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  • 1
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    Engineering entropy-driven reactions and networks catalyzed by DNA (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-17
    Description: Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, David Yu -- Turberfield, Andrew J -- Yurke, Bernard -- Winfree, Erik -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1121-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computation and Neural Systems, California Institute of Technology, MC 136-93, 1200 East California Boulevard, Pasadena, CA91125, USA. dzhang@dna.caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18006742" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Catalysis ; Chemical Engineering ; *Computers, Molecular ; DNA/*chemistry ; Entropy ; Equipment Design ; Feedback, Physiological ; Mice ; Nanotechnology ; Nucleic Acid Hybridization ; Rabbits
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Enzyme-free nucleic acid logic circuits (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-13
    Description: Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation. We report the design and experimental implementation of DNA-based digital logic circuits. We demonstrate AND, OR, and NOT gates, signal restoration, amplification, feedback, and cascading. Gate design and circuit construction is modular. The gates use single-stranded nucleic acids as inputs and outputs, and the mechanism relies exclusively on sequence recognition and strand displacement. Biological nucleic acids such as microRNAs can serve as inputs, suggesting applications in biotechnology and bioengineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seelig, Georg -- Soloveichik, David -- Zhang, David Yu -- Winfree, Erik -- New York, N.Y. -- Science. 2006 Dec 8;314(5805):1585-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17158324" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Pairing ; Base Sequence ; *Biotechnology ; *Computers, Molecular ; *Dna ; *DNA, Single-Stranded ; Logic ; Mice ; MicroRNAs ; Nanostructures ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Ultrafast chemical imaging by widefield photothermal sensing of infrared absorption (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Infrared (IR) imaging has become a viable tool for visualizing various chemical bonds in a specimen. The performance, however, is limited in terms of spatial resolution and imaging speed. Here, instead of measuring the loss of the IR beam, we use a pulsed visible light for high-throughput, widefield sensing of the transient photothermal effect induced by absorption of single mid-IR pulses. To extract these transient signals, we built a virtual lock-in camera synchronized to the visible probe and IR light pulses with precisely controlled delays, allowing submicrosecond temporal resolution determined by the probe pulse width. Our widefield photothermal sensing microscope enabled chemical imaging at a speed up to 1250 frames/s, with high spectral fidelity, while offering submicrometer spatial resolution. With the capability of imaging living cells and nanometer-scale polymer films, widefield photothermal microscopy opens a new way for high-throughput characterization of biological and material specimens.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Machine learning-enabled identification of material phase transitions based on experimental data: Exploring collective dynamics in ferroelectric relaxors (2018)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2018-03-31
    Description: Exploration of phase transitions and construction of associated phase diagrams are of fundamental importance for condensed matter physics and materials science alike, and remain the focus of extensive research for both theoretical and experimental studies. For the latter, comprehensive studies involving scattering, thermodynamics, and modeling are typically required. We present a new approach to data mining multiple realizations of collective dynamics, measured through piezoelectric relaxation studies, to identify the onset of a structural phase transition in nanometer-scale volumes, that is, the probed volume of an atomic force microscope tip. Machine learning is used to analyze the multidimensional data sets describing relaxation to voltage and thermal stimuli, producing the temperature-bias phase diagram for a relaxor crystal without the need to measure (or know) the order parameter. The suitability of the approach to determine the phase diagram is shown with simulations based on a two-dimensional Ising model. These results indicate that machine learning approaches can be used to determine phase transitions in ferroelectrics, providing a general, statistically significant, and robust approach toward determining the presence of critical regimes and phase boundaries.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Long-term viability of carbon sequestration in deep-sea sediments (2018)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2018-07-05
    Description: Sequestration of carbon dioxide in deep-sea sediments has been proposed for the long-term storage of anthropogenic CO 2 that can take advantage of the current offshore infrastructure. It benefits from the negative buoyancy effect and hydrate formation under conditions of high pressure and low temperature. However, the multiphysics process of injection and postinjection fate of CO 2 and the feasibility of subseabed disposal of CO 2 under different geological and operational conditions have not been well studied. With a detailed study of the coupled processes, we investigate whether storing CO 2 into deep-sea sediments is viable, efficient, and secure over the long term. We also study the evolution of multiphase and multicomponent flow and the impact of hydrate formation on storage efficiency. The results show that low buoyancy and high viscosity slow down the ascending plume and the forming of the hydrate cap effectively reduces permeability and finally becomes an impermeable seal, thus limiting the movement of CO 2 toward the seafloor. We identify different flow patterns at varied time scales by analyzing the mass distribution of CO 2 in different phases over time. We observe the formation of a fluid inclusion, which mainly consists of liquid CO 2 and is encapsulated by an impermeable hydrate film in the diffusion-dominated stage. The trapped liquid CO 2 and CO 2 hydrate finally dissolve into the pore water through diffusion of the CO 2 component, resulting in permanent storage. We perform sensitivity analyses on storage efficiency under variable geological and operational conditions. We find that under a deep-sea setting, CO 2 sequestration in intact marine sediments is generally safe and permanent.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA (2017)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2017-06-22
    Description: Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure–based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub–100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 x 60 nm 2 , substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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