Integrating DNA Encapsulates and Digital Microfluidics for Automated Data Storage in DNA.

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.

Preserving DNA in Biodegradable Organosilica Encapsulates.

A core-shell strategy was developed to protect synthetic DNA in organosilica particles encompassing dithiol linkages allowing for a DNA loading of 1.1 wt %. DNA stability tests involving bleach as an oxidant showed that following the procedure DNA was sandwiched between core particles of ca. 450 nm size and a protective outer layer, separating the DNA from the environment. Rapid aging tests at 60 °C and 50% relative humidity revealed that the DNA protected within this material was significantly more stable than nonprotected DNA, with an expected ambient temperature half-life of over 60 years. Still, and due to the presence of the dithiol linkages in the backbone of the organosilica material, the particles degraded in the presence of reducing agents (TCEP and glutathione) and disintegrated within several days in a simulated compost environment, which was employed to test the biodegradability of the material. This is in contrast to DNA encapsulated following state of the art procedures in pure SiO2 particles, which do not biodegrade in the investigated timeframes and conditions. The results show that synthetic DNA protected within dithiol comprising organosilica particles presents a strategy to store digital data at a high storage capacity for long time frames in a fully biodegradable format.

Paired Electrochemical Reactions and the On-Site Generation of a Chemical Reagent.

While the majority of reported paired electrochemical reactions involve carefully matched cathodic and anodic reactions, the precise matching of half reactions in an electrolysis cell is not generally necessary. During a constant current electrolysis almost any oxidation and reduction reaction can be paired, and in the presented work we capitalize on this observation by examining the coupling of anodic oxidation reactions with the production of hydrogen gas for use as a reagent in remote, Pd-catalyzed hydrogenation and hydrogenolysis reactions. To this end, an alcohol oxidation, an oxidative condensation, intramolecular anodic olefin coupling reactions, an amide oxidation, and a mediated oxidation were all shown to be compatible with the generation and use of hydrogen gas at the cathode. This pairing of an electrolysis reaction with the production of a chemical reagent or substrate has the potential to greatly expand the use of more energy efficient paired electrochemical reactions.

Paired Electrolysis in the Simultaneous Production of Synthetic Intermediates and Substrates.

In electrochemical processes, an oxidation half-reaction is always paired with a reduction half-reaction. Although systems for reactions such as the reduction of CO2 can be coupled to water oxidation to produce O2 at the anode, large-scale O2 production is of limited value. One may replace a low-value half-reaction with a compatible half-reaction that can produce a valuable chemical compound and operate at a lower potential. In doing so, both the anodic and cathodic half-reactions yield desirable products with a decreased energy demand. Here we demonstrate a paired electrolysis in the case of the oxidative condensation of syringaldehyde and o-phenylenediamine to give 2-(3,5-dimethoxy-4-hydroxyphenyl)benzimidazole coupled with the reduction of CO2 to CO mediated by molecular electrocatalysts. We also present general principles for evaluating current-voltage characteristics and power demands in paired electrolyzers.

Solvolysis, Electrochemistry, and Development of Synthetic Building Blocks from Sawdust.

Either aldehyde or cinnamyl ether products can be selectively extracted from raw sawdust by controlling the temperature and pressure of a solvolysis reaction. These materials have been used as platform chemicals for the synthesis of 15 different synthetic substrates. The conversion of the initial sawdust-derived materials into electron-rich aryl substrates often requires the use of oxidation and reduction chemistry, and the role electrochemistry can play as a sustainable method for these transformations has been defined.

Photovoltaic-driven organic electrosynthesis and efforts toward more sustainable oxidation reactions.

The combination of visible light, photovoltaics, and electrochemistry provides a convenient, inexpensive platform for conducting a wide variety of sustainable oxidation reactions. The approach presented in this article is compatible with both direct and indirect oxidation reactions, avoids the need for a stoichiometric oxidant, and leads to hydrogen gas as the only byproduct from the corresponding reduction reaction.

Microelectrode arrays: a general strategy for using oxidation reactions to site selectively modify electrode surfaces.

Oxidation reactions are powerful tools for synthesis because they allow for the functionalization of molecules. Here, we present a general method for conducting these reactions on a microelectrode array in a site-selective fashion. The reactions are run as a competition between generation of a chemical oxidant at the electrodes in the array and reduction of the oxidant by a "confining agent" in the solution above the array. The "confining agent" does not need to be more reactive than the substrate fixed to the surface of the array. In many cases, the same substrate placed on the surface of the array can also be used in solution as the confining agent.

Comparative life cycle assessment of copper and gold recovery from waste printed circuit boards: Pyrometallurgy, chemical leaching and bioleaching.

Printed circuit boards (PCBs) make up a substantial amount of electronic waste (e-waste) generated annually. Waste PCBs contain high quantities of copper and gold in comparison to natural ores. As such, "urban mining" of waste PCBs to recover these metals is of commercial interest. In this work, we used life cycle assessment to compare the environmental impact of four copper and gold recovery processes. We evaluated pyrometallurgy, chemical leaching, and bioleaching, as well as a hybrid leaching process that uses bioleaching to recover copper and chemical leaching to recover gold. Furthermore, we considered differences in environmental impact based on differences in electricity sources. If electricity comes from fossil fuels, the pyrometallurgical process results in the lowest environmental impact in all impact categories studied. If electricity comes from carbon-free sources, the pyrometallurgical process results in the lowest environmental impact in all categories studied except global warming, where the hybrid leaching process results in the lowest impact. In all cases, metal recovery from waste PCBs leads to lower environmental impact than primary metal production. Our goal is to guide e-waste recyclers towards more environmentally sustainable metal recovery processes and to provide knowledge gaps in the field to guide future research.

Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system.

DNA data storage is a potential alternative to magnetic tape for archival storage purposes, promising substantial gains in information density. Critical to the success of DNA as a storage media is an understanding of the role of environmental factors on the longevity of the stored information. In this paper, we evaluate the effect of exposure to ionizing particle radiation, a cause of data loss in traditional magnetic media, on the longevity of data in DNA data storage pools. We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. Finally, we experimentally validate our model by exposing dried DNA samples to different levels of neutron irradiation and analyzing the resulting error profile. Our results show that particle radiation is not a significant contributor to data loss in DNA data storage pools under typical storage conditions.

Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate.

Novel enzymatic methods are poised to become the dominant processes for de novo synthesis of DNA, promising functional, economic, and environmental advantages over the longstanding approach of phosphoramidite synthesis. Before this can occur, however, enzymatic synthesis methods must be parallelized to enable production of multiple DNA sequences simultaneously. As a means to this parallelization, we report a polymerase-nucleotide conjugate that is cleaved using electrochemical oxidation on a microelectrode array. The developed conjugate maintains polymerase activity toward surface-bound substrates with single-base control and detaches from the surface at mild oxidative voltages, leaving an extendable oligonucleotide behind. Our approach readies the way for enzymatic DNA synthesis on the scale necessary for DNA-intensive applications such as DNA data storage or gene synthesis.

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization.

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise-the disagreement between model and metric defined candidate rankings-minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries.

DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access.

DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access to information is a desirable property of any storage system. For DNA-based storage systems, however, this still needs to be robustly established. Here we report on a thermoconfined polymerase chain reaction, which enables multiplexed, repeated random access to compartmentalized DNA files. The strategy is based on localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable microcapsules. At low temperatures, microcapsules are permeable to enzymes, primers and amplified products, whereas at high temperatures, membrane collapse prevents molecular crosstalk during amplification. Our data show that the platform outperforms non-compartmentalized DNA storage compared with repeated random access and reduces amplification bias tenfold during multiplex polymerase chain reaction. Using fluorescent sorting, we also demonstrate sample pooling and data retrieval by microcapsule barcoding. Therefore, the thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access to archival DNA files.

Passively sensing SARS-CoV-2 RNA in public transit buses.

Affordably tracking the transmission of respiratory infectious diseases in urban transport infrastructures can inform individuals about potential exposure to diseases and guide public policymakers to prepare timely responses based on geographical transmission in different areas in the city. Towards that end, we designed and tested a method to detect SARS-CoV-2 RNA in the air filters of public buses, revealing that air filters could be used as passive fabric sensors for the detection of viral presence. We placed and retrieved filters in the existing HVAC systems of public buses to test for the presence of trapped SARS-CoV-2 RNA using phenol-chloroform extraction and RT-qPCR. SARS-CoV-2 RNA was detected in 14% (5/37) of public bus filters tested in Seattle, Washington, from August 2020 to March 2021. These results indicate that this sensing system is feasible and that, if scaled, this method could provide a unique lens into the geographically relevant transmission of SARS-CoV-2 through public transit rider vectors, pooling samples of riders over time in a passive manner without installing any additional systems on transit vehicles.

Synthetic DNA applications in information technology.

Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.

Anhydrous calcium phosphate crystals stabilize DNA for dry storage.

The resilience of ancient DNA (aDNA) in bone gives rise to the preservation of synthetic DNA with bioinorganic materials such as calcium phosphate (CaP). Accelerated aging experiments at elevated temperature and humidity displayed a positive effect of co-precipitated, crystalline dicalcium phosphate on the stability of synthetic DNA in contrast to amorphous CaP. Quantitative PXRD in combination with SEM and EDX measurements revealed distinct CaP phase transformations of calcium phosphate dihydrate (brushite) to anhydrous dicalcium phosphate (monetite) influencing DNA stability.

Information decay and enzymatic information recovery for DNA data storage.

Synthetic DNA has been proposed as a storage medium for digital information due to its high theoretical storage density and anticipated long storage horizons. However, under all ambient storage conditions, DNA undergoes a slow chemical decay process resulting in nicked (broken) DNA strands, and the information stored in these strands is no longer readable. In this work we design an enzymatic repair procedure, which is applicable to the DNA pool prior to readout and can partially reverse the damage. Through a chemical understanding of the decay process, an overhang at the 3' end of the damaged site is identified as obstructive to repair via the base excision-repair (BER) mechanism. The obstruction can be removed via the enzyme apurinic/apyrimidinic endonuclease I (APE1), thereby enabling repair of hydrolytically damaged DNA via Bst polymerase and Taq ligase. Simulations of damage and repair reveal the benefit of the enzymatic repair step for DNA data storage, especially when data is stored in DNA at high storage densities (=low physical redundancy) and for long time durations.

An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage.

Synthetic DNA has recently risen as a viable alternative for long-term digital data storage. To ensure that information is safely recovered after storage, it is essential to appropriately preserve the physical DNA molecules encoding the data. While preservation of biological DNA has been studied previously, synthetic DNA differs in that it is typically much shorter in length, it has different sequence profiles with fewer, if any, repeats (or homopolymers), and it has different contaminants. In this paper, nine different methods used to preserve data files encoded in synthetic DNA are evaluated by accelerated aging of nearly 29 000 DNA sequences. In addition to a molecular count comparison, the DNA is also sequenced and analyzed after aging. These findings show that errors and erasures are stochastic and show no practical distribution difference between preservation methods. Finally, the physical density of these methods is compared and a stability versus density trade-offs discussion provided.

Scaling DNA data storage with nanoscale electrode wells.

Synthetic DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, preservation, and sequencing technologies. Despite progress in these areas, the most challenging hurdle in deployment of DNA data storage remains the write throughput, which limits data storage capacity. We have developed the first nanoscale DNA storage writer, which we expect to scale DNA write density to 25 × 106 sequences per square centimeter, three orders of magnitude improvement over existing DNA synthesis arrays. We show confinement of DNA synthesis to an area under 1 square micrometer, parallelized over millions of nanoelectrode wells and then successfully write and decode a message in DNA. DNA synthesis on this scale will enable write throughputs to reach megabytes per second and is a key enabler to a practical DNA data storage system.

Lithium cuprate coupling reactions: evaluation of computational methods for determination of the reaction mechanisms.

Several computational methods were evaluated for determining the gas-phase reaction mechanisms of lithium dimethylcuprate and dimethylcuprate anion with chloromethane and vinyl chloride. These methods include the B3LYP and M06 density functional theory (DFT) methods, the unscaled and spin-component-scaled Moller-Plesset perturbation theory (MP2, SCS-MP2, and SCSC-MP2), CCSD, and CCSD(T). The reaction of interest is an oxidative addition of the alkyl or vinyl halide to the Cu(I) species, resulting in a Cu(III) intermediate, which undergoes reductive elimination with coupling of the two alkyl fragments. Three possible oxidative addition pathways were examined, a concerted addition to Cu(I), an S(N)2-like reaction of Cu on the alkyl halide, and a radical mechanism. A concerted reductive elimination step was also investigated.

Stabilizing synthetic DNA for long-term data storage with earth alkaline salts.

Rapid aging tests (70 °C, 50% RH) of solid state DNA dried in the presence of various salt formulations, showed the strong stabilizing effect of calcium phosphate, calcium chloride and magnesium chloride, even at high DNA loadings (>20 wt%). A DNA-based digital information storage system utilizing the stabilizing effect of MgCl2 was tested by storing a DNA file, encoding 115 kB of digital data, and the successful readout of the file by sequencing after accelerated aging.