151
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Wang X, Yan N, Song T, Wang B, Wei B, Lin L, Chen X, Tian H, Liang H. Robust Fuel Catalyzed DNA Molecular Machine for in Vivo MicroRNA Detection. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojing Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Nan Yan
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
| | - Lin Lin
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun 130022 P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Department of Polymer Science and Engineering; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
- Hefei National Laboratory for Physical Sciences at Microscale; University of Science and Technology of China; Hefei Anhui 230026 P. R. China
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152
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Lee JH, Lee SH, Baek C, Chun H, Ryu JH, Kim JW, Deaton R, Zhang BT. In vitro molecular machine learning algorithm via symmetric internal loops of DNA. Biosystems 2017; 158:1-9. [PMID: 28465242 DOI: 10.1016/j.biosystems.2017.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/12/2017] [Accepted: 04/24/2017] [Indexed: 01/11/2023]
Abstract
Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors. The model was evaluated on a data set of twenty dialogue sentences obtained from the television shows Friends and Prison Break. The wet DNA-computing experiments confirmed that the molecular learning machine was able to generalize the dialogue patterns of each show and successfully identify the show from which the sentences originated. The molecular machine learning model described here opens the way for solving machine learning problems in computer science and biology using in vitro molecular computing with the data encoded in DNA molecules.
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Affiliation(s)
- Ji-Hoon Lee
- Graduate Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Seung Hwan Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Christina Baek
- Graduate Program in Brain Science, Seoul National University, Seoul, Republic of Korea
| | - Hyosun Chun
- School of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
| | - Je-Hwan Ryu
- Graduate Program in Brain Science, Seoul National University, Seoul, Republic of Korea
| | - Jin-Woo Kim
- Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, USA; Bio/Nano Technology Laboratory, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Russell Deaton
- Electrical and Computer Engineering, University of Memphis, Memphis, TN,USA
| | - Byoung-Tak Zhang
- Graduate Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea; Graduate Program in Brain Science, Seoul National University, Seoul, Republic of Korea; School of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea; Graduate Program in Cognitive Science, Seoul National University, Seoul, Republic of Korea.
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153
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Abstract
Nonenzymatic catalytic substrates have been engineered using toehold-mediated DNA strand displacement, and their programmable applications range from medical diagnosis to molecular computation. However, the complexity, stability, scalability, and sensitivity of those systems are plagued by network leakage. A novel way to suppress leakage is to increase its energy barrier through four-way branch migration. Presented here, we designed multi-arm junction substrates that simultaneously exploit four-way branch migration, with a high-energy barrier to minimize leakage, and three-way branch migration, with a low-energy barrier to maximize catalysis. Original feed forward, autocatalytic, and cross-catalytic systems have been designed with polynomial and exponential amplification that exhibit the modularity of linear substrates and the stability of hairpin substrates, creating a new phase space for synthetic biologist, biotechnologist, and DNA nanotechnologists to explore. A key insight is that high-performing circuits can be engineered in the absence of intensive purification and/or extensive rounds of design optimization. Without adopting established leakage suppression techniques, the ratio of the catalytic rate constant to the leakage rate constant is more than 2 orders of magnitude greater than state-of-the-art linear and hairpin substrates. Our results demonstrate that multi-arm junctions have great potential to become central building blocks in dynamic DNA nanotechnology.
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Affiliation(s)
- Shohei Kotani
- Micron School of Materials Science and Engineering, Boise State University , 1910 University Dr., Boise, Idaho 83725, United States
| | - William L Hughes
- Micron School of Materials Science and Engineering, Boise State University , 1910 University Dr., Boise, Idaho 83725, United States
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154
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Gines G, Zadorin AS, Galas JC, Fujii T, Estevez-Torres A, Rondelez Y. Microscopic agents programmed by DNA circuits. NATURE NANOTECHNOLOGY 2017; 12:351-359. [PMID: 28135261 DOI: 10.1038/nnano.2016.299] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 12/14/2016] [Indexed: 05/03/2023]
Abstract
Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics.
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Affiliation(s)
- G Gines
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
| | - A S Zadorin
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - J-C Galas
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - T Fujii
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - A Estevez-Torres
- Laboratoire Jean Perrin, CNRS, Université Pierre et Marie Curie, UMR 8237, 4 place Jussieu, 75005 Paris, France
| | - Y Rondelez
- LIMMS, CNRS, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, 75005 Paris, France
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155
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Aydin C. The Posthuman as Hollow Idol: A Nietzschean Critique of Human Enhancement. THE JOURNAL OF MEDICINE AND PHILOSOPHY 2017; 42:304-327. [DOI: 10.1093/jmp/jhx002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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156
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Foo M, Kim J, Sawlekar R, Bates DG. Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes. Comput Chem Eng 2017; 99:145-157. [PMID: 28392606 PMCID: PMC5362158 DOI: 10.1016/j.compchemeng.2017.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a 'subtractor' that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a biomolecular controller that allows tracking of required changes in the outputs of enzymatic reaction processes can be designed and implemented within the framework of chemical reaction network theory. The controller architecture employs an inversion-based feedforward controller that compensates for the limitations of the one-sided subtractor that generates the error signals for a feedback controller. The proposed approach requires significantly fewer chemical reactions to implement than alternative designs, and should have wide applicability throughout the fields of synthetic biology and biological engineering.
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Affiliation(s)
- Mathias Foo
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Jongrae Kim
- School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - Rucha Sawlekar
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Declan G Bates
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry CV4 7AL, UK
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157
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Song T, Wang X, Liang H. Engineering chemical reaction modules via programming the assembly of DNA hairpins. J Mater Chem B 2017; 5:2297-2301. [PMID: 32263620 DOI: 10.1039/c6tb03098j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The architect of enzyme-free chemical reaction modules, working as building blocks in implementing complex computing tasks, was achieved by modulating the assembly of DNA hairpins, including non-catalytic and catalytic systems. The performance of heterogeneous outputted sequences, which were programmed on different hairpins for triggering the downstream reaction, was asymmetric in the non-catalytic system, whereas symmetric in the catalytic system. Furthermore, complicated DNA-only chemical modules possessing controllable species of inputs or outputs were constructed based on our strategy. The kinetic studies revealed that the performance of the chemical modules was toehold length correlated; on the basis of which, a DNA concentration monitor was constructed.
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Affiliation(s)
- Tingjie Song
- CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
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158
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Antibody-controlled actuation of DNA-based molecular circuits. Nat Commun 2017; 8:14473. [PMID: 28211541 PMCID: PMC5321729 DOI: 10.1038/ncomms14473] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/03/2017] [Indexed: 12/31/2022] Open
Abstract
DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.
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159
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Fern J, Scalise D, Cangialosi A, Howie D, Potters L, Schulman R. DNA Strand-Displacement Timer Circuits. ACS Synth Biol 2017; 6:190-193. [PMID: 27744682 DOI: 10.1021/acssynbio.6b00170] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly of biological complexes to the sequence of embryonic development. However, autonomously directing the timing of events in synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. The rates of DNA release can be tuned to the order of 1-100 nM per day. Multiple timer circuits can release different DNA strands at different rates and times in the same solution. This circuit can thus facilitate precise coordination of chemical events in vitro without external stimulation.
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Affiliation(s)
- Joshua Fern
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dominic Scalise
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Angelo Cangialosi
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dylan Howie
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Leo Potters
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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160
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Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice. Biochem Biophys Res Commun 2017; 485:492-498. [PMID: 28189681 DOI: 10.1016/j.bbrc.2017.02.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/05/2017] [Indexed: 12/14/2022]
Abstract
DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices.
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161
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Abstract
Chemical reaction networks (CRNs) provide a fundamental model in the study of molecular systems. Widely used as formalism for the analysis of chemical and biochemical systems, CRNs have received renewed attention as a model for molecular computation. This paper demonstrates that, with a new encoding, CRNs can compute any set of polynomial functions subject only to the limitation that these functions must map the unit interval to itself. These polynomials can be expressed as linear combinations of Bernstein basis polynomials with positive coefficients less than or equal to 1. In the proposed encoding approach, each variable is represented using two molecular types: a type-0 and a type-1. The value is the ratio of the concentration of type-1 molecules to the sum of the concentrations of type-0 and type-1 molecules. The proposed encoding naturally exploits the expansion of a power-form polynomial into a Bernstein polynomial. Molecular encoders for converting any input in a standard representation to the fractional representation as well as decoders for converting the computed output from the fractional to a standard representation are presented. The method is illustrated first for generic CRNs; then chemical reactions designed for an example are mapped to DNA strand-displacement reactions.
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Affiliation(s)
- Sayed Ahmad Salehi
- Department of Electrical
and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Keshab K. Parhi
- Department of Electrical
and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Marc D. Riedel
- Department of Electrical
and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
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162
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Qu X, Zhu D, Yao G, Su S, Chao J, Liu H, Zuo X, Wang L, Shi J, Wang L, Huang W, Pei H, Fan C. An Exonuclease III-Powered, On-Particle Stochastic DNA Walker. Angew Chem Int Ed Engl 2017; 56:1855-1858. [DOI: 10.1002/anie.201611777] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 12/21/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Dan Zhu
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Guangbao Yao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Shao Su
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Jie Chao
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiye Shi
- Kellogg College; University of Oxford; Oxford OX2 6PN UK
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Lianhui Wang
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Wei Huang
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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163
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Qu X, Zhu D, Yao G, Su S, Chao J, Liu H, Zuo X, Wang L, Shi J, Wang L, Huang W, Pei H, Fan C. An Exonuclease III-Powered, On-Particle Stochastic DNA Walker. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611777] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Dan Zhu
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Guangbao Yao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Shao Su
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Jie Chao
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Jiye Shi
- Kellogg College; University of Oxford; Oxford OX2 6PN UK
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Lianhui Wang
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Wei Huang
- Institute of Advanced Materials; Nanjing University of Posts and Telecommunications; Nanjing 210023 China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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164
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165
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Alistarh D, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust Detection in Leak-Prone Population Protocols. LECTURE NOTES IN COMPUTER SCIENCE 2017. [DOI: 10.1007/978-3-319-66799-7_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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166
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Yao D, Xiao S, Zhou X, Li H, Wang B, Wei B, Liang H. Stacking modular DNA circuitry in cascading self-assembly of spherical nucleic acids. J Mater Chem B 2017; 5:6256-6265. [DOI: 10.1039/c7tb01307h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Integrated circuitries are successfully built through using the cascaded modular strategy with the assistance of stochastic simulations.
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Affiliation(s)
- Dongbao Yao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Xiang Zhou
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Hui Li
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bei Wang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
| | - Bing Wei
- Hefei National Laboratory for Physical Sciences at the Microscale
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
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167
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Song J, Su P, Yang Y, Yang Y. Efficient immobilization of enzymes onto magnetic nanoparticles by DNA strand displacement: a stable and high-performance biocatalyst. NEW J CHEM 2017. [DOI: 10.1039/c7nj00284j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An efficient enzyme immobilization strategy based on toehold-mediated DNA strand displacement on modified magnetic nanoparticles was developed in this study.
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Affiliation(s)
- Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Ye Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
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168
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Fages F, Le Guludec G, Bournez O, Pouly A. Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs. COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY 2017. [DOI: 10.1007/978-3-319-67471-1_7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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169
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Merindol R, Walther A. Materials learning from life: concepts for active, adaptive and autonomous molecular systems. Chem Soc Rev 2017; 46:5588-5619. [DOI: 10.1039/c6cs00738d] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A broad overview of functional aspects in biological and synthetic out-of-equilibrium systems.
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Affiliation(s)
- Rémi Merindol
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry
- Albert-Ludwigs-University Freiburg
- 79106 Freiburg
- Germany
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170
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Zenk J, Scalise D, Wang K, Dorsey P, Fern J, Cruz A, Schulman R. Stable DNA-based reaction–diffusion patterns. RSC Adv 2017. [DOI: 10.1039/c7ra00824d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This paper demonstrates the generation of enzyme free DNA reaction–diffusion gradientsin vitrothat remain stable for tens of hours.
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Affiliation(s)
- John Zenk
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Dominic Scalise
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Kaiyuan Wang
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Phillip Dorsey
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Joshua Fern
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Ariana Cruz
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering
- Johns Hopkins University
- Baltimore
- USA
- Computer Science
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171
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Badelt S, Shin SW, Johnson RF, Dong Q, Thachuk C, Winfree E. A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities. LECTURE NOTES IN COMPUTER SCIENCE 2017. [DOI: 10.1007/978-3-319-66799-7_15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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172
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Armao JJ, Lehn JM. Nonlinear Kinetic Behavior in Constitutional Dynamic Reaction Networks. J Am Chem Soc 2016; 138:16809-16814. [DOI: 10.1021/jacs.6b11107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Joseph J. Armao
- Laboratoire de Chimie Supramoléculaire,
Institut de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire,
Institut de Science et d’Ingénierie Supramoléculaires
(ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
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173
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Foo M, Sawlekar R, Bates DG. Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry. J Biol Eng 2016; 10:15. [PMID: 27872658 PMCID: PMC5108087 DOI: 10.1186/s13036-016-0036-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/19/2016] [Indexed: 01/22/2023] Open
Abstract
Background Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours – ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic. Results In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry. We show that biomolecular circuits based on the dynamics of covalent modification cycles allow (a) the computation of nonlinear operators using far fewer chemical reactions than purely abstract designs based on chemical reaction network theory, and (b) the design of nonlinear feedback controllers with strong performance and robustness properties. Conclusions Our designs provide a more efficient route for translation of complex circuits and systems from chemical reactions to DNA strand displacement-based chemistry, thus facilitating their experimental implementation in future Synthetic Biology applications.
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Affiliation(s)
- Mathias Foo
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, CV4 7AL UK
| | - Rucha Sawlekar
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, CV4 7AL UK
| | - Declan G Bates
- Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, CV4 7AL UK
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174
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Cardelli L, Kwiatkowska M, Laurenti L. Stochastic analysis of Chemical Reaction Networks using Linear Noise Approximation. Biosystems 2016; 149:26-33. [PMID: 27816736 DOI: 10.1016/j.biosystems.2016.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 07/08/2016] [Accepted: 09/01/2016] [Indexed: 10/20/2022]
Abstract
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analyzed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species. We present an approximate model checking algorithm based on the Linear Noise Approximation (LNA) of the CME, whose computational complexity is independent of the population size of each species and polynomial in the number of different species. The algorithm requires the solution of first order polynomial differential equations. We prove that our approach is valid for any CRN close enough to the thermodynamical limit. However, we show on four case studies that it can still provide good approximation even for low molecule counts. Our approach enables rigorous analysis of CRNs that are not analyzable by solving the CME, but are far from the deterministic limit. Moreover, it can be used for a fast approximate stochastic characterization of a CRN.
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Affiliation(s)
- Luca Cardelli
- Department of Computer Science, University of Oxford, United Kingdom; Microsoft Research, Cambridge, United Kingdom.
| | - Marta Kwiatkowska
- Department of Computer Science, University of Oxford, United Kingdom.
| | - Luca Laurenti
- Department of Computer Science, University of Oxford, United Kingdom.
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175
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Briat C, Zechner C, Khammash M. Design of a Synthetic Integral Feedback Circuit: Dynamic Analysis and DNA Implementation. ACS Synth Biol 2016; 5:1108-1116. [PMID: 27345033 DOI: 10.1021/acssynbio.6b00014] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and biofuels, could be easily imagined to rely on such a control strategy in order to optimize production levels and reduce production costs, despite the presence of environmental disturbance and model uncertainty. We propose here a motif that ensures tracking and robust perfect adaptation for the controlled reaction network through integral feedback. Its metabolic load on the host is fully tunable and can be made arbitrarily close to the constitutive limit, the universal minimal metabolic load of all possible controllers. A DNA implementation of the controller network is finally provided. Computer simulations using realistic parameters demonstrate the good agreement between the DNA implementation and the ideal controller dynamics.
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Affiliation(s)
- Corentin Briat
- Department of Biosystems
Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christoph Zechner
- Department of Biosystems
Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems
Science and Engineering, ETH Zürich, Basel, Switzerland
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176
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Yang X, Tang Y, Traynor SM, Li F. Regulation of DNA Strand Displacement Using an Allosteric DNA Toehold. J Am Chem Soc 2016; 138:14076-14082. [DOI: 10.1021/jacs.6b08794] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xiaolong Yang
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Yanan Tang
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Sarah M. Traynor
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
| | - Feng Li
- Department of Chemistry,
Centre for Biotechnology, Brock University, St. Catharines, Ontario Canada, L2S 3A1
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177
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Bi S, Yue S, Wu Q, Ye J. Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing. Biosens Bioelectron 2016; 83:281-6. [DOI: 10.1016/j.bios.2016.04.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/16/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022]
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178
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Fellermann H, Markovitch O, Gilfellon O, Madsen C, Phillips A. Toward Programmable Biology. ACS Synth Biol 2016; 5:793-4. [PMID: 27539571 DOI: 10.1021/acssynbio.6b00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harold Fellermann
- Interdisciplinary Computing
and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne, U.K
| | - Omer Markovitch
- Interdisciplinary Computing
and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne, U.K
| | - Owen Gilfellon
- Interdisciplinary Computing
and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne, U.K
| | - Curtis Madsen
- Cross-disciplinary Integration of Design Automation Research Research Group and Hybrid & Networked Systems Group, Electrical & Computer Engineering Department, Boston University, Boston, Massachusetts, USA
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179
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Abstract
The development of engineered biochemical circuits that exhibit adaptive behavior is a key goal of synthetic biology and molecular computing. Such circuits could be used for long-term monitoring and control of biochemical systems, for instance, to prevent disease or to enable the development of artificial life. In this article, we present a framework for developing adaptive molecular circuits using buffered DNA strand displacement networks, which extend existing DNA strand displacement circuit architectures to enable straightforward storage and modification of behavioral parameters. As a proof of concept, we use this framework to design and simulate a DNA circuit for supervised learning of a class of linear functions by stochastic gradient descent. This work highlights the potential of buffered DNA strand displacement as a powerful circuit architecture for implementing adaptive molecular systems.
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Affiliation(s)
- Matthew R. Lakin
- Department of Chemical & Biological Engineering, ‡Department of Computer Science, and §Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Darko Stefanovic
- Department of Chemical & Biological Engineering, ‡Department of Computer Science, and §Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
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180
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Song T, Garg S, Mokhtar R, Bui H, Reif J. Analog Computation by DNA Strand Displacement Circuits. ACS Synth Biol 2016; 5:898-912. [PMID: 27363950 DOI: 10.1021/acssynbio.6b00144] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.
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Affiliation(s)
- Tianqi Song
- Department
of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Sudhanshu Garg
- Department
of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Reem Mokhtar
- Department
of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Hieu Bui
- Department
of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - John Reif
- Department
of Computer Science, Duke University, Durham, North Carolina 27708, United States
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181
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182
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Bornholt J, Lopez R, Carmean DM, Ceze L, Seelig G, Strauss K. A DNA-Based Archival Storage System. ACTA ACUST UNITED AC 2016. [DOI: 10.1145/2980024.2872397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm
3
(109 GB/mm
3
), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.
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Affiliation(s)
| | | | | | - Luis Ceze
- University of Washington, Seattle, WA, USA
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183
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184
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Genot AJ, Baccouche A, Sieskind R, Aubert-Kato N, Bredeche N, Bartolo JF, Taly V, Fujii T, Rondelez Y. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nat Chem 2016; 8:760-7. [PMID: 27442281 DOI: 10.1038/nchem.2544] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/05/2016] [Indexed: 11/09/2022]
Abstract
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.
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Affiliation(s)
- A J Genot
- LAAS, CNRS, UPR 8001, 7 av. Col. Roche, 31400 Toulouse, France.,LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan
| | - A Baccouche
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,LCBPT, CNRS, UMR 8601, Université Paris Descartes, 45 rue des Saints Pères, 75006 Paris, France
| | - R Sieskind
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,Electrical Engineering and Applied Physics department (EEA), Ecole Normale Superieure of Cachan, 61 avenue du Président Wilson, 94230 Cachan, France.,Laboratoire Gulliver, CNRS, UMR 7083, ESPCI, 10 rue Vauquelin, 75005 Paris, France
| | - N Aubert-Kato
- Ochanomizu University, 112-8610 Tokyo, Japan.,Earth- Life Science Institute (ELSI), Tokyo Institute of Technology, 152-8550 Tokyo, Japan
| | - N Bredeche
- Sorbonne Universités, UPMC Université Paris 06, CNRS, ISIR, F-75005 Paris, France
| | - J F Bartolo
- LCAMB, UMR 7199, CNRS/Université de Strasbourg, F-67400 Illkirch, France.,Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - V Taly
- Université Paris Sorbonne Cité, INSERM UMR-S1147, CNRS SNC 5014, Centre Universitaire des Saints-Pères, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - T Fujii
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan
| | - Y Rondelez
- LIMMS, CNRS-Institute of Industrial Science, UMI 2820, University of Tokyo, 153-8505 Tokyo, Japan.,Laboratoire Gulliver, CNRS, UMR 7083, ESPCI, 10 rue Vauquelin, 75005 Paris, France
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185
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Petersen RL, Lakin MR, Phillips A. A strand graph semantics for DNA-based computation. THEORETICAL COMPUTER SCIENCE 2016; 632:43-73. [PMID: 27293306 PMCID: PMC4896506 DOI: 10.1016/j.tcs.2015.07.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure.
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Affiliation(s)
| | - Matthew R Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, NM, USA
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186
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Lakin MR, Stefanovic D, Phillips A. Modular verification of chemical reaction network encodings via serializability analysis. THEORETICAL COMPUTER SCIENCE 2016; 632:21-42. [PMID: 27325906 PMCID: PMC4911709 DOI: 10.1016/j.tcs.2015.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a "commit reaction" that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of "extra tolerance", which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited.
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Affiliation(s)
- Matthew R. Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, NM, USA
| | - Darko Stefanovic
- Department of Computer Science, University of New Mexico, Albuquerque, NM, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, USA
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187
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Isothermal RNA detection through the formation of DNA concatemers containing HRP-mimicking DNAzymes on the surface of gold nanoparticles. Biosens Bioelectron 2016; 80:67-73. [DOI: 10.1016/j.bios.2016.01.047] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/16/2016] [Accepted: 01/18/2016] [Indexed: 12/21/2022]
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188
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Chen J, Wen J, Zhuang L, Zhou S. An enzyme-free catalytic DNA circuit for amplified detection of aflatoxin B1 using gold nanoparticles as colorimetric indicators. NANOSCALE 2016; 8:9791-9797. [PMID: 27119550 DOI: 10.1039/c6nr01381c] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An enzyme-free biosensor for the amplified detection of aflatoxin B1 has been constructed based on a catalytic DNA circuit. Three biotinylated hairpin DNA probes (H1, H2, and H3) were designed as the assembly components to construct the sensing system (triplex H1-H2-H3 product). Cascaded signal amplification capability was obtained through toehold-mediated strand displacement reactions to open the hairpins and recycle the trigger DNA. By the use of streptavidin-functionalized gold nanoparticles as the signal indicators, the colorimetric readout can be observed by the naked eye. In the presence of a target, the individual nanoparticles (red) aggregate into a cross-linked network of nanoparticles (blue) via biotin-streptavidin coupling. The colorimetric assay is ultrasensitive, enabling the visual detection of trace levels of aflatoxin B1 (AFB1) as low as 10 pM without instrumentation. The calculated limit of detection (LOD) is 2 pM in terms of 3 times standard deviation over the blank response. The sensor is robust and works even when challenged with complex sample matrices such as rice samples. Our sensing platform is simple and convenient in operation, requiring only the mixing of several solutions at room temperature to achieve visible and intuitive results, and holds great promise for the point-of-use monitoring of AFB1 in environmental and food samples.
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Affiliation(s)
- Junhua Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
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189
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Sawlekar R, Montefusco F, Kulkarni VV, Bates DG. Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions. IEEE Trans Nanobioscience 2016; 15:443-454. [PMID: 27164599 DOI: 10.1109/tnb.2016.2560764] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.
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190
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Abstract
The invention of the Kalman filter is a crowning achievement of filtering theory-one that has revolutionized technology in countless ways. By dealing effectively with noise, the Kalman filter has enabled various applications in positioning, navigation, control, and telecommunications. In the emerging field of synthetic biology, noise and context dependency are among the key challenges facing the successful implementation of reliable, complex, and scalable synthetic circuits. Although substantial further advancement in the field may very well rely on effectively addressing these issues, a principled protocol to deal with noise-as provided by the Kalman filter-remains completely missing. Here we develop an optimal filtering theory that is suitable for noisy biochemical networks. We show how the resulting filters can be implemented at the molecular level and provide various simulations related to estimation, system identification, and noise cancellation problems. We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using flow cytometry measurements of a light-inducible circuit in Escherichia coli.
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191
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Chen SX, Seelig G. An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes. J Am Chem Soc 2016; 138:5076-86. [PMID: 27010123 DOI: 10.1021/jacs.6b00277] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.
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Affiliation(s)
- Sherry Xi Chen
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States.,Department of Computer Science & Engineering, University of Washington , Seattle, Washington 98195, United States
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192
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Bornholt J, Lopez R, Carmean DM, Ceze L, Seelig G, Strauss K. A DNA-Based Archival Storage System. ACTA ACUST UNITED AC 2016. [DOI: 10.1145/2954680.2872397] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | | | | | - Luis Ceze
- University of Washington, Seattle, WA, USA
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193
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Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids. Anal Chim Acta 2016; 910:68-74. [DOI: 10.1016/j.aca.2016.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/02/2016] [Accepted: 01/07/2016] [Indexed: 12/25/2022]
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194
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Groves B, Chen YJ, Zurla C, Pochekailov S, Kirschman JL, Santangelo PJ, Seelig G. Computing in mammalian cells with nucleic acid strand exchange. NATURE NANOTECHNOLOGY 2016; 11:287-294. [PMID: 26689378 PMCID: PMC4777654 DOI: 10.1038/nnano.2015.278] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/26/2015] [Indexed: 05/03/2023]
Abstract
DNA strand displacement has been widely used for the design of molecular circuits, motors, and sensors in cell-free settings. Recently, it has been shown that this technology can also operate in biological environments, but capabilities remain limited. Here, we look to adapt strand displacement and exchange reactions to mammalian cells and report DNA circuitry that can directly interact with a native mRNA. We began by optimizing the cellular performance of fluorescent reporters based on four-way strand exchange reactions and identified robust design principles by systematically varying the molecular structure, chemistry and delivery method. Next, we developed and tested AND and OR logic gates based on four-way strand exchange, demonstrating the feasibility of multi-input logic. Finally, we established that functional siRNA could be activated through strand exchange, and used native mRNA as programmable scaffolds for co-localizing gates and visualizing their operation with subcellular resolution.
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Affiliation(s)
- Benjamin Groves
- Department of Electrical Engineering, University of Washington
| | - Yuan-Jyue Chen
- Department of Electrical Engineering, University of Washington
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
| | | | - Jonathan L. Kirschman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University
- To whom correspondence should be addressed: or
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington
- Department of Computer Science & Engineering, University of Washington
- To whom correspondence should be addressed: or
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195
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Milligan JN, Ellington AD. Using RecA protein to enhance kinetic rates of DNA circuits. Chem Commun (Camb) 2016; 51:9503-6. [PMID: 25967118 DOI: 10.1039/c5cc02261d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While DNA circuits are becoming increasingly useful as signal transducers, their utility is inhibited by their slow catalytic rate. Here, we demonstrate how RecA, a recombination enzyme that catalyzes sequence specific strand exchange, can be used to increase circuit rates up to 9-fold. We also show how the introduction of RNA into DNA circuits further controls the specificity of RecA strand exchange, improving signal-to-noise.
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Affiliation(s)
- J N Milligan
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway, Austin, TX, USA.
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196
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Li W, Zhang F, Yan H, Liu Y. DNA based arithmetic function: a half adder based on DNA strand displacement. NANOSCALE 2016; 8:3775-84. [PMID: 26814628 DOI: 10.1039/c5nr08497k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biomolecular programming utilizes the reactions and information stored in biological molecules, such as proteins and nucleic acids, for computational purposes. DNA has proven itself an excellent candidate for building logic operating systems due to its highly predictable molecular behavior. In this work we designed and realized an XOR logic gate and an AND logic gate based on DNA strand displacement reactions. These logic gates utilize ssDNA as input and output signals. The XOR gate and the AND gate were used as building blocks for constructing a half adder logic circuit, which is a primary step in constructing a full adder, a basic arithmetic unit in computing. This work provides the field of DNA molecular programming with a potential universal arithmetic tool.
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Affiliation(s)
- Wei Li
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Fei Zhang
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Hao Yan
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
| | - Yan Liu
- Center of Molecular Design and Biomimetics at The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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197
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Jung C, Allen PB, Ellington AD. A stochastic DNA walker that traverses a microparticle surface. NATURE NANOTECHNOLOGY 2016; 11:157-63. [PMID: 26524397 PMCID: PMC4740228 DOI: 10.1038/nnano.2015.246] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 09/20/2015] [Indexed: 05/18/2023]
Abstract
Molecular machines have previously been designed that are propelled by DNAzymes, protein enzymes and strand displacement. These engineered machines typically move along precisely defined one- and two-dimensional tracks. Here, we report a DNA walker that uses hybridization to drive walking on DNA-coated microparticle surfaces. Through purely DNA:DNA hybridization reactions, the nanoscale movements of the walker can lead to the generation of a single-stranded product and the subsequent immobilization of fluorescent labels on the microparticle surface. This suggests that the system could be of use in analytical and diagnostic applications, similar to how strand exchange reactions in solution have been used for transducing and quantifying signals from isothermal molecular amplification assays. The walking behaviour is robust and the walker can take more than 30 continuous steps. The traversal of an unprogrammed, inhomogeneous surface is also due entirely to autonomous decisions made by the walker, behaviour analogous to amorphous chemical reaction network computations, which have been shown to lead to pattern formation.
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Affiliation(s)
- C. Jung
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, United States
| | - P. B. Allen
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, United States
| | - A. D. Ellington
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, United States
- To whom correspondence should be addressed. Tel: +1 512 471 6445; Fax: +1 512 471 7014;
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198
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Briat C, Gupta A, Khammash M. Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks. Cell Syst 2016; 2:15-26. [PMID: 27136686 DOI: 10.1016/j.cels.2016.01.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/10/2015] [Accepted: 01/06/2016] [Indexed: 10/22/2022]
Abstract
The ability to adapt to stimuli is a defining feature of many biological systems and critical to maintaining homeostasis. While it is well appreciated that negative feedback can be used to achieve homeostasis when networks behave deterministically, the effect of noise on their regulatory function is not understood. Here, we combine probability and control theory to develop a theory of biological regulation that explicitly takes into account the noisy nature of biochemical reactions. We introduce tools for the analysis and design of robust homeostatic circuits and propose a new regulation motif, which we call antithetic integral feedback. This motif exploits stochastic noise, allowing it to achieve precise regulation in scenarios where similar deterministic regulation fails. Specifically, antithetic integral feedback preserves the stability of the overall network, steers the population of any regulated species to a desired set point, and adapts perfectly. We suggest that this motif may be prevalent in endogenous biological circuits and useful when creating synthetic circuits.
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Affiliation(s)
- Corentin Briat
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ankit Gupta
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.
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199
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Zhang C, Yang J, Jiang S, Liu Y, Yan H. DNAzyme-Based Logic Gate-Mediated DNA Self-Assembly. NANO LETTERS 2016; 16:736-741. [PMID: 26647640 DOI: 10.1021/acs.nanolett.5b04608] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Controlling DNA self-assembly processes using rationally designed logic gates is a major goal of DNA-based nanotechnology and programming. Such controls could facilitate the hierarchical engineering of complex nanopatterns responding to various molecular triggers or inputs. Here, we demonstrate the use of a series of DNAzyme-based logic gates to control DNA tile self-assembly onto a prescribed DNA origami frame. Logic systems such as "YES," "OR," "AND," and "logic switch" are implemented based on DNAzyme-mediated tile recognition with the DNA origami frame. DNAzyme is designed to play two roles: (1) as an intermediate messenger to motivate downstream reactions and (2) as a final trigger to report fluorescent signals, enabling information relay between the DNA origami-framed tile assembly and fluorescent signaling. The results of this study demonstrate the plausibility of DNAzyme-mediated hierarchical self-assembly and provide new tools for generating dynamic and responsive self-assembly systems.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Peking University , Beijing, China
- School of Molecular Sciences, Center for Molecule Design and Biomimetics at the Biodesign Institute, Arizona State University , Tempe, Arizona 85281, United States
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University , Beijing, China
- School of Molecular Sciences, Center for Molecule Design and Biomimetics at the Biodesign Institute, Arizona State University , Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- School of Molecular Sciences, Center for Molecule Design and Biomimetics at the Biodesign Institute, Arizona State University , Tempe, Arizona 85281, United States
| | - Yan Liu
- School of Molecular Sciences, Center for Molecule Design and Biomimetics at the Biodesign Institute, Arizona State University , Tempe, Arizona 85281, United States
| | - Hao Yan
- School of Molecular Sciences, Center for Molecule Design and Biomimetics at the Biodesign Institute, Arizona State University , Tempe, Arizona 85281, United States
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200
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Mendoza O, Mergny JL, Aimé JP, Elezgaray J. G-Quadruplexes Light up Localized DNA Circuits. NANO LETTERS 2016; 16:624-628. [PMID: 26717099 DOI: 10.1021/acs.nanolett.5b04354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA circuits tethered to nanoplatforms can perform cascade reactions for signal amplification. One DNA single strand activates a strand-displacement cascade generating numerous outputs, and therefore amplifying the signal. These localized circuits present, however, an important limitation: the spontaneous activation of the cascade reaction. Current methods to stabilize these circuits employ combination of protective DNA strands, which need to be removed to activate the device. This protection-deprotection process generates an important amount of unwanted side reactions. This is indeed an important limitation for the large potential application of these amplification circuits. In the present work, G-quadruplex DNA structures were used to stabilize localized DNA circuits. This new protocol generates nanoplatforms that no longer requires protective-deprotective systems and is therefore completely neutral to the sample. In addition, cations such as Pb(2+) or Ca(2+) can be also employed to activate the device enlarging the potential applications from biosensors devices to metal detector sensors.
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Affiliation(s)
- Oscar Mendoza
- Université de Bordeaux , 33600 Bordeaux, France
- CBMN, CNRS UMR-5248 , F-33600 Pessac, France
| | - Jean-Louis Mergny
- Université de Bordeaux , 33600 Bordeaux, France
- Inserm, U1212, CNRS, ARNA laboratory, IECB , F-33600 Pessac, France
| | - Jean-Pierre Aimé
- Université de Bordeaux , 33600 Bordeaux, France
- CBMN, CNRS UMR-5248 , F-33600 Pessac, France
| | - Juan Elezgaray
- Université de Bordeaux , 33600 Bordeaux, France
- CBMN, CNRS UMR-5248 , F-33600 Pessac, France
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