification.
“Consequently, the observed substitution errors must have been introduced in steps preceding the aging process, which include DNA synthesis and PCR amplification.”
Quote in the paperSubstantial claim - Premisereasoning
During PCR, the uracil is falsely interpreted as a thymine resulting in a T-A base pair instead of C-G.
“During PCR, the uracil is falsely interpreted as a thymine resulting in a T-A base pair instead of C-G.”
Quote in the paperNot a substantial claim - Interpretationreasoning
Assuming 50 spots per glass plate, a DNA rack would store up to 188 PB.
“Assuming we can fit 50 spots on a glass plate, such a DNA rack would store up to 188 PB.”
Quote in the paperSubstantial claim- The authors state this as an assumption: 50 spots can fit on a glass plate.
- Interpretationcitation
A potential data load of nearly 280 TB per spot is already feasible today, considering particles with optimized DNA loading and a coding scheme with increased net information density.
“Considering the usage of particles with a more optimized DNA loading and a coding scheme featuring increased net information density, [5,22] a potential data load of nearly 280 TB per spot is already feasible today.”
Quote in the paperNot a substantial claim0 of 2 sources checked - Interpretationreasoning
Active cooling is avoided by using these nanoparticles.
“Thus, active cooling, which generates considerably higher energy consumption and requires more sophisticated infrastructure, is avoided.”
Quote in the paperSubstantial claim - Interpretationreasoning
With a spot load of 280 TB, the DNA rack storage would increase to 2.24 EB.
“With a spot load of 280 TB, this number would even be increased to 2.24 EB.”
Quote in the paperSubstantial claim- The authors state this as an assumption: 50 spots can fit on a glass plate.
- Interpretationreasoning
DNA storage is 6144× denser than tape storage.
“This translates to 6144× denser storage in DNA compared to tape.”
- Also stated in: § DNA Library Aging and Sequencing: · plain
“As a result, the storage density is more than 6000× larger, compared to a standard 19”
Quote in the paperSubstantial claim- Rests on an assumption: A standard 19-inch rack storing LTO-9 magnetic tapes (18 TB each) can host 9.4 PB and has a storage density of 8.2 GB cm-3.
- Also stated in: § DNA Library Aging and Sequencing: · plain
- Interpretationreasoning
The use of DMF in conjunction with advanced nanoparticles facilitates DNA storage at industrial scale.
“We demonstrate that the use of DMF in conjunction with advanced nanoparticles, facilitates DNA storage at industrial scale.”
Quote in the paperSubstantial claim - Interpretationcitation
In conjunction with anticipated lower-cost and rapid DNA synthesis technologies, this will present a viable alternative in terms of ecological, dense, and automated data storage.
“In conjunction with anticipated lower-cost and rapid DNA synthesis technologies, [2] this will present a viable alternative in terms of ecological, dense, and automated data storage.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [2] source
Not checked in the free run.
- May combine two claims. 20
- Classified as probably not a substantial claim. 23
May combine two claims.
Findingown dataFirst experiments of moving droplets containing dispersions of conventionally synthesized DNA particles were unreliable, as agglomeration of silica particles was observed, resulting in unsteady flow of the droplet.
“First experiments of moving droplets containing dispersions of these particles was unreliable, as agglomeration of silica particles could be observed, resulting in unsteady flow of the droplet.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
FindingcitationThe adaptation was accomplished by a more dilute condensation reaction as opposed to previously reported synthesis procedures.
“This was accomplished by a more dilute condensation reaction as opposed to previously reported synthesis procedures. [22,22,26]”
Quote in the paperSubstantial claim0 of 2 sources checkedMay combine two claims.
Findingnone givenThe particles are compatible with a DMF device and allow for efficient storage and retrieval in an automated fashion.
“The particles are compatible with a DMF device and allow for efficient storage and retrieval in an automated fashion.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataIn a particle storage experiment, after driving droplets to a designated location on the electrode array, they were allowed to dry, resulting in particle pellets that were hard to dissolve by using BOE only.
“In a particle storage experiment, after driving droplets to a designated location on the electrode array, they were allowed to dry.This resulted in particle pellets that were hard to dissolve by using BOE only.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataLow amounts of salt did not produce enough gaseous agitation to help break up the particle pellet, whereas too much salt sometimes gave bubbles that were expanding the droplet and thereby immobilizing it.
“Low amounts of salt did not produce enough gaseous agitation to help break up the particle pellet, whereas too much salt sometimes gave bubbles that were expanding the droplet and thereby immobilizing it.”
Quote in the paperSubstantial claimMay combine two claims.
FindingreasoningTo compensate for the relatively low DNA loading of the particles (≈0.5 wt%), high particle concentrations were used, thus achieving a large data capacity.
“To compensate for the relatively low DNA loading of the particles (≈0.5 wt%), we used high particle concentrations, thus achieving a large data capacity.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataTreatment with BOE produced a clear solution devoid of polymers or other solids and could be amplified by PCR following 1:20 dilution with water or after purification with a silica column.
“Treatment with BOE produced a clear solution devoid of polymers or other solids and could be amplified by PCR following 1:20 dilution with water or after the purification with a silica column.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S4 (based).
Findingnone givenThe particles were engineered to be compatible with DMF.
“Moreover, the particles were engineered to be compatible with DMF.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataUnder accelerated aging conditions (70 °C and 50% RH for up to 9 days), unprotected DNA is degrading rapidly whereas the encapsulated DNA is stable.
“It is evident, that under these conditions, unprotected DNA is degrading rapidly whereas the encapsulated DNA is stable.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn both experiments, only a low percentage of sequences were lost, so that the authors were able to perfectly decode the file from the encapsulated DNA library.
“In both experiments, only a low percentage of sequences were lost, so that we were able to perfectly decode the file from the encapsulated DNA library.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataIn contrast, the unprotected DNA library had been degraded almost completely, which made a file recovery impossible.
“In contrast to this, the unprotected DNA library had been degraded almost completely, which made a file recovery impossible (Figure 6b).”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataThe engineered DNA nanoparticles withstand agglomeration in high-voltage electric fields and can be used in droplets at high concentration.
“The engineered DNA nanoparticles withstand agglomeration in high-voltage electric fields and can be used in droplets at high concentration.”
- Also stated in: § DNA Library Aging and Sequencing: · plain
“PD particles show a more resilient nature and are stable in the dispersion.”
Quote in the paperSubstantial claim- Also stated in: § DNA Library Aging and Sequencing: · plain
May combine two claims.
PremisecitationDNA offers massive parallelization of copy, delete, and read operations; it takes the same amount of time for one or billions of molecules.
“As a molecular storage system, DNA offers massive parallelization of copy, delete, and read operations; it takes the same amount of time for one or billions of molecules.”
Quote in the paperNot a substantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationMore advanced applications, such as random number generation or arithmetic operations, prove the versatility of DNA as an information medium.
“More advanced applications, for example, random number generation or the possibility to perform arithmetic operations, prove the versatility of DNA as an information medium.[11,12]”
Quote in the paperNot a substantial claim0 of 2 sources checkedMay combine two claims.
PremisecitationEncapsulation of DNA in silica nanoparticles is one of the most effective methods for DNA preservation and was employed in this work.
“One of the most effective methods is the encapsulation of DNA in silica nanoparticles, which has been versatilely used in the recent past and was therefore also employed in this work.[10,21,22]”
Quote in the paperSubstantial claim0 of 3 sources checkedClassified as probably not a substantial claim.
PremisecitationDNA encoded data has a storage density in the Exabyte/gram range.
“With a storage density in the Exabyte/gram range and improbable format obsolescence due to its importance in medicine and bioscience, DNA encoded data gains more relevance in today's information technology.[1,6]”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [1] source
Not checked in the free run.
- cites [6]
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThere are several different solutions for the preservation of DNA at room temperature, such as filter paper, anaerobic encapsulation, sugar-matrices, and inorganic salts.
“There are several different solutions for the preservation of DNA at room temperature, such as filter paper, anaerobic encapsulation, sugar-matrices, and inorganic salts.[16][17][18][19][20]”
Quote in the paperNot a substantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S2 (checkable), S4 (based).
Interpretationnone givenUsing DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency.
“Using DNA as a durable, high-density storage medium with eternal format relevance can address a future data storage deficiency.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationIf stored properly, DNA can be preserved for more than one million years.
“If stored properly, DNA can be preserved for more than one million years, DNA data storage.[16]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [16] source
Not checked in the free run.
Classified as probably not a substantial claim.
PremisecitationDNA has emerged as an attractive alternative as conventional data storage media converge on their physical limits.
“As conventional data storage media steadily converge on their physical limits, DNA has emerged as an attractive alternative.[1][2][3][4][5]”
Quote in the paperSubstantial claim0 of 3 sources checkedMay combine two claims.
InterpretationreasoningThe use of acids other than BOE would entail disadvantages: the needed addition of BOE to dissolve the silica particles would add an extra step to the process, and due to the low pH in the HCl solution, this retrieval method would additionally require neutralization immediately after the retrieval.
“The use of acids other than BOE would entail several disadvantages: The needed addition of BOE to dissolve the silica particles would add an extra step to the process.Due to the low pH in the HCl solution, this retrieval method would additionally require neutralization immediately after the retrieval.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningIf applied at an industrial scale, chilling dried unprotected DNA would significantly increase operating cost and decrease storage density, if overhead infrastructure is included.
“If applied at an industrial scale, this would significantly increase operating cost and decrease the storage density, if overhead infrastructure is included.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningReducing retrieval droplet size could enable better access through more densely spotted particles on a glass plate.
“which reduces retrieval droplet size and could enable better access through more densely spotted particles on a glass plate.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationnone givenPermanent liquid storage severely reduces the storage density and would be impractical for the use in DMF devices.
“Permanent liquid storage, however, severely reduces the storage density and would be impractical for the use in DMF devices.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningDNA has to be protected when stored at room temperature and encapsulation in silica nanoparticles is a suitable method to achieve this.
“The two preceding paragraphs show that DNA has to be protected when stored at room temperature and encapsulation in silica nanoparticles is a suitable method to achieve this.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Interpretationown dataThis degradation shows the necessity of finding a suitable method to stabilize DNA for storage without active cooling.
“This shows the necessity of finding a suitable method to stabilize DNA for storage without active cooling.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationIt is generally expected that the cost of DNA synthesis will decrease in the coming years making automated storage solutions necessary.
“However, it is generally expected [2,6] that the cost of DNA synthesis will decrease in the coming years making automated storage solutions necessary.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [2] source
Not checked in the free run.
- cites [6]
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
InterpretationcitationThe slightly higher sequence loss in the 500 μg particle sample could be explained by the effect of subsampling to equalize the concentration of both samples before sequencing preparation.
“The slightly higher sequence loss in the 500 µg particle sample could be explained by the effect of subsampling to equalize the concentration of both samples (100 and 500 µg) before sequencing preparation.[31]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [31] source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisereasoningDue to amplification and handling prior to a particle synthesis, the DNA library is double-stranded.
“Due to amplification and handling prior to a particle synthesis, the DNA library is double-stranded.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe most prevalent substitution errors (T2C, A2G, and C2T, G2A) have been previously described to stem from DNA transitions.
“The most prevalent substitution errors (T2C, A2G, and C2T, G2A) have been previously described to stem from DNA transitions.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Study design and conductnone givenDue to the current prohibitive cost of synthesizing large DNA databases, this work has to extrapolate from a small example file.
“Due to the current prohibitive cost of synthesizing large DNA databases, this work has to extrapolate from a small example file.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationT2C/A2G transitions are known in biology and are the result of a tautomeric shift of adenine, from its amine to its imine form.
“T2C/A2G transitions are known in biology and are the result of a tautomeric shift of adenine, from its amine to its imine form.[32]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [32] source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationC2T/G2A transitions are a result of the hydrolysis of cytosine to give uracil.
“Similarly, C2T/G2A transitions are a result of the hydrolysis of cytosine to give uracil.[10]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [10] source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationAs these errors stem from synthesis and subsequent PCR steps, the prevalence of these errors depends on synthesis technique and employed PCR enzymes.
“As these errors stem from synthesis and subsequent PCR steps, the prevalence of these errors depends on synthesis technique and employed PCR enzymes.[33]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [33] source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Interpretationnone givenData storage per spot could be further improved by using slightly bigger droplets and exhausting the particle concentration.
“This could be further improved by using slightly bigger droplets and exhausting the particle concentration.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationcitationParticles comprising higher DNA concentrations than those used here would aid to further increase data density.
“Also, particles comprising higher DNA concentrations than the ones used here, would aid to further increase data density.[22]”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [22] source
Not checked in the free run.
May combine two claims.
InterpretationreasoningThe storage density would be 50 TB cm-3 for the 188 PB rack and 595 TB cm-3 for the 2.24 EB rack.
“The storage density would be 50 TB cm -3 ,and 595 TB cm -3 , respectively.”
Quote in the paperSubstantial claimMay combine two claims.
InterpretationreasoningA fully functioning DNA storage rack will feature significantly higher storage density and storage stability than current archival storage solutions.
“However, it is evident, that a fully functioning DNA storage rack will feature a significantly higher storage density and storage stability than current archival storage solutions.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing), S4 (based).
Study design and conductnone givenIt is paramount for the success of a synthesis that particles were well suspended at all times.
“It was paramount for the success of a synthesis, that particles were well suspended at all times.”
Quote in the paperNot a substantial claimClassified as probably not a substantial claim.
Interpretationnone givenA 50 cm high rack can comfortably accommodate 160 slides.
“For the storage of glass plates similar to drives mounted in a server rack, one could comfortably accommodate 160 slides efficiently into a 50 cm high rack.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
Interpretationnone givenEvery layer of the core-shell structured particles serves a specific purpose, to enable simple handling, stable storage, and DMF compatibility.
“Every layer of the core-shell structured particles serves a specific purpose, to enable simple handling, stable storage, and DMF compatibility.”
Quote in the paperSubstantial claim
The paper relies on this without support.
The accelerated aging conditions (4 days at 70 °C, 50% RH) correspond to 116 years at room temperature.
“corresponding to 116 years at room temperature”
The paper relies on this without support.
None of the existing room-temperature DNA preservation methods have been developed in combination with a scalable and automated technology that can potentially reach wide deployment.
“Although most methods are reliable and simple to use, none have been developed in combination with a scalable and automated technology that can potentially reach wide deployment.”
The paper relies on this without support.
The liquid manipulations required on the macro-level, including diluting, mixing, and splitting, are still mostly performed manually.
“The liquid manipulations required on the macro-level, including diluting, mixing, and splitting, are still mostly performed manually.”
The paper relies on this without support.
Long-term decay studies of synthetic DNA in the literature are scarce.
“Since long-term decay studies of synthetic DNA in the literature are scarce”
The paper relies on this without support.
The proposed storage format has a theoretical capacity of more than 20 TB per spot.
“at a theoretical capacity of more than 20 TB per spot”
The paper relies on this without support.
The smallest informational unit in DNA is one base pair, with an average molecular weight of 650 g/mol.
“Therefore, the smallest informational unit exists as one base pair, which has an average molecular weight of 650 g mol -1 .”
The paper relies on this without support.
Formulations to stabilize DNA comprising significantly more than 10 wt% of DNA have not yet been reported.
“However, this has its limitations, as formulations to stabilize DNA comprising significantly more than 10 wt% of DNA have not yet been Small 2022, 18, 2107381 reported.”
The authors state this as an assumption.
50 spots can fit on a glass plate.
“Assuming we can fit 50 spots on a glass plate, such a DNA rack would store up to 188 PB.”
The paper relies on this without support.
A standard 19-inch rack storing LTO-9 magnetic tapes (18 TB each) can host 9.4 PB and has a storage density of 8.2 GB cm-3.
“In comparison, a standardly used 19”
The authors state this as an assumption.
The specific configuration and required volume of synthesis, PCR, and sequencing can be neglected in the storage density calculation.
“As the specific configuration and required volume of synthesis, PCR, and sequencing is hard to estimate, they have been neglected in this calculation.”
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?
The maximum data that can be stored within a single macroscopic storage container has been estimated to lie between a few TB up to a few hundred TB.
“This represents the maximum data that can be stored within a single macroscopic storage container, and has been estimated to lie between a few TB up to a few hundred TB.56,6,70”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [56]
Despite DNA's long-term stability in well-controlled environments such as ancient bone, both aqueous solutions and dried DNA only exhibit a half-life on the order of months to a few years under ambient conditions.
“Despite DNA’s long-term stability in well-controlled environments such as ancient bone, with storage durations as long as several hundred thousand years,54,55 both aqueous solutions and dried DNA only exhibit a half-life on the order of months to a few years under ambient conditions.56”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [56]
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.
Conflicting particle amounts for the accelerated-aging spots
MajorThe Figure 4 caption states that 100 μg of particles were used per spot, while the experimental procedure for the accelerated-aging test specifies 1 μg per spot-a 100-fold difference.
“b) Accelerated DNA aging test on the DMF compatible glass slide: PD particles with 20 wt% NaHCO 3 added (based on the amount of particles), compared to unprotected, dried DNA at 70 °C, 50% RH. 100 µg of particles used per spot.”
“For accelerated aging experiments, bare (10 ng) and encapsulated DNA with 20 wt% of NaHCO 3 (1 µg particles corresponding to 10 ng DNA, loading ≈1 wt%) were pipetted manually on a Teflon-coated glass top plate and stored in a desiccator for 9 days at 70 °C and 50% RH.”
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High‐Fidelity Data Retrieval from Synthetic DNA Pools via Machine Learning Model
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Toward Portable DNA Data Storage: A Paper-Based System for Rewritable and Random Access
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Investigating enhanced stability in CTAB(C)-compacted DNA under aging conditions for data storage
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Condensed DNA Nanosphere for DNA Origami Cryptography
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- Authors
- Antkowiak, P. L., Koch, J., Nguyen, B. H., Stark, W. J., Strauss, K., Ceze, L., & Grass, R. N.
- Affiliations
- ETH Zurich (CH)
- Microsoft (United States) (US)
- Paul G. Allen School of Computer Science & Engineering University of Washington 185 E Stevens Way NE Seattle WA 98195 USA
- Corresponding author
- Grass, Robert N.
- ORCID
- Venue
- Small
- Publisher
- Wiley
- Published
- 2022-02-26
- Volume
- 18
- Issue
- 15
- Pages
- e2107381-e2107381
- ISSN
- 1613-6810 (ISSN-L)
- 1613-6829
- OpenAlex
- W4214575994
- Semantic Scholar
- 153d55053538f31ab6e2732f9a72d6f7e8d68d83
- Cited by
- 65
- References
- 33
- Citations by year
- 2026: 16 · 2025: 23 · 2024: 8 · 2023: 14 · 2022: 4
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Small (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- 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 › Engineering › Electrical and Electronic Engineering › Electrowetting and Microfluidic Technologies
- Keywords
- DNA data storage, DNA encapsulation, silica nanoparticles, digital microfluidics, data archiving, automated data retrieval, storage capacity, accelerated aging, DNA libraries
- MeSH terms
- DNA, Glass, Temperature, Information Storage and Retrieval, Microfluidics
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