101
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Razavi S, Su S, Inoue T. Cellular signaling circuits interfaced with synthetic, post-translational, negating Boolean logic devices. ACS Synth Biol 2014; 3:676-85. [PMID: 25000210 PMCID: PMC4169742 DOI: 10.1021/sb500222z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 12/11/2022]
Abstract
A negating functionality is fundamental to information processing of logic circuits within cells and computers. Aiming to adapt unutilized electronic concepts to the interrogation of signaling circuits in cells, we first took a bottom-up strategy whereby we created protein-based devices that perform negating Boolean logic operations such as NOT, NOR, NAND, and N-IMPLY. These devices function in living cells within a minute by precisely commanding the localization of an activator molecule among three subcellular spaces. We networked these synthetic gates to an endogenous signaling circuit and devised a physiological output. In search of logic functions in signal transduction, we next took a top-down approach and computationally screened 108 signaling pathways to identify commonalities and differences between these biological pathways and electronic circuits. This combination of synthetic and systems approaches will guide us in developing foundations for deconstruction of intricate cell signaling, as well as construction of biomolecular computers.
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Affiliation(s)
- Shiva Razavi
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Steven Su
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
| | - Takanari Inoue
- Department of Biomedical Engineering, Department of Cell Biology, and Center for Cell
Dynamics, Johns Hopkins University School
of Medicine, Baltimore, Maryland 21205, United
States
- Japan
Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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102
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Nikitin MP, Shipunova VO, Deyev SM, Nikitin PI. Biocomputing based on particle disassembly. NATURE NANOTECHNOLOGY 2014; 9:716-722. [PMID: 25129073 DOI: 10.1038/nnano.2014.156] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Nanoparticles with biocomputing capabilities could potentially be used to create sophisticated robotic devices with a variety of biomedical applications, including intelligent sensors and theranostic agents. DNA/RNA-based computing techniques have already been developed that can offer a complete set of Boolean logic functions and have been used, for example, to analyse cells and deliver molecular payloads. However, the computing potential of particle-based systems remains relatively unexplored. Here, we show that almost any type of nanoparticle or microparticle can be transformed into autonomous biocomputing structures that are capable of implementing a functionally complete set of Boolean logic gates (YES, NOT, AND and OR) and binding to a target as result of a computation. The logic-gating functionality is incorporated into self-assembled particle/biomolecule interfaces (demonstrated here with proteins) and the logic gating is achieved through input-induced disassembly of the structures. To illustrate the capabilities of the approach, we show that the structures can be used for logic-gated cell targeting and advanced immunoassays.
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Affiliation(s)
- Maxim P Nikitin
- 1] Prokhorov General Physics Institute, Russian Academy of Sciences, Natural Science Centre, 38 Vavilov St, Moscow 119991, Russia [2] Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia [3] Moscow Institute of Physics and Technology, 9 Institutskii per., Dolgoprudny, Moscow Region 141700, Russia
| | - Victoria O Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia
| | - Sergey M Deyev
- 1] Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, Moscow 117997, Russia [2] Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Av., Nizhny Novgorod 603950, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute, Russian Academy of Sciences, Natural Science Centre, 38 Vavilov St, Moscow 119991, Russia
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103
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Singh V. Recent advances and opportunities in synthetic logic gates engineering in living cells. SYSTEMS AND SYNTHETIC BIOLOGY 2014; 8:271-82. [PMID: 26396651 DOI: 10.1007/s11693-014-9154-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 08/09/2014] [Accepted: 08/23/2014] [Indexed: 01/03/2023]
Abstract
Recently, a number of synthetic biologic gates including AND, OR, NOR, NOT, XOR and NAND have been engineered and characterized in a wide range of hosts. The hope in the emerging synthetic biology community is to construct an inventory of well-characterized parts and install distinct gene and circuit behaviours that are externally controllable. Though the field is still growing and major successes are yet to emerge, the payoffs are predicted to be significant. In this review, we highlight specific examples of logic gates engineering with applications towards fundamental understanding of network complexity and generating a novel socially useful applications.
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Affiliation(s)
- Vijai Singh
- Department of Biotechnology, Invertis University, Bareilly- Lucknow National Highway-24, Bareilly, 243123 India ; Synthetic Biology Laboratory, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulju-gun, Ulsan, 689-798 Republic of Korea
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104
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Yang B, Zhang XB, Kang LP, Huang ZM, Shen GL, Yu RQ, Tan W. Intelligent layered nanoflare: "lab-on-a-nanoparticle" for multiple DNA logic gate operations and efficient intracellular delivery. NANOSCALE 2014; 6:8990-8996. [PMID: 24969570 DOI: 10.1039/c4nr01676a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA strand displacement cascades have been engineered to construct various fascinating DNA circuits. However, biological applications are limited by the insufficient cellular internalization of naked DNA structures, as well as the separated multicomponent feature. In this work, these problems are addressed by the development of a novel DNA nanodevice, termed intelligent layered nanoflare, which integrates DNA computing at the nanoscale, via the self-assembly of DNA flares on a single gold nanoparticle. As a "lab-on-a-nanoparticle", the intelligent layered nanoflare could be engineered to perform a variety of Boolean logic gate operations, including three basic logic gates, one three-input AND gate, and two complex logic operations, in a digital non-leaky way. In addition, the layered nanoflare can serve as a programmable strategy to sequentially tune the size of nanoparticles, as well as a new fingerprint spectrum technique for intelligent multiplex biosensing. More importantly, the nanoflare developed here can also act as a single entity for intracellular DNA logic gate delivery, without the need of commercial transfection agents or other auxiliary carriers. By incorporating DNA circuits on nanoparticles, the presented layered nanoflare will broaden the applications of DNA circuits in biological systems, and facilitate the development of DNA nanotechnology.
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Affiliation(s)
- Bin Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P.R. China.
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105
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Shong J, Collins CH. Quorum sensing-modulated AND-gate promoters control gene expression in response to a combination of endogenous and exogenous signals. ACS Synth Biol 2014; 3:238-46. [PMID: 24175658 DOI: 10.1021/sb4000965] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have constructed and characterized two synthetic AND-gate promoters that require both a quorum-sensing (QS) signal and an exogenously added inducer to turn on gene expression. The engineered promoters, LEE and TTE, contain binding sites for the QS-dependent repressor, EsaR, and either LacI or TetR, and they are induced by an acyl-homoserine lactone (AHL) signal and IPTG or aTc. Although repression of both LEE and TTE by wild-type EsaR was observed, induction of gene expression at physiologically relevant concentrations of AHL required the use of an EsaR variant with higher signal sensitivity. Gene expression from both LEE and TTE was shown to require both signal molecules, and gene expression above background levels was not observed with either signal alone. We added endogenous production of AHL to evaluate the ability of the promoters to function in a QS-dependent manner and observed that gene expression increased as a function of cell density only in the presence of exogenously added IPTG or aTc. Cell-cell communication-dependent AND-gate behaviors were demonstrated using an agar plate assay, where cells containing the engineered promoters were shown to respond to AHL produced by a second E. coli strain only in the presence of exogenously added IPTG or aTc. The promoters described in this work demonstrate that EsaR and its target DNA sequence can be used to engineer new promoters to respond to cell density or cell-cell communication. Further, the AND-gate promoters described here may serve as a template for new regulatory systems that integrate QS and the presence of key metabolites or other environmental cues to enable dynamic changes in gene expression for metabolic engineering applications.
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Affiliation(s)
- Jasmine Shong
- Department of Chemical
and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York 12180 United States of America
- Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York 12180 United States of America
| | - Cynthia H. Collins
- Department of Chemical
and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York 12180 United States of America
- Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York 12180 United States of America
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy New
York 12180 United States of America
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106
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Hettie KS, Klockow JL, Glass TE. Three-Input Logic Gates with Potential Applications for Neuronal Imaging. J Am Chem Soc 2014; 136:4877-80. [DOI: 10.1021/ja501211v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kenneth S. Hettie
- Department of Chemistry, University of Missouri 601 South College Avenue, Columbia, Missouri 65211, United States
| | - Jessica L. Klockow
- Department of Chemistry, University of Missouri 601 South College Avenue, Columbia, Missouri 65211, United States
| | - Timothy E. Glass
- Department of Chemistry, University of Missouri 601 South College Avenue, Columbia, Missouri 65211, United States
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107
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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108
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Lin JH, Tseng WL. Design of two and three input molecular logic gates using non-Watson–Crick base pairing-based molecular beacons. Analyst 2014; 139:1436-41. [DOI: 10.1039/c3an02298f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A single, resettable, and sensitive molecular beacon has been developed to operate two-input, three-input, and set–reset logic gates.
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Affiliation(s)
- Jia-Hui Lin
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry
- National Sun Yat-sen University
- Kaohsiung 80424, Taiwan
- School of Pharmacy
- College of Pharmacy
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109
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Privman V, Zavalov O, Halámková L, Moseley F, Halámek J, Katz E. Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application. J Phys Chem B 2013; 117:14928-39. [DOI: 10.1021/jp408973g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | - Lenka Halámková
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | | | - Jan Halámek
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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110
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Hemphill J, Deiters A. DNA Computation in Mammalian Cells: MicroRNA Logic Operations. J Am Chem Soc 2013; 135:10512-8. [DOI: 10.1021/ja404350s] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James Hemphill
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
| | - Alexander Deiters
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United
States
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111
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Moe-Behrens GH. The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 2013; 7:e201304003. [PMID: 24688733 PMCID: PMC3962179 DOI: 10.5936/csbj.201304003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 01/21/2023] Open
Abstract
Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
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112
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Huynh L, Tsoukalas A, Köppe M, Tagkopoulos I. SBROME: a scalable optimization and module matching framework for automated biosystems design. ACS Synth Biol 2013; 2:263-73. [PMID: 23654271 DOI: 10.1021/sb300095m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The development of a scalable framework for biodesign automation is a formidable challenge given the expected increase in part availability and the ever-growing complexity of synthetic circuits. To allow for (a) the use of previously constructed and characterized circuits or modules and (b) the implementation of designs that can scale up to hundreds of nodes, we here propose a divide-and-conquer Synthetic Biology Reusable Optimization Methodology (SBROME). An abstract user-defined circuit is first transformed and matched against a module database that incorporates circuits that have previously been experimentally characterized. Then the resulting circuit is decomposed to subcircuits that are populated with the set of parts that best approximate the desired function. Finally, all subcircuits are subsequently characterized and deposited back to the module database for future reuse. We successfully applied SBROME toward two alternative designs of a modular 3-input multiplexer that utilize pre-existing logic gates and characterized biological parts.
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Affiliation(s)
- Linh Huynh
- Department of Computer Science and UC Davis
Genome Center and ‡Department of Mathematics, University of California, Davis, California 95616 United States
| | - Athanasios Tsoukalas
- Department of Computer Science and UC Davis
Genome Center and ‡Department of Mathematics, University of California, Davis, California 95616 United States
| | - Matthias Köppe
- Department of Computer Science and UC Davis
Genome Center and ‡Department of Mathematics, University of California, Davis, California 95616 United States
| | - Ilias Tagkopoulos
- Department of Computer Science and UC Davis
Genome Center and ‡Department of Mathematics, University of California, Davis, California 95616 United States
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113
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Abstract
Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.
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Affiliation(s)
- Jerome Bonnet
- Department of Bioengineering, Y2E2-269B, 473 Via Ortega, Stanford, CA 94305-4201, USA
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114
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MacVittie K, Halámek J, Privman V, Katz E. A bioinspired associative memory system based on enzymatic cascades. Chem Commun (Camb) 2013; 49:6962-4. [DOI: 10.1039/c3cc43272f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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