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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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Singh NK, Wang Y, Wen C, Davis B, Wang X, Lee K, Wang Y. High-affinity one-step aptamer selection using a non-fouling porous hydrogel. Nat Biotechnol 2023:10.1038/s41587-023-01973-8. [PMID: 37798416 DOI: 10.1038/s41587-023-01973-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023]
Abstract
Aptamers, commonly referred to as chemical antibodies, are used in a wide range of applications including drug delivery and biosensing. However, the process of aptamer selection poses a substantial challenge, as it requires numerous cycles of enrichment and involves issues with nonspecific binding. We present a simple, fast instrument-free method for aptamer enrichment and selection based on a diffusion-binding process in a three-dimensional non-fouling porous hydrogel with immobilized target proteins. Low-affinity aptamer candidates can be rapidly released from the hydrogel, whereas high-affinity candidates are restricted due to their strong binding to the immobilized protein targets. Consequently, a one-step enriched aptamer pool can strongly bind the protein targets. This enrichment is consistent across five proteins with isoelectric points in varying ranges. With thrombin as a representative model, the anti-thrombin aptamer identified from an enriched aptamer pool has been found to have a binding affinity that is comparable to those identified over ten cycles of selection using traditional methods.
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Affiliation(s)
- Naveen K Singh
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, Delhi, New Delhi, India
| | - Yixun Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Connie Wen
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Xuelin Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA.
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3
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Takiguchi S, Kambara F, Tani M, Sugiura T, Kawano R. Simultaneous Recognition of Over- and Under-Expressed MicroRNAs Using Nanopore Decoding. Anal Chem 2023; 95:14675-14685. [PMID: 37675494 PMCID: PMC10797591 DOI: 10.1021/acs.analchem.3c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023]
Abstract
This paper describes a strategy for simultaneous recognition of over- and under-expressed microRNAs (miRNAs) using the method of signal classification-based nanopore decoding. MiRNA has attracted attention as a promising biomarker for cancer diagnosis owing to its cancer-type-specific expression patterns. While nanopore technology has emerged as a simple and label-free method to detect miRNAs and their expression patterns, recognizing patterns involving simultaneous over/under-expression is still challenging due to the inherent working principles. Here, inspired by the sequence design for DNA computation with nanopore decoding, we designed diagnostic DNA probes targeting two individual over/under-expressed miRNAs in the serum of oral squamous cell carcinoma. Through nanopore measurements, our designed probes exhibited characteristic current signals depending on the hybridized miRNA species, which were plotted on the scatter plot of duration versus current blocking ratio. The classified signals reflected the relative abundance of target miRNAs, thereby enabling successful pattern recognition of over/under-expressed miRNAs, even when using clinical samples. We believe that our method paves the way for miRNA-targeting simple diagnosis as a liquid biopsy.
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Affiliation(s)
- Sotaro Takiguchi
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Fumika Kambara
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Mika Tani
- Department
of Maxillofacial Diagnostic and Surgical Science, Field of Oral and
Maxillofacial Rehabilitation, Graduate School of Medical and Dental
Science, Kagoshima University, Kagoshima 890-8544, Japan
| | - Tsuyoshi Sugiura
- Department
of Maxillofacial Diagnostic and Surgical Science, Field of Oral and
Maxillofacial Rehabilitation, Graduate School of Medical and Dental
Science, Kagoshima University, Kagoshima 890-8544, Japan
- Division
of Oral and Maxillofacial Oncology and Surgical Sciences, Graduate
School of Dentistry, Tohoku University, Miyagi 980-8577, Japan
| | - Ryuji Kawano
- Department
of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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4
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DNA Computing: Concepts for Medical Applications. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The branch of informatics that deals with construction and operation of computers built of DNA, is one of the research directions which investigates issues related to the use of DNA as hardware and software. This concept assumes the use of DNA computers due to their biological origin mainly for intelligent, personalized and targeted diagnostics frequently related to therapy. Important elements of this concept are (1) the retrieval of unique DNA sequences using machine learning methods and, based on the results of this process, (2) the construction/design of smart diagnostic biochip projects. The authors of this paper propose a new concept of designing diagnostic biochips, the key elements of which are machine-learning methods and the concept of biomolecular queue automata. This approach enables the scheduling of computational tasks at the molecular level by sequential events of cutting and ligating DNA molecules. We also summarize current challenges and perspectives of biomolecular computer application and machine-learning approaches using DNA sequence data mining.
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Wang GA, Xu J, Traynor SM, Chen H, Eljabu F, Wu X, Yan H, Li F. DNA Balance for Native Characterization of Chemically Modified DNA. J Am Chem Soc 2021; 143:13655-13663. [PMID: 34404208 DOI: 10.1021/jacs.1c05236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chemical modification is a powerful approach to expand the chemical diversity and functionality of natural DNA. However, when chemically modified oligonucleotides are employed in DNA-based reactions or structures, it becomes quite difficult to predict, understand, and control their kinetics and thermodynamics. To address this challenge, we introduce a rationally designed DNA balance capable of measuring critical thermodynamic and kinetic properties of chemically modified DNA in their native environment. Our DNA balance is operated using the principle of toehold-exchange, where a panel of weight probes were designed by tuning the lengths of forward and reverse toeholds. Once placed on the DNA balance, the chemical modification will be interrogated using the weight probes to determine changes in both Gibbs free energy and hybridization rate constant. Using cyclic-azobenzene (cAB)-modified DNA as a model system, we demonstrated that our DNA balance could not only measure stable chemical modifications, but also solve more challenging issues where unstable chemical modifications and transient isomerization reactions were involved. We anticipate that our DNA balance will find wide uses for measuring important thermodynamic and kinetic parameters for DNA carrying various chemical modifications, as well as for probing transient chemical changes in DNA.
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Affiliation(s)
- Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Junpeng Xu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Sarah M Traynor
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Haodi Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Fatma Eljabu
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Xinghong Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Hongbin Yan
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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6
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Implementation of biomolecular logic gate using DNA and electrically doped GaAs nano-pore: a first principle paradigm. J Mol Model 2021; 27:23. [PMID: 33410979 DOI: 10.1007/s00894-020-04623-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022]
Abstract
One of the emerging areas of today's research arena is molecular modeling and molecular computing. The molecular logic gate can be theoretically implemented from single-strand DNA which consists of four basic nucleobases. In this study, the electronic transmission characteristics of DNA chain are investigated to form the logic gate. This biomolecular single-strand DNA chain is passed through an electrically doped gallium-arsenide nano-pore to achieve reasonably improved transmission along <1 1 1> direction. Current-voltage characteristic and device density of states with HOMO-LUMO plot of the device are explained along with the conductivity of the device to confirm the characteristics of some important logic gates like a universal gate. Ultimately the property of resistivity proves the law of Boolean logic of AND gate and universal logic gate, viz., NAND and NOR gate. All the electronic properties of the Boolean logic gate are explored based on the first principle approach by non-equilibrium Green's function coupled with density functional theory in room temperature.
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Deng J, Walther A. ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002629. [PMID: 32881127 DOI: 10.1002/adma.202002629] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.
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Affiliation(s)
- Jie Deng
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg, D-79110, Germany
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8
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Abstract
The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.
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Roy P, Dey D, De D. First principle approach towards logic design using hydrogen-doped single-strand DNA. IET Nanobiotechnol 2019; 13:77-83. [PMID: 30964042 PMCID: PMC8676674 DOI: 10.1049/iet-nbt.2018.5027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/09/2018] [Accepted: 07/30/2018] [Indexed: 04/05/2024] Open
Abstract
Molecular logic gate has been proposed using single-strand DNA (ssDNA) consisting of basic four nucleobases. In this study, density functional theory and non-equilibrium Green's function based first principle approach is applied to investigate the electronic transmission characteristics of ssDNA chain. The heavily hydrogen-doped-ssDNA (H-ssDNA) chain is connected with gold electrode to achieve enhanced quantum-ballistic transmission along 〈1 1 1〉 direction. Logic gates OR, Ex-OR, NXOR have been implemented using this analytical model of H-ssDNA device. Enhanced logic properties have been observed for ssDNA after H adsorption due to improved electronic transmission. Dense electron cloud is considered as logic 'high' (1) output in presence of hydrogen molecule and on the contrary sparse cloud indicate logic 'low' (0) in the absence of hydrogen molecule. Device current is significantly increased from 0.2 nA to 2.4 µA (approx.) when ssDNA chain is heavily doped with hydrogen molecule. The current-voltage characteristics confirm the formation of various Boolean logic gate operations.
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Affiliation(s)
- Pradipta Roy
- Department of Computer Science & Engineering, Swami Vivekananda Institute of Science and Technology, Dakshin Gobindapur, P.S.: Sonarpur, Kolkata 700 145, West Bengal, India.
| | - Debarati Dey
- Department of Computer Science & Engineering, Maulana Abul Kalam Azad University of Technology, BF-142, Sector 1, Salt Lake City, Kolkata 700 064, West Bengal, India
| | - Debashis De
- Department of Physics, University of Western Australia, M013, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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10
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Chu D, Spinney RE. A thermodynamically consistent model of finite-state machines. Interface Focus 2018; 8:20180037. [PMID: 30443334 DOI: 10.1098/rsfs.2018.0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 01/26/2023] Open
Abstract
Finite-state machines (FSMs) are a theoretically and practically important model of computation. We propose a general, thermodynamically consistent model of FSMs and characterize the resource requirements of these machines. We model FSMs as time-inhomogeneous Markov chains. The computation is driven by instantaneous manipulations of the energy levels of the states. We calculate the entropy production of the machine, its error probability, and the time required to complete one update step. We find that a sequence of generalized bit-setting operations is sufficient to implement any FSM.
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Affiliation(s)
- Dominique Chu
- School of Computing, University of Kent, Canterbury CT2 7NF, UK
| | - Richard E Spinney
- Centre for Complex Systems, The University of Sydney, Sydney, New South Wales 2006, Australia
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12
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Kawano R. Nanopore Decoding of Oligonucleotides in DNA Computing. Biotechnol J 2018; 13:e1800091. [PMID: 30076732 DOI: 10.1002/biot.201800091] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/24/2018] [Indexed: 12/17/2022]
Abstract
In conventional DNA-computation methods involving logic gate operations, the output molecules are detected and decoded mainly by gel electrophoresis or fluorescence measurements. To employ rapid and label-free decoding, nanopore technology, an emerging methodology for single-molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations. This review describes recent approaches to decoding DNA computation using label-free and electrical nanopore measurements. Several attempts have been successful in DNA decoding with the nanopore either through enzymatic reactions or in water-in-oil droplets. Additionally, DNA computing combined with nanopore decoding has clinical applications, including microRNA detection for early diagnosis of cancers. Because this decoding methodology is still in development and not yet widely accepted, this review aims to inform the scientific community regarding usefulness.
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Affiliation(s)
- Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Harumicho, Fuchu, Tokyo 183-8538, Japan
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13
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Bader A, Cockroft SL. Simultaneous G-Quadruplex DNA Logic. Chemistry 2018; 24:4820-4824. [DOI: 10.1002/chem.201800756] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh, Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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14
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Sakowski S, Krasinski T, Waldmajer J, Sarnik J, Blasiak J, Poplawski T. Biomolecular computers with multiple restriction enzymes. Genet Mol Biol 2017; 40:860-870. [PMID: 29064510 PMCID: PMC5738618 DOI: 10.1590/1678-4685-gmb-2016-0132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/16/2017] [Indexed: 11/24/2022] Open
Abstract
The development of conventional, silicon-based computers has several limitations,
including some related to the Heisenberg uncertainty principle and the von
Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are
largely free of these disadvantages and, along with quantum computers, are
reasonable alternatives to their conventional counterparts in some applications.
The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann
Institute of Science was developed using one restriction enzyme as hardware and
DNA fragments (the transition molecules) as software and input/output signals.
This computer represented a two-state two-symbol finite automaton that was
subsequently extended by using two restriction enzymes. In this paper, we
propose the idea of a multistate biomolecular computer with multiple
commercially available restriction enzymes as hardware. Additionally, an
algorithmic method for the construction of transition molecules in the DNA
computer based on the use of multiple restriction enzymes is presented. We use
this method to construct multistate, biomolecular, nondeterministic finite
automata with four commercially available restriction enzymes as hardware. We
also describe an experimental applicaton of this theoretical model to a
biomolecular finite automaton made of four endonucleases.
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Affiliation(s)
- Sebastian Sakowski
- Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland
| | - Tadeusz Krasinski
- Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland
| | - Jacek Waldmajer
- Logic, Language and Information Group, Department of Philosophy, University of Opole, Opole, Poland
| | - Joanna Sarnik
- Department of Molecular Genetics, University of Lodz, Lodz, Poland
| | - Janusz Blasiak
- Department of Molecular Genetics, University of Lodz, Lodz, Poland
| | - Tomasz Poplawski
- Department of Molecular Genetics, University of Lodz, Lodz, Poland
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15
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Sakowski S, Krasiński T, Sarnik J, Blasiak J, Waldmajer J, Poplawski T. A detailed experimental study of a DNA computer with two endonucleases. ACTA ACUST UNITED AC 2017; 72:303-313. [PMID: 28432850 DOI: 10.1515/znc-2016-0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/26/2017] [Indexed: 11/15/2022]
Abstract
Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.
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Affiliation(s)
- Sebastian Sakowski
- Faculty of Mathematics and Computer Science, University of Lodz, Banacha 22, 90-238 Lodz, Poland
| | - Tadeusz Krasiński
- Faculty of Mathematics and Computer Science, University of Lodz, Banacha 22, 90-238 Lodz, Poland
| | - Joanna Sarnik
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Janusz Blasiak
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Jacek Waldmajer
- Department of Philosophy, University of Opole, Katowicka 89, 45-061 Opole, Poland
| | - Tomasz Poplawski
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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16
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Cheng N, Zhu P, Xu Y, Huang K, Luo Y, Yang Z, Xu W. High-sensitivity assay for Hg (II) and Ag (I) ion detection: A new class of droplet digital PCR logic gates for an intelligent DNA calculator. Biosens Bioelectron 2016; 84:1-6. [DOI: 10.1016/j.bios.2016.04.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 12/21/2022]
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17
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Rawtani D, Kuntmal B, Agrawal Y. Charge transfer in DNA and its diverse modelling approaches. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1207570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Deepak Rawtani
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Binal Kuntmal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
| | - Y. Agrawal
- Institute of Research and Development, Gujarat Forensic Sciences University, Gandhi Nagar, Gujarat, India
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18
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Lu CH, Cecconello A, Willner I. Recent Advances in the Synthesis and Functions of Reconfigurable Interlocked DNA Nanostructures. J Am Chem Soc 2016; 138:5172-85. [DOI: 10.1021/jacs.6b00694] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chun-Hua Lu
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alessandro Cecconello
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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19
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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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20
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Generative and Recognising Devices for Biological Processes. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Varghese S, Elemans JAAW, Rowan AE, Nolte RJM. Molecular computing: paths to chemical Turing machines. Chem Sci 2015; 6:6050-6058. [PMID: 28717447 PMCID: PMC5504628 DOI: 10.1039/c5sc02317c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/06/2015] [Indexed: 11/21/2022] Open
Abstract
In this perspective, we highlight some of the recent advances in the development of molecular and biomolecular systems for performing logic operations and computing. We also present a blueprint of a chemical Turing machine using a processive catalytic approach.
To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.
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Affiliation(s)
- Shaji Varghese
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Johannes A A W Elemans
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Alan E Rowan
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
| | - Roeland J M Nolte
- Radboud University , Institute for Molecules and Materials , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands . ;
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22
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Jiang YS, Bhadra S, Li B, Wu YR, Milligan JN, Ellington AD. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal Chem 2015; 87:3314-20. [PMID: 25708458 DOI: 10.1021/ac504387c] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) of DNA is a powerful isothermal nucleic acid amplification method that can generate upward of 10(9) copies from less than 100 copies of template DNA within an hour. Unfortunately, although the amplification reactions are extremely powerful, real-time and specific detection of LAMP products remains analytically challenging. In order to both improve the specificity of LAMP detection and to make readout simpler and more reliable, we have replaced the intercalating dye typically used for monitoring in real-time fluorescence with a toehold-mediated strand exchange reaction termed one-step strand displacement (OSD). Due to the inherent sequence specificity of toehold-mediated strand exchange, the OSD reporter could successfully distinguish side products from true amplicons arising from templates corresponding to the biomedically relevant M. tuberculosis RNA polymerase (rpoB) and the melanoma-related biomarker BRAF. OSD allowed the Yes/No detection of rpoB in a complex mixture such as synthetic sputum and also demonstrated single nucleotide specificity in Yes/No detection of a mutant BRAF allele (V600E) in the presence of 20-fold more of the wild-type gene. Real-time detection of different genes in multiplex LAMP reactions also proved possible. The development of simple, readily designed, modular equivalents of TaqMan probes for isothermal amplification reactions should generally improve the applicability of these reactions and may eventually assist with the development of point-of-care tests.
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Affiliation(s)
- Yu Sherry Jiang
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sanchita Bhadra
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bingling Li
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yuefeng Rose Wu
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - John N Milligan
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D Ellington
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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23
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Complexity Measures and Physical Principles. ISCS 2014: INTERDISCIPLINARY SYMPOSIUM ON COMPLEX SYSTEMS 2015. [DOI: 10.1007/978-3-319-10759-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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24
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 486] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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25
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Song C, Wang ZG, Ding B. Smart nanomachines based on DNA self-assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2382-92. [PMID: 23776091 DOI: 10.1002/smll.201300824] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/28/2013] [Indexed: 05/09/2023]
Abstract
DNA-based nanomachines are self-assembled DNA superstructures that harness chemical free energy to perform mechanical work. The development of DNA machines has benefited greatly from the achievements in both structural and dynamic DNA nanotechnology. In this review, the configurations of DNA machines, fuel systems, and operations are discussed to outline the evolving paths of DNA machines. The focus is on the smart mechanical behavior of DNA machines, from the standpoint of upgrading the complexity of DNA nanostructures, cooperative activation of multimachinary systems, and the establishment of a network of the mechanical states. In the end, the challenges are highlighted and possible solutions are proposed to push forward smart DNA nanomachines, with the goal of creating biomimicking systems. Insights are also provided into the potential applications of the DNA machines with designable intelligence.
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Affiliation(s)
- Chen Song
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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26
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Moe-Behrens GH. The biological microprocessor, or how to build a computer with biological parts. Comput Struct Biotechnol J 2013; 7:e201304003. [PMID: 24688733 PMCID: PMC3962179 DOI: 10.5936/csbj.201304003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 01/21/2023] Open
Abstract
Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system.
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28
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Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates. Proc Natl Acad Sci U S A 2012; 109:21228-33. [PMID: 23236131 DOI: 10.1073/pnas.1219672110] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg(2+)-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli's and Fredkin's logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine.
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29
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DNA biosensors that reason. Biosystems 2012; 109:91-104. [DOI: 10.1016/j.biosystems.2012.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 01/23/2012] [Accepted: 02/16/2012] [Indexed: 11/18/2022]
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30
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Benenson Y. Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 2012; 13:455-68. [PMID: 22688678 DOI: 10.1038/nrg3197] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.
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Affiliation(s)
- Yaakov Benenson
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), Mattenstrasse 26, 4058 Basel, Switzerland.
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31
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Shen X, Atamas NA, Zhang FS. Competition between Na⁺ and Rb⁺ in the minor groove of DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:051913. [PMID: 23004793 DOI: 10.1103/physreve.85.051913] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Indexed: 06/01/2023]
Abstract
The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.
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Affiliation(s)
- X Shen
- Key Laboratory of Beam Technology and Material Modification of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China
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32
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Shapiro E. A mechanical Turing machine: blueprint for a biomolecular computer. Interface Focus 2012; 2:497-503. [PMID: 22649583 PMCID: PMC3363030 DOI: 10.1098/rsfs.2011.0118] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 02/22/2012] [Indexed: 12/26/2022] Open
Abstract
We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may ‘compute’ synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.
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Affiliation(s)
- Ehud Shapiro
- Department of Computer Science and Applied Math and Department of Biological Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
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33
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34
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Affiliation(s)
- Ofer I. Wilner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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35
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36
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Abstract
Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity-heat agitation and the cause-and-effect determinism of nature's orderliness-cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.
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37
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Gil B, Kahan-Hanum M, Skirtenko N, Adar R, Shapiro E. Detection of multiple disease indicators by an autonomous biomolecular computer. NANO LETTERS 2011; 11:2989-2996. [PMID: 21671655 DOI: 10.1021/nl2015872] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The promise of biomolecular computers is their ability to interact with naturally occurring biomolecules, enabling in the future the development of context-dependent programmable drugs. Here we show a context-sensing mechanism of a biomolecular automaton that can simultaneously sense different types of molecules, allowing future integration of biomedical knowledge on a broad range of molecular disease symptoms in the decision of a biomolecular computer to release a drug molecule.
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Affiliation(s)
- Binyamin Gil
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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38
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39
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40
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Simeonov PL. Integral biomathics: A post-Newtonian view into the logos of bios. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 102:85-121. [DOI: 10.1016/j.pbiomolbio.2010.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 01/29/2010] [Indexed: 11/29/2022]
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44
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Affiliation(s)
- Tamar Ratner
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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45
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Zhang Y, Yu H, Qin J, Lin B. A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis. BIOMICROFLUIDICS 2009; 3:44105. [PMID: 20216967 PMCID: PMC2835285 DOI: 10.1063/1.3259628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/17/2009] [Indexed: 05/08/2023]
Abstract
Boolean logic performs a logical operation on one or more logic input and produces a single logic output. Here, we describe a microfluidic DNA computing processor performing Boolean logic operations for gene expression analysis and gene drug synthesis. Multiple cancer-related genes were used as input molecules. Their expression levels were identified by interacting with the computing related DNA strands, which were designed according to the sequences of cancer-related genes and the suicide gene. When all the expressions of the cancer-related genes fit in with the diagnostic criteria, positive diagnosis would be confirmed and then a complete suicide gene (gene drug) could be synthesized as an output molecule. Microfluidic chip was employed as an effective platform to realize the computing process by integrating multistep biochemical reactions involving hybridization, displacement, denaturalization, and ligation. By combining the specific design of the computing related molecules and the integrated functions of the microfluidics, the microfluidic DNA computing processor is able to analyze the multiple gene expressions simultaneously and realize the corresponding gene drug synthesis with simplicity and fast speed, which demonstrates the potential of this platform for DNA computing in biomedical applications.
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46
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Ran T, Kaplan S, Shapiro E. Molecular implementation of simple logic programs. NATURE NANOTECHNOLOGY 2009; 4:642-648. [PMID: 19809454 DOI: 10.1038/nnano.2009.203] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 07/01/2009] [Indexed: 05/28/2023]
Abstract
Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications. Biomolecular implementations of finite automata and logic gates have already been developed. Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) <-- Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision. A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.
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Affiliation(s)
- Tom Ran
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
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47
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Phillips A, Cardelli L. A programming language for composable DNA circuits. J R Soc Interface 2009; 6 Suppl 4:S419-36. [PMID: 19535415 PMCID: PMC2843959 DOI: 10.1098/rsif.2009.0072.focus] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/13/2009] [Indexed: 11/12/2022] Open
Abstract
Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.
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Abstract
Biocomputers are man-made biological networks whose goal is to probe and control biological hosts--cells and organisms--in which they operate. Their key design features, informed by computer science and engineering, are programmability, modularity and versatility. While still a work in progress, biocomputers will eventually enable disease diagnosis and treatment with single-cell precision, lead to "designer" cell functions for biotechnology, and bring about a new generation of biological measurement tools. This review describes the intellectual foundation of the "biocomputer" concept as well as surveys the state of the art in the field.
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Affiliation(s)
- Yaakov Benenson
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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49
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Ali MM, Imoto S, Li Y, Sasaki S, Nagatsugi F. Incorporation of an inducible nucleotide analog into DNA by DNA polymerases. Bioorg Med Chem 2009; 17:2859-63. [PMID: 19286386 DOI: 10.1016/j.bmc.2009.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 02/12/2009] [Accepted: 02/13/2009] [Indexed: 11/28/2022]
Abstract
Non-natural nucleotides with diverse functionalities are highly useful in many areas of basic research and practical applications. We have previously developed an efficient method for post-synthetic modifications of 2-amino-6-vinylpurine (AVP)-containing oligonucleotides, which permits conjugations of a variety of useful functional appendages to the AVP moiety in DNA. Here we report an investigation on the ability of various DNA polymerases to use 5'-triphosphate of 2'-deoxyribosyl-2-amino-6-(2-methylthioethyl)purine (a stable precursor of AVP) as the substrate for templated DNA synthesis.
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Affiliation(s)
- Md Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Canada ON L8N 3Z5
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50
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Sahu S, LaBean TH, Reif JH. A DNA nanotransport device powered by polymerase phi29. NANO LETTERS 2008; 8:3870-3878. [PMID: 18939810 DOI: 10.1021/nl802294d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Polymerases are a family of enzymes responsible for copying or replication of nucleic acids (DNA or RNA) templates and hence sustenance of life processes. In this paper, we present a method to exploit a strand-displacing polymerase phi29 as a driving force for nanoscale transportation devices. The principal idea behind the device is strong strand displacement ability of phi29, which can displace any DNA strand from its template while extending a primer hybridized to the template. This capability of phi29 is used to power the movement of a target nanostructure on a DNA track. The major advantage of using a polymerase driven nanotransportation device as compared to other existing nanorobotical devices is its speed. phi29 polymerase can travel at the rate of 2000 nucleotides per minute at room temperature, which translates to approximately 680 nm min(-1) on a nanostructure. We also demonstrate transportation of a DNA cargo on a DNA track with the help of fluorescence resonance electron transfer data.
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Affiliation(s)
- Sudheer Sahu
- Department of Computer Science, Box 90129, 3101 French Family Sciences Center, Box 90345, Duke University, Durham, North Carolina 27708, USA
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