1
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Smith FG, Goertz JP, Jurinović K, Stevens MM, Ouldridge TE. Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics. NANOSCALE 2024; 16:17624-17637. [PMID: 39235130 DOI: 10.1039/d4nr00542b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Strand displacement reactions underlie dynamic nucleic acid nanotechnology. The kinetic and thermodynamic features of DNA-based displacement reactions are well understood and well predicted by current computational models. By contrast, understanding of RNA/DNA hybrid strand displacement kinetics is limited, restricting the design of increasingly complex RNA/DNA hybrid reaction networks with more tightly regulated dynamics. Given the importance of RNA as a diagnostic biomarker, and its critical role in intracellular processes, this shortfall is particularly limiting for the development of strand displacement-based therapeutics and diagnostics. Herein, we characterise 22 RNA/DNA hybrid strand displacement systems, alongside 11 DNA/DNA systems, varying a range of common design parameters including toehold length and branch migration domain length. We observe that differences in stability between RNA-DNA hybrids and DNA-DNA duplexes have large effects on strand displacement rates, with rates for equivalent sequences differing by up to 3 orders of magnitude. Crucially, however, this effect is strongly sequence-dependent, with RNA invaders strongly favoured in a system with RNA strands of high purine content, and disfavoured in a system when the RNA strands have low purine content. These results lay the groundwork for more general design principles, allowing for creation of de novo reaction networks with novel complexity while maintaining predictable reaction kinetics.
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Affiliation(s)
- Francesca G Smith
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - John P Goertz
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
| | - Križan Jurinović
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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2
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Karar M, Barkale HV, Vasishtha SD, Dey N. Designing Unconventional Molecular Ternary INHIBIT Logic Gate and Crafting Multifunctional Molecular Logic Systems. J Phys Chem B 2024; 128:6684-6692. [PMID: 38980697 DOI: 10.1021/acs.jpcb.4c01145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The paper describes an improved method for building flexible interswitchable logic gates such as rare-type molecular ternary INHIBIT and combinational logic circuits using a specially designed pyridine-end oligo-p-phenylenevinylene compound featuring alkyl substituents (-C16H33) in a THF medium. The probe molecule showed distinct opto-chemical signals upon interaction with Cu(II) and Hg(II) in THF medium. It is interesting to note that the presence of certain anions (S2-, I-, and CN-) could specifically mask the interaction of either of these metal ions or both. The most exciting thing is that we used a completely new gate design technique to construct a rare-type ternary INHIBIT logic gate using Cu(II), Hg(II), and CN- ions as three chemical inputs. With the identical set of chemical inputs, two more ternary combinational logic circuits were created out of these case-specific, independent reversible and irreversible spectroscopic studies. Finally, we were able to design adaptive molecular logic systems composed of several logic gates, including NOR, AND, IMPLICATION, INHIBIT, TRANSFER, and COMPLEMENT, that in this specific situation change the sort of logic sense by effortless optical toggling.
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Affiliation(s)
- Monaj Karar
- MLR Institute of Technology, Hyderabad, Hyderabad, India 500043
| | - Harshal V Barkale
- Department of Chemistry, BITS-Pilani, Hyderabad Campus, Hyderabad, India 500078
| | - Sahil D Vasishtha
- Department of Chemistry, BITS-Pilani, Hyderabad Campus, Hyderabad, India 500078
| | - Nilanjan Dey
- Department of Chemistry, BITS-Pilani, Hyderabad Campus, Hyderabad, India 500078
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3
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Liu Y, Zhai Y, Hu H, Liao Y, Liu H, Liu X, He J, Wang L, Wang H, Li L, Zhou X, Xiao X. Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400011. [PMID: 38698560 PMCID: PMC11234411 DOI: 10.1002/advs.202400011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/09/2024] [Indexed: 05/05/2024]
Abstract
DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
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Affiliation(s)
- Yizhou Liu
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuxuan Zhai
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hao Hu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuheng Liao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Huan Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiao Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Jiachen He
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Limei Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hongxun Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Longjie Li
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000China
| | - Xianjin Xiao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
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4
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Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
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5
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Mei T, Liu W, Xu G, Chen Y, Wu M, Wang L, Xiao K. Ionic Transistors. ACS NANO 2024. [PMID: 38285731 DOI: 10.1021/acsnano.3c06190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Biological voltage-gated ion channels, which behave as life's transistors, regulate ion transport precisely and selectively through atomic-scale selectivity filters to sustain important life activities. By this inspiration, voltage-adaptable ionic transistors that use ions as signal carriers may provide an alternative information processing unit beyond solid-state electronic devices. This review provides a comprehensive overview of the first generation of biomimetic ionic transistors, including their operating mechanisms, device architecture development, and property characterizations. Despite its infancy, significant progress has been made in the applications of ionic transistors in fields such as DNA detection, drug delivery, and ionic circuits. Challenges and prospects of full exploitation of ionic transistors for a broad spectrum of practical applications are also discussed.
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Affiliation(s)
- Tingting Mei
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Wenchao Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Guoheng Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Yuanxia Chen
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Minghui Wu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Li Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Kai Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
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6
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Seet I, Ouldridge TE, Doye JPK. Simulation of reversible molecular mechanical logic gates and circuits. Phys Rev E 2023; 107:024134. [PMID: 36932514 DOI: 10.1103/physreve.107.024134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/21/2022] [Indexed: 06/18/2023]
Abstract
Landauer's principle places a fundamental lower limit on the work required to perform a logically irreversible operation. Logically reversible gates provide a way to avoid these work costs and also simplify the task of making the computation as a whole thermodynamically reversible. The inherent reversibility of mechanical logic gates would make them good candidates for the design of practical logically reversible computing systems if not for the relatively large size and mass of such systems. In this paper we outline the design and simulation of reversible molecular mechanical logic gates that come close to the limits of thermodynamic reversibility even under the effects of thermal noise, and outline associated circuit components from which arbitrary combinatorial reversible circuits can be constructed and simulated. We demonstrate that isolated components can be operated in a thermodynamically reversible manner, and explore the complexities of combining components to implement more complex computations. Finally, we demonstrate a method to construct arbitrarily large reversible combinatorial circuits using multiple external controls and signal boosters with a working half-adder circuit.
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Affiliation(s)
- Ian Seet
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, Royal School of Mines, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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7
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Cui M, Zhang D, Wang Q, Chao J. An intelligent, autocatalytic, DNAzyme biocircuit for amplified imaging of intracellular microRNAs. NANOSCALE 2023; 15:578-587. [PMID: 36533380 DOI: 10.1039/d2nr05165f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
DNAzymes hold great promise as transducing agents for the analysis of intracellular biomarkers. However, their low intracellular delivery efficiency and limited signal amplification capability (including an additional supply of cofactors) hinder their application in low-abundance biomarker analysis. Herein, a general strategy to design an intelligent, autocatalytic, DNAzyme biocircuit is developed for amplified microRNA imaging in living cells. The DNAzyme biocircuit is constructed based on a nanodevice composed of catalytic hairpin assembly (CHA) and DNAzyme biocatalytic functional units, sustained by Au nanoparticles (AuNPs) and MnO2 nanosheets (CD/AM nanodevices). Once the CD/AM nanodevices are endocytosed by cells, the MnO2 nanosheets are reduced by intracellular glutathione (GSH), which not only releases the different units of the DNAzyme circuit, but also generates the cofactor Mn2+ for DNAzyme autocatalysis. The intracellular analytes could trigger the coordinated cross-activation of CHA and autocatalytic DNAzymes on AuNPs, enabling reliable and accurate detection of miRNAs in living cells. This intelligent autocatalytic multilayer DNAzyme biocircuit can effectively avoid signal leakage and obtain high amplification gain, expanding the application of programmable complex DNA nanocircuits in biosensing, nanomaterial assembly, and biomedicine.
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Affiliation(s)
- Meirong Cui
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Dan Zhang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Qingfu Wang
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
| | - Jie Chao
- State Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China.
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8
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Okumura S, Gines G, Lobato-Dauzier N, Baccouche A, Deteix R, Fujii T, Rondelez Y, Genot AJ. Nonlinear decision-making with enzymatic neural networks. Nature 2022; 610:496-501. [PMID: 36261553 DOI: 10.1038/s41586-022-05218-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/09/2022] [Indexed: 12/22/2022]
Abstract
Artificial neural networks have revolutionized electronic computing. Similarly, molecular networks with neuromorphic architectures may enable molecular decision-making on a level comparable to gene regulatory networks1,2. Non-enzymatic networks could in principle support neuromorphic architectures, and seminal proofs-of-principle have been reported3,4. However, leakages (that is, the unwanted release of species), as well as issues with sensitivity, speed, preparation and the lack of strong nonlinear responses, make the composition of layers delicate, and molecular classifications equivalent to a multilayer neural network remain elusive (for example, the partitioning of a concentration space into regions that cannot be linearly separated). Here we introduce DNA-encoded enzymatic neurons with tuneable weights and biases, and which are assembled in multilayer architectures to classify nonlinearly separable regions. We first leverage the sharp decision margin of a neuron to compute various majority functions on 10 bits. We then compose neurons into a two-layer network and synthetize a parametric family of rectangular functions on a microRNA input. Finally, we connect neural and logical computations into a hybrid circuit that recursively partitions a concentration plane according to a decision tree in cell-sized droplets. This computational power and extreme miniaturization open avenues to query and manage molecular systems with complex contents, such as liquid biopsies or DNA databases.
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Affiliation(s)
- S Okumura
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - G Gines
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - N Lobato-Dauzier
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - A Baccouche
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - R Deteix
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - T Fujii
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Y Rondelez
- Laboratoire Gulliver, PSL Research University, Paris, France
| | - A J Genot
- LIMMS, CNRS-Institute of Industrial Science, University of Tokyo, Tokyo, Japan.
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9
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Todisco M, Szostak JW. Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides. Nucleic Acids Res 2022; 50:9647-9662. [PMID: 36099434 PMCID: PMC9508827 DOI: 10.1093/nar/gkac784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt–12nt) that exhibit no expected secondary structure as simple functions of oligonucleotide length, CG content, ΔG of hybridization and ΔG of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.
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Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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10
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Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold-Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022; 61:e202201929. [PMID: 35315568 PMCID: PMC9324813 DOI: 10.1002/anie.202201929] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 12/31/2022]
Abstract
Here we show a general approach to achieve dissipative control over toehold-mediated strand-displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re-engineering the classic strand displacement reaction such that the high-energy invader strand (fuel) is converted into a low-energy waste product through an energy-dissipating reaction allowing the spontaneous return to the original state over time. We show that such dissipative control over the toehold-mediated strand displacement process is reversible (up to 10 cycles), highly controllable and enables unique temporal activation of DNA systems. We show here two possible applications of this strategy: the transient labelling of DNA structures and the additional temporal control of cascade reactions.
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Affiliation(s)
- Erica Del Grosso
- Department of ChemistryUniversity of Rome Tor VergataVia della Ricerca Scientifica00133RomeItaly
| | - Patrick Irmisch
- Molecular Biophysics GroupPeter Debye Institute for Soft Matter PhysicsUniversität Leipzig04103LeipzigGermany
| | - Serena Gentile
- Department of ChemistryUniversity of Rome Tor VergataVia della Ricerca Scientifica00133RomeItaly
| | - Leonard J. Prins
- Department of Chemical fSciencesUniversity of PaduaVia Marzolo 135131PaduaItaly
| | - Ralf Seidel
- Molecular Biophysics GroupPeter Debye Institute for Soft Matter PhysicsUniversität Leipzig04103LeipzigGermany
| | - Francesco Ricci
- Department of ChemistryUniversity of Rome Tor VergataVia della Ricerca Scientifica00133RomeItaly
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11
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Xie N, Li M, Wang Y, Lv H, Shi J, Li J, Li Q, Wang F, Fan C. Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions. J Am Chem Soc 2022; 144:9479-9488. [DOI: 10.1021/jacs.2c03258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nuli Xie
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Hui Lv
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Wang J, Law CS, Gunenthiran S, Que Tran HN, Tran KN, Lim SY, Abell AD, Santos A. Structural Engineering of the Barrier Oxide Layer of Nanoporous Anodic Alumina for Iontronic Sensing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:21181-21197. [PMID: 35485719 DOI: 10.1021/acsami.2c02369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The hemispherical barrier oxide layer (BOL) closing the bottom tips of hexagonally distributed arrays of cylindrical nanochannels in nanoporous anodic alumina (NAA) membranes is structurally engineered by anodizing aluminum substrates in three distinct acid electrolytes at their corresponding self-ordering anodizing potentials. These nanochannels display a characteristic ionic current rectification (ICR) signal between high and low ionic conduction states, which is determined by the thickness and chemical composition of the BOL and the pH of the ionic electrolyte solution. The rectification efficiency of the ionic current associated with the flow of ions across the anodic BOL increases with its thickness, under optimal pH conditions. The inner surface of the nanopores in NAA membranes was chemically modified with thiol-terminated functional molecules. The resultant NAA-based iontronic system provides a model platform to selectively detect gold metal ions (Au3+) by harnessing dynamic ICR signal shifts as the core sensing principle. The sensitivity of the system is proportional to the thickness of the barrier oxide layer, where NAA membranes produced in phosphoric acid at 195 V with a BOL thickness of 232 ± 6 nm achieve the highest sensitivity and low limit of detection in the sub-picomolar range. This study provides exciting opportunities to engineer NAA structures with tailorable ICR signals for specific applications across iontronic sensing and other nanofluidic disciplines.
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Affiliation(s)
- Juan Wang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Cheryl Suwen Law
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Monash Institute of Pharmaceutics Science, Monash University, Victoria 3052, Melbourne, Australia
| | - Satyathiran Gunenthiran
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Huong Nguyen Que Tran
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Khoa Nhu Tran
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Siew Yee Lim
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Department of Chemistry, The University of Adelaide, South Australia 5005, Adelaide, Australia
| | - Abel Santos
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, South Australia 5005, Adelaide, Australia
- Institute for Photonics and Advanced Sensing, The University of Adelaide, South Australia 5005, Adelaide, Australia
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13
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Del Grosso E, Irmisch P, Gentile S, Prins LJ, Seidel R, Ricci F. Dissipative Control over the Toehold‐Mediated DNA Strand Displacement Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Patrick Irmisch
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Serena Gentile
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Leonard J. Prins
- Department of Chemical fSciences University of Padua Via Marzolo 1 35131 Padua Italy
| | - Ralf Seidel
- Molecular Biophysics Group Peter Debye Institute for Soft Matter Physics Universität Leipzig 04103 Leipzig Germany
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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14
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Zhang C, Ma X, Zheng X, Ke Y, Chen K, Liu D, Lu Z, Yang J, Yan H. Programmable allosteric DNA regulations for molecular networks and nanomachines. SCIENCE ADVANCES 2022; 8:eabl4589. [PMID: 35108052 PMCID: PMC8809682 DOI: 10.1126/sciadv.abl4589] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.
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Affiliation(s)
- Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing 100871, China
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
| | - Xueying Ma
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
- Bio-evidence Sciences Academy, Xi’an Jiaotong University, Xi’an, Shaanxi 710049, China
| | - Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Kuiting Chen
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zuhong Lu
- The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 211189, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author. (C.Z.); (J.Y.); (H.Y.)
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15
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Liu L, Hu Q, Zhang W, Li W, Zhang W, Ming Z, Li L, Chen N, Wang H, Xiao X. Multifunctional Clip Strand for the Regulation of DNA Strand Displacement and Construction of Complex DNA Nanodevices. ACS NANO 2021; 15:11573-11584. [PMID: 34213302 DOI: 10.1021/acsnano.1c01763] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Strand displacement reactions are important bricks for the construction of various DNA nanodevices, among which the toehold-mediated strand displacement reaction is the most prevalently adopted. However, only a limited number of tools could be used to finely regulate the toehold reaction, thus restricting DNA nanodevices from being more multifunctional and powerful. Herein, we developed a regulation tool, Clip, and achieved multiple regulatory functions, including subtle adjustment of the reaction rates, allosteric strand displacement, selective activation, and resetting of the reaction. Taking advantages of the multiple functions, we constructed Clip-toehold-based DNA walking machines. They showed behaviors of controllable walking, concatenation, and programmable pathways. Furthermore, we built Clip-toehold-based AND and OR logic gates and integrated those logic gates to construct multilayer circuits, which could be reset and reused to process different input signals. We believe that the proposed Clip tool has expanded the functionality of DNA strand displacement-based nanodevices to a much more complex and diverse level and anticipate that the tool will be widely adopted in DNA nanotechnology.
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Affiliation(s)
- Liquan Liu
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingyi Hu
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenkai Zhang
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenhao Li
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Zhang
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhihao Ming
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Longjie Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering. Huazhong University of Science and Technology, Wuhan 430074, China
| | - Na Chen
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hongbo Wang
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianjin Xiao
- Institute of Reproductive Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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16
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Synthesis Strategy of Reversible Circuits on DNA Computers. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA computers and quantum computers are gaining attention as alternatives to classical digital computers. DNA is a biological material that can be reprogrammed to perform computing functions. Quantum computing performs reversible computations by nature based on the laws of quantum mechanics. In this paper, DNA computing and reversible computing are combined to propose novel theoretical methods to implement reversible gates and circuits in DNA computers based on strand displacement reactions, since the advantages of reversible logic gates can be exploited to improve the capabilities and functionalities of DNA computers. This paper also proposes a novel universal reversible gate library (URGL) for synthesizing n-bit reversible circuits using DNA to reduce the average length and cost of the constructed circuits when compared with previous methods. Each n-bit URGL contains building blocks to generate all possible permutations of a symmetric group of degree n. Our proposed group (URGL) in the paper is a permutation group. The proposed implementation methods will improve the efficiency of DNA computer computations as the results of DNA implementations are better in terms of quantum cost, DNA cost, and circuit length.
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17
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Zimmers ZA, Adams NM, Haselton FR. Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal. Biosens Bioelectron 2021; 188:113354. [PMID: 34034212 DOI: 10.1016/j.bios.2021.113354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
DNA amplification circuits that rely on thermodynamically-driven hybridization events triggered by a target nucleic acid are becoming increasingly utilized due to their relative simplicity. A drawback of these circuits is that non-specific amplification, or circuit leakage, must be estimated using a separate "no-target" control reaction to eliminate false positives. Aside from requiring an additional reaction, the problem with this approach is the difficulty of creating a no-target control for biological specimens. To overcome this limitation, we propose a strategy that combines both reactions into the same tube using naturally-occurring right-handed D-DNA circuit elements for the target detection reaction and identical synthetic mirror-image left-handed L-DNA circuit elements for the no-target control reaction. We illustrate this approach using catalyzed hairpin assembly (CHA), one of the most studied DNA amplification circuits. In a dual-chirality CHA design, the right-handed circuit signal is produced by target-specific amplification and circuit leakage, whereas the left-handed circuit signal is produced only by circuit leakage. The target-specific amplification is calculated as the difference between the two signals. The limit of detection of this dual-chirality CHA reaction was found to be similar to that of traditional CHA (81 vs 92 pM, respectively). Furthermore, the left-handed no-target signal matched the right-handed leakage across a wide range of sample conditions including background DNA, increased salt concentration, increased temperature, and urine. These results demonstrate the robustness of a dual-chirality design and the potential utility of left-handed DNA in the development of new DNA amplification circuits better-suited for target detection applications in biological samples.
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Affiliation(s)
- Zackary A Zimmers
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA.
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18
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Zou C, Wei X, Zhang Q, Zhou C, Zhou S. Encryption Algorithm Based on DNA Strand Displacement and DNA Sequence Operation. IEEE Trans Nanobioscience 2021; 20:223-234. [PMID: 33577453 DOI: 10.1109/tnb.2021.3058399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA strand displacement is introduced in this study and used to construct an analog DNA strand displacement chaotic system based on six reaction modules in nanoscale size. The DNA strand displacement circuit is employed in encryption as a chaotic generator to produce chaotic sequences. In the encryption algorithm, we convert chaotic sequences to binary ones by comparing the concentration of signal DNA strand. Simulation results show that the encryption scheme is sensitive to the keys, and key space is large enough to resist the brute-force attacks, furthermore algorithm has a high capacity to resist statistic attack. Based on robustness analysis, our proposed encryption scheme is robust to the DNA strand displacement reaction rate control, noise and concentration detection to a certain extent.
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19
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Zhou Z, Wang J, Levine RD, Remacle F, Willner I. DNA-based constitutional dynamic networks as functional modules for logic gates and computing circuit operations. Chem Sci 2021; 12:5473-5483. [PMID: 34168788 PMCID: PMC8179666 DOI: 10.1039/d1sc01098k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 11/21/2022] Open
Abstract
A nucleic acid-based constitutional dynamic network (CDN) is introduced as a single computational module that, in the presence of different sets of inputs, operates a variety of logic gates including a half adder, 2 : 1 multiplexer and 1 : 2 demultiplexer, a ternary multiplication matrix and a cascaded logic circuit. The CDN-based computational module leads to four logically equivalent outputs for each of the logic operations. Beyond the significance of the four logically equivalent outputs in establishing reliable and robust readout signals of the computational module, each of the outputs may be fanned out, in the presence of different inputs, to a set of different logic circuits. In addition, the ability to intercommunicate constitutional dynamic networks (CDNs) and to construct DNA-based CDNs of higher complexity provides versatile means to design computing circuits of enhanced complexity.
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Affiliation(s)
- Zhixin Zhou
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - R D Levine
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Francoise Remacle
- Theoretical Physical Chemistry, UR MolSys B6c, University of Liège B4000 Liège Belgium
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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20
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Molden TA, Grillo MC, Kolpashchikov DM. Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors. Chemistry 2020; 27:2421-2426. [DOI: 10.1002/chem.202003959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/30/2020] [Indexed: 01/27/2023]
Affiliation(s)
- Tatiana A. Molden
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
| | - Marcella C. Grillo
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
| | - Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
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21
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Zou C, Zhang Q, Wei X. Compilation of a Coupled Hyper-Chaotic Lorenz System Based on DNA Strand Displacement Reaction Network. IEEE Trans Nanobioscience 2020; 20:92-104. [PMID: 33055027 DOI: 10.1109/tnb.2020.3031360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ideal formal chemical reaction network is an effective programming language to design complex system dynamical behavior. In this article, a coupled hyper-chaotic Lorenz system can be described by the ordinary differential equations of an ideal formal reaction network, which is constructed by catalysis, annihilation and adjust reaction modules, where the variables of system are represented by the difference in concentration of two chemical species. The ideal formal reaction network can be implemented by DNA strand displacement reaction network. Through Lyapunov exponent, we have analyzed hyper-chaotic dynamical behavior of coupled Lorenz system. In discussion and analysis, we have analyzed effect of noise, reaction rate control error and concentration detection error to DNA strand displacement reaction network.
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22
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Fan D, Wang J, Wang E, Dong S. Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001766. [PMID: 33344121 PMCID: PMC7740092 DOI: 10.1002/advs.202001766] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Indexed: 05/11/2023]
Abstract
DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- Present address:
Institute of ChemistryThe Hebrew University of JerusalemJerusalem91904Israel
| | - Juan Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022China
- University of Science and Technology of ChinaHefeiAnhui230026China
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23
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Accelerating the Finite-Element Method for Reaction-Diffusion Simulations on GPUs with CUDA. MICROMACHINES 2020; 11:mi11090881. [PMID: 32971889 PMCID: PMC7569852 DOI: 10.3390/mi11090881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology offers a fine control over biochemistry by programming chemical reactions in DNA templates. Coupled to microfluidics, it has enabled DNA-based reaction-diffusion microsystems with advanced spatio-temporal dynamics such as traveling waves. The Finite Element Method (FEM) is a standard tool to simulate the physics of such systems where boundary conditions play a crucial role. However, a fine discretization in time and space is required for complex geometries (like sharp corners) and highly nonlinear chemistry. Graphical Processing Units (GPUs) are increasingly used to speed up scientific computing, but their application to accelerate simulations of reaction-diffusion in DNA nanotechnology has been little investigated. Here we study reaction-diffusion equations (a DNA-based predator-prey system) in a tortuous geometry (a maze), which was shown experimentally to generate subtle geometric effects. We solve the partial differential equations on a GPU, demonstrating a speedup of ∼100 over the same resolution on a 20 cores CPU.
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24
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Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
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Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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25
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Nakama T, Takezawa Y, Sasaki D, Shionoya M. Allosteric Regulation of DNAzyme Activities through Intrastrand Transformation Induced by Cu(II)-Mediated Artificial Base Pairing. J Am Chem Soc 2020; 142:10153-10162. [PMID: 32396728 DOI: 10.1021/jacs.0c03129] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Allosteric regulation is gaining increasing attention as a basis for the production of stimuli-responsive materials in many research areas including DNA nanotechnology. We expected that metal-mediated artificial base pairs, consisting of ligand-type nucleotides and a bridging metal ion, could serve as allosteric units that regulate the function of DNA molecules. In this study, we established a rational design strategy for developing CuII-responsive allosteric DNAzymes by incorporating artificial hydroxypyridone ligand-type nucleotides (H) that form a CuII-mediated base pair (H-CuII-H). We devised a new enzymatic method using a standard DNA polymerase and a ligase to prepare DNA strands containing H nucleotides. Previously reported DNAzymes were modified by introducing a H-H pair into the stem region, and the stem-loop sequences were altered so that the structure becomes catalytically inactive in the absence of CuII ions. The formation of a H-CuII-H base pair triggers intrastrand transformation from the inactive to the active structure, enabling allosteric regulation of the DNAzyme activity in response to CuII ions. The activity of the H-modified DNAzyme was reversibly switched by the addition and removal of CuII ions under isothermal conditions. Similarly, by incorporating a H-CuII-H pair into an in vitro-selected AgI-dependent DNAzyme, we have developed a DNAzyme that exhibits an AND logic-gate response to CuII and AgI ions. The rational design strategy and the easy enzymatic synthetic method presented here provide a versatile way to develop a variety of metal-responsive allosteric DNA materials, including molecular machines and logic circuits, based on metal-mediated artificial base pairing.
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Affiliation(s)
- Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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26
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Scalise D, Rubanov M, Miller K, Potters L, Noble M, Schulman R. Programming the Sequential Release of DNA. ACS Synth Biol 2020; 9:749-755. [PMID: 32212717 DOI: 10.1021/acssynbio.9b00398] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This study presents a mechanism for releasing a series of different short DNA sequences from sequestered complexes, one after another, using coupled biochemical reactions. The process uses stages of coupled DNA strand-displacement reactions that first release an output molecule and then trigger the initiation of the next release stage. We demonstrate the sequential release of 25 nM of four different sequences of DNA over a day, both with and without a centralized "clock" mechanism to regulate release timing. We then demonstrate how the presence of a target input molecule can determine which of several different release pathways are activated, analogous to branching conditional statements in computer programming. This sequential release circuit offers a means to schedule downstream chemical events, such as steps in the assembly of a nanostructure, or stages in a material's response to a stimulus.
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27
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Bader A, Cockroft SL. Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices. Chem Commun (Camb) 2020; 56:5135-5138. [DOI: 10.1039/d0cc00882f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Simple design principles improve conformational stability and decrease strand leakage by two orders of magnitude.
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Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
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28
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Harding BI, Pollak NM, Stefanovic D, Macdonald J. Repeated Reuse of Deoxyribozyme-Based Logic Gates. NANO LETTERS 2019; 19:7655-7661. [PMID: 31615207 DOI: 10.1021/acs.nanolett.9b02326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Deoxyribozymes (DNAzymes) have demonstrated a significant capacity for biocomputing and hold promise for information processing within advanced biological devices if several key capabilities are developed. One required capability is reuse-having DNAzyme logic gates be cyclically, and controllably, activated and deactivated. We designed an oligonucleotide-based system for DNAzyme reuse that could (1) remove previously bound inputs by addition of complementary oligonucleotides via toe-hold mediated binding and (2) diminish output signal through the addition of quencher-labeled oligonucleotides complementary to the fluorophore-bound substrate. Our system demonstrated, for the first time, the ability for DNAzymes to have their activity toggled, with activity returning to 90-125% of original activity. This toggling could be performed multiple times with control being exerted over when the toggling occurs, with three clear cycles observed before the variability in activity became too great. Our data also demonstrated that fluorescent output of the DNAzyme activity could be actively removed and regenerated. This reuse system can increase the efficiency of DNAzyme-based logic circuits by reducing the number of redundant oligonucleotides and is critical for future development of reusable biodevices controlled by logical operations.
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Affiliation(s)
- Bradley I Harding
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
| | - Nina M Pollak
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
- CSIRO Synthetic Biology Future Science Platform , GPO Box 1700, Canberra , ACT 2601 , Australia
| | - Darko Stefanovic
- Department of Computer Science , University of New Mexico , Albuquerque , New Mexico 87131 , United States
- Center for Biomedical Engineering , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Joanne Macdonald
- Genecology Research Centre, School of Science and Engineering , University of the Sunshine Coast , Sippy Downs , QLD 4556 , Australia
- Division of Experimental Therapeutics, Department of Medicine , Columbia University , New York , New York 10032 , United States
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29
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Zhang C, Wang Z, Liu Y, Yang J, Zhang X, Li Y, Pan L, Ke Y, Yan H. Nicking-Assisted Reactant Recycle To Implement Entropy-Driven DNA Circuit. J Am Chem Soc 2019; 141:17189-17197. [DOI: 10.1021/jacs.9b07521] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
- College of Medical Technology, Peking University Health Science Center, Beijing 100871, China
| | - Zhiyu Wang
- Huazhong University of Science and Technology, Wuhan 430074, Hubei China
| | | | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Xinxin Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yifan Li
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Linqiang Pan
- Huazhong University of Science and Technology, Wuhan 430074, Hubei China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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30
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On the importance of reaction networks for synthetic living systems. Emerg Top Life Sci 2019; 3:517-527. [DOI: 10.1042/etls20190016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022]
Abstract
The goal of creating a synthetic cell necessitates the development of reaction networks which will underlie all of its behaviours. Recent developments in in vitro systems, based upon both DNA and enzymes, have created networks capable of a range of behaviours e.g. information processing, adaptation and diffusive signalling. These networks are based upon reaction motifs that when combined together produce more complex behaviour. We highlight why it is inevitable that networks, based on enzymes or enzyme-like catalysts, will be required for the construction of a synthetic cell. We outline several of the challenges, including (a) timing, (b) regulation and (c) energy distribution, that must be overcome in order to transition from the simple networks we have today to much more complex networks capable of a variety of behaviours and which could find application one day within a synthetic cell.
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31
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Seo J, Kim S, Park HH, Choi DY, Nam JM. Nano-bio-computing lipid nanotablet. SCIENCE ADVANCES 2019; 5:eaau2124. [PMID: 30801008 PMCID: PMC6386558 DOI: 10.1126/sciadv.aau2124] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/11/2019] [Indexed: 05/02/2023]
Abstract
Using nanoparticles as substrates for computation enables algorithmic and autonomous controls of their unique and beneficial properties. However, scalable architecture for nanoparticle-based computing systems is lacking. Here, we report a platform for constructing nanoparticle logic gates and circuits at the single-particle level on a supported lipid bilayer. Our "lipid nanotablet" platform, inspired by cellular membranes that are exploited to compartmentalize and control signaling networks, uses a lipid bilayer as a chemical circuit board and nanoparticles as computational units. On a lipid nanotablet, a single-nanoparticle logic gate senses molecules in solution as inputs and triggers particle assembly or disassembly as an output. We demonstrate a set of Boolean logic operations, fan-in/fan-out of logic gates, and a combinational logic circuit such as a multiplexer. We envisage that our approach to modularly implement nanoparticle circuits on a lipid bilayer will create new paradigms and opportunities in molecular computing, nanoparticle circuits, and systems nanoscience.
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32
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Yang S, Yang C, Huang D, Song L, Chen J, Yang Q. Recent Progress in Fluorescence Signal Design for DNA-Based Logic Circuits. Chemistry 2019; 25:5389-5405. [PMID: 30328639 DOI: 10.1002/chem.201804420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/16/2018] [Indexed: 01/06/2023]
Abstract
DNA-based logic circuits, encoding algorithms in DNA and processing information, are pushing the frontiers of molecular computers forward, owing to DNA's advantages of stability, accessibility, manipulability, and especially inherent biological significance and potential medical application. In recent years, numerous logic functions, from arithmetic to nonarithmetic, have been realized based on DNA. However, DNA can barely provide a detectable signal by itself, so that the DNA-based circuits depend on extrinsic signal actuators. The signal strategy of carrying out a response is becoming one of the design focuses in DNA-based logic circuit construction. Although work on sequence and structure design for DNA-based circuits has been well reviewed, the strategy on signal production lacks comprehensive summary. In this review, we focused on the latest designs of fluorescent output for DNA-based logic circuits. Several basic strategies are summarized and a few designs for developing multi-output systems are provided. Finally, some current difficulties and possible opportunities were also discussed.
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Affiliation(s)
- Shu Yang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Chunrong Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Dan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Lingbo Song
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jianchi Chen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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33
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Berleant J, Berlind C, Badelt S, Dannenberg F, Schaeffer J, Winfree E. Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems. J R Soc Interface 2018; 15:20180107. [PMID: 30958232 PMCID: PMC6303802 DOI: 10.1098/rsif.2018.0107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 11/05/2018] [Indexed: 12/11/2022] Open
Abstract
As an engineering material, DNA is well suited for the construction of biochemical circuits and systems, because it is simple enough that its interactions can be rationally designed using Watson-Crick base pairing rules, yet the design space is remarkably rich. When designing DNA systems, this simplicity permits using functional sections of each strand, called domains, without considering particular nucleotide sequences. However, the actual sequences used may have interactions not predicted at the domain-level abstraction, and new rigorous analysis techniques are needed to determine the extent to which the chosen sequences conform to the system's domain-level description. We have developed a computational method for verifying sequence-level systems by identifying discrepancies between the domain-level and sequence-level behaviour. This method takes a DNA system, as specified using the domain-level tool Peppercorn, and analyses data from the stochastic sequence-level simulator Multistrand and sequence-level thermodynamic analysis tool NUPACK to estimate important aspects of the system, such as reaction rate constants and secondary structure formation. These techniques, implemented as the Python package KinDA, will allow researchers to predict the kinetic and thermodynamic behaviour of domain-level systems after sequence assignment, as well as to detect violations of the intended behaviour.
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Affiliation(s)
| | | | | | | | | | - Erik Winfree
- California Institute of Technology, Pasadena, CA, USA
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34
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Wang H, Zheng J, Sun Y, Li T. Cellular environment-responsive intelligent DNA logic circuits for controllable molecular sensing. Biosens Bioelectron 2018; 117:729-735. [DOI: 10.1016/j.bios.2018.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/12/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022]
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35
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Fern J, Schulman R. Modular DNA strand-displacement controllers for directing material expansion. Nat Commun 2018; 9:3766. [PMID: 30217991 PMCID: PMC6138645 DOI: 10.1038/s41467-018-06218-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/17/2018] [Indexed: 12/05/2022] Open
Abstract
Soft materials that swell or change shape in response to external stimuli show extensive promise in regenerative medicine, targeted therapeutics, and soft robotics. Generally, a stimulus for shape change must interact directly with the material, limiting the types of stimuli that may be used and necessitating high stimulus concentrations. Here, we show how DNA strand-displacement controllers within hydrogels can mediate size change by interpreting, amplifying, and integrating stimuli and releasing signals that direct the response. These controllers tune the time scale and degree of DNA-crosslinked hydrogel swelling and can actuate dramatic material size change in response to <100 nM of a specific biomolecular input. Controllers can also direct swelling in response to small molecules or perform logic. The integration of these stimuli-responsive materials with biomolecular circuits is a major step towards autonomous soft robotic systems in which sensing and actuation are implemented by biomolecular reaction networks. Materials which change shape in response to a trigger are of interest for soft robotics and targeted therapeutic delivery. Here, the authors report on the development of DNA-crosslinked hydrogels which can expand upon the detection of different biomolecular inputs mediated by DNA strand-displacement.
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Affiliation(s)
- Joshua Fern
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.
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36
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Abstract
A buffer reaction actively resists changes to the concentration of a chemical species. Typically, buffering reactions have only been able to regulate the concentration of hydronium (i.e., pH) and other ions. Here, we develop a new class of buffers that regulate the concentrations of short sequences of DNA (i.e., oligonucleotides). A buffer's behavior is determined by its set point concentration, capacity to resist disturbances, and response time after a disturbance. We provide simple mathematical formulas for selecting rate constants to tune each of these properties and show how to design DNA sequences and concentrations to implement the desired rate constants. We demonstrate several oligonucleotide buffers that maintain oligonucleotide set point concentrations between 10 and 80 nM in the presence of disturbances of 50 to 500 nM, with response times of less than 10 min to 1.5 h. Multiple buffers can regulate different sequences of DNA in parallel without crosstalk. Oligonucleotide buffers could stabilize and restore reactant concentrations in DNA circuits or in self-assembly processes, allowing such systems to operate reliably for extended durations. These buffers might also be coupled to other reactions to buffer molecules other than DNA. In general, an oligonucleotide buffer can be viewed as a chemical "battery" that maintains the total chemical potential of a buffered species in a closed system.
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37
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Sawaya NPD, Rappoport D, Tabor DP, Aspuru-Guzik A. Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling. ACS NANO 2018; 12:6410-6420. [PMID: 29920202 DOI: 10.1021/acsnano.8b00584] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we introduce a proposal for a molecular exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. Our proposal relies on excitation migration via the second excited singlet (S2) state of the gate molecule. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: picosecond time scale actuation, amplification/gain behavior, and a lack of molecular rearrangement. We demonstrate that the device can be used to produce universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux.
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Affiliation(s)
- Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
- Intel Laboratories , Santa Clara , California 95054 , United States
| | - Dmitrij Rappoport
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Daniel P Tabor
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
- Senior Fellow, Canadian Institute for Advanced Research, Bioinspired Solar Energy Program , Toronto , ON M5G 1Z8 , Canada
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38
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Garg S, Shah S, Bui H, Song T, Mokhtar R, Reif J. Renewable Time-Responsive DNA Circuits. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801470. [PMID: 30022600 DOI: 10.1002/smll.201801470] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/29/2018] [Indexed: 06/08/2023]
Abstract
DNA devices have been shown to be capable of evaluating Boolean logic. Several robust designs for DNA circuits have been demonstrated. Some prior DNA-based circuits are use-once circuits since the gate motifs of the DNA circuits get permanently destroyed as a side effect of the computation, and hence cannot respond correctly to subsequent changes in inputs. Other DNA-based circuits use a large reservoir of buffered gates to replace the working gates of the circuit and can be used to drive a finite number of computation cycles. In many applications of DNA circuits, the inputs are inherently asynchronous, and this necessitates that the DNA circuits be asynchronous: the output must always be correct regardless of differences in the arrival time of inputs. This paper demonstrates: 1) renewable DNA circuits, which can be manually reverted to their original state by addition of DNA strands, and 2) time-responsive DNA circuits, where if the inputs change over time, the DNA circuit can recompute the output correctly based on the new inputs, that are manually added after the system has been reset. The properties of renewable, asynchronous, and time-responsiveness appear to be central to molecular-scale systems; for example, self-regulation in cellular organisms.
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Affiliation(s)
- Sudhanshu Garg
- LinkedIn Inc., 1000 W Maude Ave, Sunnyvale, CA, 94085, USA
| | - Shalin Shah
- Department of Electrical & Computer Engineering, Duke University, Durham, NC, 27705, USA
| | - Hieu Bui
- National Research Council, 500 Fifth Street NW, Keck 576, Washington, DC, 20001, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Tianqi Song
- Department of Computer Science, Duke University, Durham, NC, 27705, USA
| | - Reem Mokhtar
- Department of Computer Science, Duke University, Durham, NC, 27705, USA
| | - John Reif
- Department of Electrical & Computer Engineering, Duke University, Durham, NC, 27705, USA
- Department of Computer Science, Duke University, Durham, NC, 27705, USA
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39
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Abstract
Herein, we report a carbazole (Cz) ligand that displays distinct turn-on fluorescence signals upon interaction with human telomeric G-quadruplex ( h-TELO) and nuclease enzymes. Interestingly, Cz selectively binds and stabilizes the mixed hybrid topology of h-TELO G-quadruplex that withstands digestion by exonucleases and nuclease S1. The distinct fluorescence signatures of Cz-stabilized h-TELO with nucleases are used to design conceptually novel DNA devices for selectively detecting the enzymatic activity of DNase I as well as performing logic operations. An INHIBIT logic gate is constructed using h-TELO and DNase I as the inputs while the inputs of h-TELO and nuclease S1 form a YES logic gate. Furthermore, a two-input two-output reusable logic device with "multireset" function is developed by using h-TELO and DNase I as inputs. On the basis of this platform, combinatorial logic systems (INHIBIT-INHIBIT and NOR-OR) have been successfully installed using different combinations of nucleases as inputs. Moreover, this new strategy of using a synthetic dual emissive probe and enzyme/DNA inputs for constructing reusable logic device may find important applications in biological computing and information processing.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Rakesh Paul
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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40
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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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41
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Masaki Y, Cayer D, McBride R, Ghadiri MR. A kinetically controlled, isothermal method for the detection of single nucleotide mismatches. Bioorg Med Chem Lett 2018; 28:2754-2758. [PMID: 29500066 DOI: 10.1016/j.bmcl.2018.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/13/2018] [Indexed: 11/28/2022]
Abstract
We describe an isothermal, enzyme-free method to detect single nucleotide differences between oligonucleotides of close homology. The approach exploits kinetic differences in toe-hold-mediated, nucleic acid strand-displacement reactions to detect single nucleotide polymorphisms (SNPs) with essentially "digital" precision. The theoretical underpinning, experimental analyses, predictability, and accuracy of this new method are reported. We demonstrate detection of biologically relevant SNPs and single nucleotide differences in the let-7 family of microRNAs. The method is adaptable to microarray formats, as demonstrated with on-chip detection of SNP variants involved in susceptibility to the therapeutic agents abacavir, Herceptin, and simvastatin.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Devon Cayer
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Ryan McBride
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - M Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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42
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Ran X, Wang Z, Ju E, Pu F, Song Y, Ren J, Qu X. An intelligent 1:2 demultiplexer as an intracellular theranostic device based on DNA/Ag cluster-gated nanovehicles. NANOTECHNOLOGY 2018; 29:065501. [PMID: 29226844 DOI: 10.1088/1361-6528/aaa09a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The logic device demultiplexer can convey a single input signal into one of multiple output channels. The choice of the output channel is controlled by a selector. Several molecules and biomolecules have been used to mimic the function of a demultiplexer. However, the practical application of logic devices still remains a big challenge. Herein, we design and construct an intelligent 1:2 demultiplexer as a theranostic device based on azobenzene (azo)-modified and DNA/Ag cluster-gated nanovehicles. The configuration of azo and the conformation of the DNA ensemble can be regulated by light irradiation and pH, respectively. The demultiplexer which uses light as the input and acid as the selector can emit red fluorescence or a release drug under different conditions. Depending on different cells, the intelligent logic device can select the mode of cellular imaging in healthy cells or tumor therapy in tumor cells. The study incorporates the logic gate with the theranostic device, paving the way for tangible applications of logic gates in the future.
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Affiliation(s)
- Xiang Ran
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, People's Republic of China. School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230031, People's Republic of China
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43
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Deng J, Tao Z, Liu Y, Lin X, Qian P, Lyu Y, Li Y, Fu K, Wang S. A target-induced logically reversible logic gate for intelligent and rapid detection of pathogenic bacterial genes. Chem Commun (Camb) 2018. [DOI: 10.1039/c8cc00178b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A target-induced Feynman gate acts as an intelligent biosensor to distinguish all information of the targets from the output signal patterns.
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Affiliation(s)
- Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Zhanhui Tao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Pengcheng Qian
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yanlong Lyu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Yunfei Li
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Kejing Fu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education)
- Tianjin Key Laboratory of Food Nutrition and Safety
- Tianjin University of Science and Technology
- Tianjin
- China
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44
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Li Q, Tian C, Li X, Mao C. Can strand displacement take place in DNA triplexes? Org Biomol Chem 2018; 16:372-375. [PMID: 29265153 DOI: 10.1039/c7ob02871g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Toehold-mediated strand displacement can take place in the context of DNA triplexes, slowly.
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Affiliation(s)
- Qian Li
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Cheng Tian
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Xiang Li
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
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45
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Chandrasekaran AR, Levchenko O, Patel DS, MacIsaac M, Halvorsen K. Addressable configurations of DNA nanostructures for rewritable memory. Nucleic Acids Res 2017; 45:11459-11465. [PMID: 28977499 PMCID: PMC5737491 DOI: 10.1093/nar/gkx777] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA serves as nature's information storage molecule, and has been the primary focus of engineered systems for biological computing and data storage. Here we combine recent efforts in DNA self-assembly and toehold-mediated strand displacement to develop a rewritable multi-bit DNA memory system. The system operates by encoding information in distinct and reversible conformations of a DNA nanoswitch and decoding by gel electrophoresis. We demonstrate a 5-bit system capable of writing, erasing, and rewriting binary representations of alphanumeric symbols, as well as compatibility with 'OR' and 'AND' logic operations. Our strategy is simple to implement, requiring only a single mixing step at room temperature for each operation and standard gel electrophoresis to read the data. We envision such systems could find use in covert product labeling and barcoding, as well as secure messaging and authentication when combined with previously developed encryption strategies. Ultimately, this type of memory has exciting potential in biomedical sciences as data storage can be coupled to sensing of biological molecules.
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Affiliation(s)
| | - Oksana Levchenko
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Dhruv S Patel
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Molly MacIsaac
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
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46
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Pan L, Wang Z, Li Y, Xu F, Zhang Q, Zhang C. Nicking enzyme-controlled toehold regulation for DNA logic circuits. NANOSCALE 2017; 9:18223-18228. [PMID: 29164226 DOI: 10.1039/c7nr06484e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA strand displacement is widely used in DNA-related nanoengineering for its remarkable specificity and predictability. We report a nicking enzyme-assisted mechanism to regulate strand displacement, where DNA toeholds are dynamically controlled. To demonstrate the strategy, a protein/DNA-based Boolean operation system is constructed and based on it a two-channel multiplexer controlled by three different nicking enzymes is realized. The proposed regulatory mechanism can be used for switch logic statement and bridges protein and DNA logic circuits.
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Affiliation(s)
- Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
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47
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Li J, Green AA, Yan H, Fan C. Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. Nat Chem 2017; 9:1056-1067. [PMID: 29064489 PMCID: PMC11421837 DOI: 10.1038/nchem.2852] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions. In this Review, we summarize the current abilities of DNA/RNA nanotechnology to realize applications in live cells and then discuss the key problems that must be solved to fully exploit the useful properties of nanostructures. Finally, we provide viewpoints on how to integrate the tools provided by DNA/RNA nanotechnology and related new technologies to construct nucleic acid nanostructure-based molecular circuitry for synthetic biology.
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Affiliation(s)
- Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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48
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Gao J, Liu Y, Lin X, Deng J, Yin J, Wang S. Implementation of cascade logic gates and majority logic gate on a simple and universal molecular platform. Sci Rep 2017; 7:14014. [PMID: 29070871 PMCID: PMC5656625 DOI: 10.1038/s41598-017-14416-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 10/11/2017] [Indexed: 12/18/2022] Open
Abstract
Wiring a series of simple logic gates to process complex data is significantly important and a large challenge for untraditional molecular computing systems. The programmable property of DNA endows its powerful application in molecular computing. In our investigation, it was found that DNA exhibits excellent peroxidase-like activity in a colorimetric system of TMB/H2O2/Hemin (TMB, 3,3′, 5,5′-Tetramethylbenzidine) in the presence of K+ and Cu2+, which is significantly inhibited by the addition of an antioxidant. According to the modulated catalytic activity of this DNA-based catalyst, three cascade logic gates including AND-OR-INH (INHIBIT), AND-INH and OR-INH were successfully constructed. Interestingly, by only modulating the concentration of Cu2+, a majority logic gate with a single-vote veto function was realized following the same threshold value as that of the cascade logic gates. The strategy is quite straightforward and versatile and provides an instructive method for constructing multiple logic gates on a simple platform to implement complex molecular computing.
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Affiliation(s)
- Jinting Gao
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Yaqing Liu
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
| | - Xiaodong Lin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jiankang Deng
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Jinjin Yin
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety (Ministry of Education of China), College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin Economic and Technological Development Area, the 13th Avenue, No. 29, Tianjin, 300457, China.
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Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing. Sci Rep 2017; 7:10017. [PMID: 28855676 PMCID: PMC5577262 DOI: 10.1038/s41598-017-10459-y] [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: 06/15/2017] [Accepted: 08/08/2017] [Indexed: 11/15/2022] Open
Abstract
Toehold-mediated DNA strand displacement reaction (SDR) plays pivotal roles for the construction of diverse dynamic DNA nanodevices. To date, many elements have been introduced into SDR system to achieve controllable activation and fine regulation. However, as the most relevant stimuli for nucleic acid involved reaction, nucleic acid-recognizing enzymes (NAEs) have received nearly no attention so far despite SDR often takes place in NAEs-enriched environment (i.e., biological fluids). Herein, we report a set of NAEs-controlled SDR strategies, which take full advantage of NAEs’ properties. In this study, three different kinds of enzymes belonging to several classes (i.e., exonuclease, endonuclease and polymerase) have been used to activate or inhibit SDR, and more importantly, some mechanisms behind these strategies on how NAEs affect SDR have also been revealed. The exploration to use NAEs as possible cues to operate SDR will expand the available toolbox to build novel stimuli-fueled DNA nanodevices and could open the door to many applications including enzyme-triggered biocomputing and biosensing.
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50
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Idili A, Ricci F, Vallée-Bélisle A. Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves. Nucleic Acids Res 2017; 45:7571-7580. [PMID: 28605461 PMCID: PMC5737623 DOI: 10.1093/nar/gkx498] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/13/2022] Open
Abstract
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson-Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers.
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Affiliation(s)
- Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors and Nanomachines, Département de Chimie, Université de Montréal, Montreal, Québec H3T-1J4, Canada
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