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      A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami

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          Abstract

          Here we design a DNA origami-based site-specific molecular capture and release platform operated by a DNAzyme-mediated logic gate process.

          Abstract

          Here we design a DNA origami-based site-specific molecular capture and release platform operated by a DNAzyme-mediated logic gate process. We show the programmability and versatility of this platform with small molecules, proteins, and nanoparticles, which may also be controlled by external light signals.

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          A logic-gated nanorobot for targeted transport of molecular payloads.

          Shawn M. Douglas, Ido Bachelet, George M. Church (2012)
          We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery. The device can be loaded with a variety of materials in a highly organized fashion and is controlled by an aptamer-encoded logic gate, enabling it to respond to a wide array of cues. We implemented several different logical AND gates and demonstrate their efficacy in selective regulation of nanorobot function. As a proof of principle, nanorobots loaded with combinations of antibody fragments were used in two different types of cell-signaling stimulation in tissue culture. Our prototype could inspire new designs with different selectivities and biologically active payloads for cell-targeting tasks.
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            Dynamic DNA nanotechnology using strand-displacement reactions.

            David Zhang, Georg Seelig (2011)
            The specificity and predictability of Watson-Crick base pairing make DNA a powerful and versatile material for engineering at the nanoscale. This has enabled the construction of a diverse and rapidly growing set of DNA nanostructures and nanodevices through the programmed hybridization of complementary strands. Although it had initially focused on the self-assembly of static structures, DNA nanotechnology is now also becoming increasingly attractive for engineering systems with interesting dynamic properties. Various devices, including circuits, catalytic amplifiers, autonomous molecular motors and reconfigurable nanostructures, have recently been rationally designed to use DNA strand-displacement reactions, in which two strands with partial or full complementarity hybridize, displacing in the process one or more pre-hybridized strands. This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour.
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              Enzyme-free nucleic acid logic circuits.

              Georg Seelig, David Soloveichik, David Yu Zhang … (2006)
              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.
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                Author and article information

                Journal
                Journal ID (publisher-id): CHCOFS
                Title: Chemical Communications
                Abbreviated Title: Chem. Commun.
                Publisher: Royal Society of Chemistry (RSC)
                ISSN (Print): 1359-7345
                ISSN (Electronic): 1364-548X
                Publication date Created: 2016
                Publication date (Electronic): 2016
                Volume: 52
                Issue: 54
                Pages: 8369-8372
                Affiliations
                [1 ]School of Mechanical Engineering
                [2 ]Purdue University
                [3 ]West Lafayette
                [4 ]USA
                [5 ]Centre for Bio/Molecular Science and Engineering
                [6 ]Code 6900 U.S. Naval Research Laboratory
                [7 ]Washington DC 20375
                Article
                DOI: 10.1039/C6CC02989B
                PubMed ID: 27211274
                SO-VID: 8ffb9624-3ae0-4bf3-9f73-74caeb3dc31a
                Copyright © © 2016
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