DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

In support of the publication "DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access" we share the following datasets and code: AutoCAD drawing of the microfluidic trapping device. Sequences of the DNA used to encode the 25 files used in the current study. FASTQ-files of the sequencing experiments of Figures 5b and d. Python scripts that allow for the reproduction of our sequencing data analysis. The code has been tested on MacOS 13.0.1, Python 3.7.13, samtools 1.16.1 and BWA 0.7.17

Towards Sustainable Electrochemistry: Applications from Femtomolar to Preparative Scale

Electrochemistry provides a versatile method for a variety of synthetic transformations. It has been used in the Moeller lab to generate reactive intermediates to trigger intramolecular cyclization reactions, recycle chemical oxidants on microelectrode arrays, and to study binding interactions of molecules attached to the arrays with biological receptors in solution. Electrochemical techniques have also been demonstrated as a green chemical alternative to many traditional processes. While organic electrochemistry has been widely accepted by the electrochemical community, the synthetic chemistry community has failed to fully appreciate its utility. The goal of this thesis is to demonstrate the versatility and scope of electrochemical techniques from the femtomolar to preparative scale and to emphasize electrochemistry as a sustainable process. First, a series of electrochemically mediated chemical oxidations was explored. Since the selectivity of a chemical oxidant is not always based on oxidation potential and can be influenced by chirality, chelation, and other factors, electrochemical mediated oxidations are an important tool for organic synthesis. In addition, traditional stoichiometric metal oxidants generate a stoichiometric reduction metal waste product that can be avoided in an electrochemically mediated oxidation reaction. The chemical oxidants were recycled on a microelectrode array to functionalize the polymer surface and then scaled to the preparative scale. In doing so, chemical oxidation reactions were performed in an environmentally benign, sustainable manner. On the preparative scale, the electricity used to power the mediated oxidation reactions was supplied by a photovoltaic cell. This was done to emphasize that for electrochemistry to be a green alternative to traditional oxidation methods, it requires a green source of electricity. For electrochemical oxidations to be sustainable the whole process must be considered and that includes the source of the electricity consumed. In a similar vein, the origins of the chemicals used in any electrolysis reaction must be evaluated. Chemicals obtained from biorenewable resources would be an ideal alternative to chemicals derived from petroleum feedstocks. Towards that effort, lignin disassembly to small aromatic monomers was explored. Under solvolytic conditions, raw sawdust could be converted to electron-rich aromatic aldehyde- and cinammyl- monomers. These monomers were then electrochemically processed into synthetic precursors, and their synthetic utility is currently being further studied. Finally, the energy demands and economics of an electrochemical process were investigated. Every electrochemical oxidation is by nature paired with an electrochemical reduction. Only considering the oxidative half reaction is thereby energetically wasteful. For a more efficient electrochemical process, the anodic oxidation reaction must be paired with a useful cathodic reduction reaction. In preliminary studies, the oxidation of lignin-derived substrates was paired with H2 production for in situ generation of H2 for hydrogenation reactions. Currently, the paired electrochemical reduction of CO2 to CO is being explored for use in hydroformylation reactions. In this manner, chemical reagents can be generated on site thus bypassing the costs associated with shipping and storage

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

Improved Environmental Chemistry Property Prediction of Molecules with Graph Machine Learning

Rapid prediction of environmental chemistry properties is critical towards the green and sustainable development of chemical industry and drug discovery. Machine learning methods can be applied to learn the relations between chemical structures and their environmental impact. Graph machine learning, by learning the representations directly from molecular graphs, may enable better predictive power than conventional feature-based models. In this work, we leveraged graph neural networks to predict environmental chemistry properties of molecules. To systematically evaluate the model performance, we selected a representative list of datasets, ranging from solubility to reactivity, and compare directly to commonly used methods. We found that the graph model achieved near state-of-the-art accuracy for all tasks and, for several, improved the accuracy by a large margin over conventional models that rely on human-designed chemical features. This demonstrates that graph machine learning can be a powerful tool to do representation learning for environmental chemistry. Further, we compared the data efficiency of conventional feature-based models and graph neural networks, providing guidance for model selection dependent on the size of datasets and feature requirements

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

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.ISSN:1359-7345ISSN:1364-548

Preparation of Biobased Printed Circuit Board Prototypes Using Poly(furfuryl alcohol) Resin

The present study explores the processability and properties of poly(furfuryl alcohol) (PFA)-based composites and draws comparisons with the industry-standard epoxy resin matrices used in printed circuit board applications. A poly(furfuryl alcohol)-based fiberglass prepreg was used to manufacture composite cores laminated with copper foil, which were then integrated in situ into printed circuit board prototypes through industry-typical manufacturing and assembly processes. Both copper cores and printed boards were tested to characterize the electrical properties and overall quality of the prototypes. The fabrication of the copper cores and manufacturing methods of the printed boards are described, alongside the results from the characterization of the cores and the testing of the printed boards. The inherent advantages and disadvantages of the material are highlighted, and areas of improvement for the processability of the material and reliability of the technology are discussed

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 <i>o</i>-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