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Xu J, Wu ZS, Shen W, Xu H, Li H, Jia L. Cascade DNA nanomachine and exponential amplification biosensing. Biosens Bioelectron 2015; 73:19-25. [DOI: 10.1016/j.bios.2015.05.045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/15/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023]
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2
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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3
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Hockenberry AJ, Jewett MC. Synthetic in vitro circuits. Curr Opin Chem Biol 2012; 16:253-9. [PMID: 22676890 PMCID: PMC3424401 DOI: 10.1016/j.cbpa.2012.05.179] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/17/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022]
Abstract
Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality.
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Affiliation(s)
- Adam J. Hockenberry
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Northwestern University, 303 E. Superior, Chicago, IL 60611, USA
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4
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Ayukawa S, Sakai Y, Kiga D. An aptazyme-based molecular device that converts a small-molecule input into an RNA output. Chem Commun (Camb) 2012; 48:7556-8. [PMID: 22543508 DOI: 10.1039/c2cc31886e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the construction of an aptazyme-based molecular device that converts, through a cascade of reactions, a small-molecule input into output RNA strands. This device is applicable as an interface between a small molecule and a molecular system that accepts only nucleic acid input.
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Affiliation(s)
- Shotaro Ayukawa
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan 226-8503
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5
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Shin J, Noireaux V. An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth Biol 2012; 1:29-41. [PMID: 23651008 DOI: 10.1021/sb200016s] [Citation(s) in RCA: 275] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cell-free protein synthesis is becoming a powerful technique to construct and to study complex informational processes in vitro. Engineering synthetic gene circuits in a test tube, however, is seriously limited by the transcription repertoire of modern cell-free systems, composed of only a few bacteriophage regulatory elements. Here, we report the construction and the phenomenological characterization of synthetic gene circuits engineered with a cell-free expression toolbox that works with the seven E. coli sigma factors. The E. coli endogenous holoenzyme E(70) is used as the primary transcription machinery. Elementary circuit motifs, such as multiple stage cascades, AND gate and negative feedback loops are constructed with the six other sigma factors, two bacteriophage RNA polymerases, and a set of repressors. The circuit dynamics reveal the importance of the global mRNA turnover rate and of passive competition-induced transcriptional regulation. Cell-free reactions can be carried out over long periods of time with a small-scale dialysis reactor or in phospholipid vesicles, an artificial cell system. This toolbox is a unique platform to study complex transcription/translation-based biochemical systems in vitro.
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Affiliation(s)
- Jonghyeon Shin
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota
55455, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota
55455, United States
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6
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Timing molecular motion and production with a synthetic transcriptional clock. Proc Natl Acad Sci U S A 2011; 108:E784-93. [PMID: 21921236 DOI: 10.1073/pnas.1100060108] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of "load" processes such as the operation of a DNA-based nanomechanical device ("DNA tweezers") or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an "insulator circuit" was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems.
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9
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Noireaux V, Maeda YT, Libchaber A. Development of an artificial cell, from self-organization to computation and self-reproduction. Proc Natl Acad Sci U S A 2011; 108:3473-80. [PMID: 21317359 PMCID: PMC3048108 DOI: 10.1073/pnas.1017075108] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This article describes the state and the development of an artificial cell project. We discuss the experimental constraints to synthesize the most elementary cell-sized compartment that can self-reproduce using synthetic genetic information. The original idea was to program a phospholipid vesicle with DNA. Based on this idea, it was shown that in vitro gene expression could be carried out inside cell-sized synthetic vesicles. It was also shown that a couple of genes could be expressed for a few days inside the vesicles once the exchanges of nutrients with the outside environment were adequately introduced. The development of a cell-free transcription/translation toolbox allows the expression of a large number of genes with multiple transcription factors. As a result, the development of a synthetic DNA program is becoming one of the main hurdles. We discuss the various possibilities to enrich and to replicate this program. Defining a program for self-reproduction remains a difficult question as nongenetic processes, such as molecular self-organization, play an essential and complementary role. The synthesis of a stable compartment with an active interface, one of the critical bottlenecks in the synthesis of artificial cell, depends on the properties of phospholipid membranes. The problem of a self-replicating artificial cell is a long-lasting goal that might imply evolution experiments.
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Affiliation(s)
- Vincent Noireaux
- University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455; and
| | - Yusuke T. Maeda
- The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Albert Libchaber
- The Rockefeller University, 1230 York Avenue, New York, NY 10021
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10
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Karzbrun E, Shin J, Bar-Ziv RH, Noireaux V. Coarse-grained dynamics of protein synthesis in a cell-free system. PHYSICAL REVIEW LETTERS 2011; 106:048104. [PMID: 21405367 DOI: 10.1103/physrevlett.106.048104] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Indexed: 05/30/2023]
Abstract
A complete gene expression reaction is reconstituted in a cell-free system comprising the entire endogenous transcription, translation, as well as mRNA and protein degradation machinery of E. coli. In dissecting the major reaction steps, we derive a coarse-grained enzymatic description of biosynthesis and degradation, from which ten relevant rate constants and concentrations are determined. Governed by zeroth-order degradation, protein expression follows a sharp transition from undetectable levels to constant-rate accumulation, without reaching steady state.
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Affiliation(s)
- Eyal Karzbrun
- Department of Materials and Interfaces, the Weizmann Institute of Science, Rehovot, Israel
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11
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Zhou M, Liang X, Mochizuki T, Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed Engl 2010; 49:2167-70. [PMID: 20175178 DOI: 10.1002/anie.200907082] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mengguang Zhou
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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12
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Zhou M, Liang X, Mochizuki T, Asanuma H. A Light-Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907082] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Ren X, He F, Xu QH. Direct Visualization of Conformational Switch of i-Motif DNA with a Cationic Conjugated Polymer. Chem Asian J 2010; 5:1094-8. [DOI: 10.1002/asia.200900496] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Bar M, Bar-Ziv RH. Spatially resolved DNA brushes on a chip: gene activation by enzymatic cascade. NANO LETTERS 2009; 9:4462-4466. [PMID: 19835406 DOI: 10.1021/nl902748g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We assemble on a chip spatially resolved DNA polymer brushes with density that can be controlled along continuous gradients, from dilute to dense packing, with 20-30 nm between DNA molecules. Investigation of DNA digestion in a approximately 1 kb DNA brush showed that endonucleases can digest within the brush, yet their activity is impeded at high DNA density and for restriction sites near the bottom. Local gene activation-a form of switch-was then demonstrated by a digestion-ligation cascade between two spatially resolved DNA brushes, leading to the in situ expression of green fluorescent protein upon a diffusion-controlled DNA swapping.
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Affiliation(s)
- Maya Bar
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
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15
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Buxboim A, Daube SS, Bar-Ziv R. Ultradense synthetic gene brushes on a chip. NANO LETTERS 2009; 9:909-913. [PMID: 19170553 DOI: 10.1021/nl8039124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Dense brushes of linear DNA polymers are assembled on a biochip with approximately 30 nm between anchorage points, amounting to a few mega-base-pairs/microm(3). In bulk solution, a barrier incurs to conjugate more than two end-functionalized DNAs. However, such doublets bind the surface with almost equal efficiency to singlets, suggesting that extended brush buildup reduces the barrier. On-chip transcription reveals that doublets are roughly 2-fold inefficient compared to singlets, a manifestation of the interaction of the enzymatic machinery with the dense brush. Synthetic gene brushes made of DNA conjugates provide simple means to regulate expression on a chip.
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Affiliation(s)
- Amnon Buxboim
- Department of Materials and Interfaces and Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Ko SH, Chen Y, Shu D, Guo P, Mao C. Reversible switching of pRNA activity on the DNA packaging motor of bacteriophage phi29. J Am Chem Soc 2009; 130:17684-7. [PMID: 19049308 DOI: 10.1021/ja806075d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper reports a reversible switching of the biological activity of an RNA molecule, packaging RNA (pRNA), which is a central component of the DNA packaging motor of bacteriophage phi29. The switching mechanism contains two components: (1) inhibition of pRNA by a short antisense DNA (asDNA) that can bind to the 3' end of the pRNA and inactivate the packaging motor; and (2) reactivation of pRNA by isothermal removal of asDNA from pRNA through a strand displacement strategy. The switching process can be repeated for multiple cycles and has been demonstrated by gel electrophoresis and a virion assembly assay.
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Affiliation(s)
- Seung Hyeon Ko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
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17
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Synthetic gene brushes: a structure-function relationship. Mol Syst Biol 2008; 4:181. [PMID: 18414482 PMCID: PMC2387232 DOI: 10.1038/msb.2008.20] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 02/25/2008] [Indexed: 11/09/2022] Open
Abstract
We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end-immobilized linear double-stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene-to-protein relationship of firefly luciferase under the T7/E.Coli-extract expression system, as well as transcription-only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A 'structure-function' picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two-dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells.
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18
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Jungmann R, Renner S, Simmel FC. From DNA nanotechnology to synthetic biology. HFSP JOURNAL 2008; 2:99-109. [PMID: 19404476 DOI: 10.2976/1.2896331] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Indexed: 01/16/2023]
Abstract
Attempts to construct artificial systems from biological molecules such as DNA and RNA by self-assembly are compatible with the recent development of synthetic biology. Genetic mechanisms can be used to produce or control artificial structures made from DNA and RNA, and these structures can in turn be used as artificial gene regulatory elements, in vitro as well as in vivo. Artificial biochemical circuits can be incorporated into cell-like reaction compartments, which opens up the possibility to operate them permanently out of equilibrium. In small systems, stochastic effects become noticeable and will have to be accounted for in the design of future systems.
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Affiliation(s)
- Ralf Jungmann
- Physics Department E14, Technical University Munich, James-Franck-Strasse, 85748 Garching, Germany
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19
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Nakayama K, Tachikawa T, Majima T. Protein recording material: photorecord/erasable protein array using a UV-eliminative linker. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:1625-1628. [PMID: 18211110 DOI: 10.1021/la703354c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Protein patterning on solid surfaces is a topic of significant importance in the fields of biosensors, diagnostic assays, cell adhesion technologies, and biochip microarrays. In this letter, we have established a novel, rapid method for the fabrication of a "protein recording material", which enables us to spatiotemporally regulate the recording, reading, and erasing of a fluorescent protein array as information by a photochemical technique. A photolinker that we synthesized here was used to control the protein array spatiotemporally. The recording process was almost completed after 1 min of photoirradiation to read a clear pattern consisting of a specific protein-ligand complex with high spatiotemporal resolution. The erasing of the protein array was then achieved by photoirradiation onto the entire patterned surface.
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Affiliation(s)
- Koji Nakayama
- The Institute of Scientific and Industrial Research (ISIR), Osaka University Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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20
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Abstract
DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.
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Affiliation(s)
- Friedrich C Simmel
- Technical University Munich, Physics Department E14, James-Franck-Straße D-85748 Garching, Germany
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21
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Affiliation(s)
- Roy Bar-Ziv
- The author is in the Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
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Nakashima T, Sakashita M, Nonoguchi Y, Kawai T. Sensitized Photopolymerization of an Ionic Liquid-Based Monomer by Using CdTe Nanocrystals. Macromolecules 2007. [DOI: 10.1021/ma0707988] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Takuya Nakashima
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Makiko Sakashita
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshiyuki Nonoguchi
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tsuyoshi Kawai
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Abstract
We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.
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Affiliation(s)
- Jonathan Bath
- University of Oxford, Department of Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK
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Kay ER, Leigh DA, Zerbetto F. Synthetic molecular motors and mechanical machines. Angew Chem Int Ed Engl 2007; 46:72-191. [PMID: 17133632 DOI: 10.1002/anie.200504313] [Citation(s) in RCA: 2047] [Impact Index Per Article: 120.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.
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Affiliation(s)
- Euan R Kay
- School of Chemistry, University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, UK
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25
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Kay E, Leigh D, Zerbetto F. Synthetische molekulare Motoren und mechanische Maschinen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200504313] [Citation(s) in RCA: 587] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Abstract
Long admired for its informational role in the cell, DNA is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered DNA sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid DNA structures that serve as scaffolds for the organization of matter at the molecular scale, and can build simple DNA-computing devices, diagnostic machines and DNA motors. The integration of biological and engineering advances offers great potential for therapeutic and diagnostic applications, and for nanoscale electronic engineering.
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Affiliation(s)
- Anne Condon
- The Department of Computer Science, 2366 Main Mall, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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Beyer S, Simmel FC. A modular DNA signal translator for the controlled release of a protein by an aptamer. Nucleic Acids Res 2006; 34:1581-7. [PMID: 16547201 PMCID: PMC1409677 DOI: 10.1093/nar/gkl075] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 03/03/2006] [Accepted: 03/03/2006] [Indexed: 11/14/2022] Open
Abstract
Owing to the intimate linkage of sequence and structure in nucleic acids, DNA is an extremely attractive molecule for the development of molecular devices, in particular when a combination of information processing and chemomechanical tasks is desired. Many of the previously demonstrated devices are driven by hybridization between DNA 'effector' strands and specific recognition sequences on the device. For applications it is of great interest to link several of such molecular devices together within artificial reaction cascades. Often it will not be possible to choose DNA sequences freely, e.g. when functional nucleic acids such as aptamers are used. In such cases translation of an arbitrary 'input' sequence into a desired effector sequence may be required. Here we demonstrate a molecular 'translator' for information encoded in DNA and show how it can be used to control the release of a protein by an aptamer using an arbitrarily chosen DNA input strand. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences.
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Affiliation(s)
- Stefan Beyer
- Department of Physics and Center for Nanoscience, LMU MünchenGeschwister-Scholl-Platz 1, 80539 München, Germany
| | - Friedrich C. Simmel
- Department of Physics and Center for Nanoscience, LMU MünchenGeschwister-Scholl-Platz 1, 80539 München, Germany
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28
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Abstract
Nucleic acids include substantial information in their base sequence and their hybridization-complexation motifs. Recent research efforts attempt to utilize this biomolecular information to develop DNA nanostructures exhibiting machine-like functions. DNA nano-assemblies revealing tweezers, motor, and walker activities exemplify a few such machines. The DNA-based machines provide new components that act as sensitive sensors, transporters, or drug delivery systems.
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Affiliation(s)
- Moritz K Beissenhirtz
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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