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Hu M, Wang L, Xi S, Liu R, Dong Y. A biosensor based on interchain reactions for the detection of acetamipirid and the construction of basics logic gates OR and AND. IEEE Trans Nanobioscience 2021; 21:330-340. [PMID: 34962872 DOI: 10.1109/tnb.2021.3139079] [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: 11/05/2022]
Abstract
An enzyme-free and label-free fluorescent DNA aptasensor was constructed with computer assistance based on thermodynamic deviation driving interchain reactions. In this work, in the presence of target acetamiprid, the released trigger strand C-apt could open hairpin Hp1, which in turn triggered the strand displacement reaction and catalyzed the self-assembly of hairpins Hp1 and Hp2, so that the guanine base rich stem in Hp2 was opened. In the presence of K+ and NMM, the G-rich moiety could form a G-quadruplex and emit strong fluorescence at a specific excitation wavelength. The proposed strategy enables sensitive detection of acetamiprid at concentrations as low as 54.3 pM. Most importantly, computer-assisted analysis of the thermodynamic properties of nucleic acid strands and simulation of the reaction process and conditions of the proposed model before conducting biological experiments theoretically proves this strategy feasible and may simplify subsequent biological experiments. In addition, basic molecular logic gates, including OR and AND, were constructed based on this detection principle, and simulation tests and biological experiments were performed. The final results show that this strategy can not only have some applications in the field of food safety and environmental monitoring, but also provide a certain way for the development of molecular logic computing.
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2
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Gonzàlez-Rosell A, Cerretani C, Mastracco P, Vosch T, Copp SM. Structure and luminescence of DNA-templated silver clusters. NANOSCALE ADVANCES 2021; 3:1230-1260. [PMID: 36132866 PMCID: PMC9417461 DOI: 10.1039/d0na01005g] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/21/2021] [Indexed: 05/05/2023]
Abstract
DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.
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Affiliation(s)
- Anna Gonzàlez-Rosell
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
| | - Cecilia Cerretani
- Nanoscience Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
| | - Peter Mastracco
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
| | - Tom Vosch
- Nanoscience Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen Denmark
| | - Stacy M Copp
- Department of Materials Science and Engineering, University of California Irvine California 92697-2585 USA
- Department of Physics and Astronomy, University of California Irvine California 92697-4575 USA
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3
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Trifoi LA, Hodgson GK, Dogantzis NP, Impellizzeri S. A Reconfigurable, Dual-Output INHIBIT and IMPLICATION Molecular Logic Gate. Front Chem 2020; 8:470. [PMID: 32582639 PMCID: PMC7290064 DOI: 10.3389/fchem.2020.00470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022] Open
Abstract
Molecules that respond to input stimulations to produce detectable outputs can be exploited to mimic Boolean logic operators and reproduce basic arithmetic functions. We have designed a two-state fluorescent probe with tunable emission wavelength for the construction of a molecular logic gate with reconfigurable single– or dual–output capability. The system is based on a BODIPY skeleton coupled with 4-(dimethylamino)benzaldehyde. The behavior of the molecular logic gate can be easily investigated in solution with fluorescence spectroscopy, and the optical readout (fluorescence) can be monitored in one (green) or two (green and red) channels. Depending on the solvent of choice, single INHIBIT or dual INHIBIT/IMPLY logic functions can be achieved using chemical inputs (acid and base). Reconfiguration from single– to dual–output is thus made possible by operating the system in acetonitrile (single output) or toluene (dual output), respectively. The logic gate can be switched by manipulating the fluorescence emission via protonation or deprotonation, even when immobilized onto a glass substrate. At the solid state, the resulting output can be stored for extended periods of time. This feature provides two added benefits: (i) memory function and (ii) “set/reset” capability of the logic gate. Our design thus provides a proof-of-concept interface between the molecular and electronic domains.
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Affiliation(s)
- Lavinia A Trifoi
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Gregory K Hodgson
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Nicholas P Dogantzis
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Stefania Impellizzeri
- Laboratory for Nanomaterials and Molecular Plasmonics, Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
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4
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Arabahmadi R. A reversible fluorescence “ON–OFF–ON” sensor for sequential detection of F− and Cu2+ ions and its application as a molecular-scale logic device and security keypad lock. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1595604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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5
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Physical Insights into Molecular Sensors, Molecular Logic Gates, and Photosensitizers in Photodynamic Therapy. J CHEM-NY 2019. [DOI: 10.1155/2019/6793490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this article, the importance of charge/electron transfer in two rapidly growing areas of science is highlighted. In the field of molecular sensors, it plays a considerable role on the detection of molecular systems to serve as fluorescence sensors, switches, and molecular logic gates (MLG) replacing the semiconductor electronics, while in the field of photodynamic therapy, it acts competitive. On these scientific fields, a lot of research has been conducted in the last decades to find out potential candidates. In the field of fluorescent sensors, switches, and molecular logic gates, the fluorescent photo-induced electron transfer switching principle is responsible for the quenching of fluorescence. The manipulation of the quenching can lead to the design of an ideal candidate for complicated molecular logic operation. In the field of photodynamic therapy (PDT), the intersystem crossings occurring between excited singlet and triplet states are the key for an ideal photosensitizer (PS) candidate. The triplets must present relatively long lifetimes, and they must lie near or above the energy which is needed for the excitation of molecular oxygen. It this case, charge/electron phenomena can act competitive, and they are not desirable. However, there are a few complexes which are good PSs of singlet oxygen despite the charge transfer (CT) nature of their lowest excited state.
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An enzymatic calculation system based on electrochemiluminescence and fluorescence of luminol and cyclic voltammetry of ferrocene methanol. Biosens Bioelectron 2018; 118:44-50. [DOI: 10.1016/j.bios.2018.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022]
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7
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Erbas-Cakmak S, Kolemen S, Sedgwick AC, Gunnlaugsson T, James TD, Yoon J, Akkaya EU. Molecular logic gates: the past, present and future. Chem Soc Rev 2018; 47:2228-2248. [PMID: 29493684 DOI: 10.1039/c7cs00491e] [Citation(s) in RCA: 352] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The field of molecular logic gates originated 25 years ago, when A. P. de Silva published a seminal article in Nature. Stimulated by this ground breaking research, scientists were inspired to join the race to simulate the workings of the fundamental components of integrated circuits using molecules. The rules of this game of mimicry were flexible, and have evolved and morphed over the years. This tutorial review takes a look back on and provides an overview of the birth and growth of the field of molecular logics. Spinning-off from chemosensor research, molecular logic gates quickly proved themselves to be more than intellectual exercises and are now poised for many potential practical applications. The ultimate goal of this vein of research became clearer only recently - to "boldly go where no silicon-based logic gate has gone before" and seek out a new deeper understanding of life inside tissues and cells.
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Affiliation(s)
- Sundus Erbas-Cakmak
- Department of Molecular Biology and Genetics, Konya Food and Agriculture University, 42080 Konya, Turkey
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8
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Turan IS, Gunaydin G, Ayan S, Akkaya EU. Molecular demultiplexer as a terminator automaton. Nat Commun 2018; 9:805. [PMID: 29476048 PMCID: PMC5824880 DOI: 10.1038/s41467-018-03259-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/31/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular logic gates are expected to play an important role on the way to information processing therapeutic agents, especially considering the wide variety of physical and chemical responses that they can elicit in response to the inputs applied. Here, we show that a 1:2 demultiplexer based on a Zn2+-terpyridine-Bodipy conjugate with a quenched fluorescent emission, is efficient in photosensitized singlet oxygen generation as inferred from trap compound experiments and cell culture data. However, once the singlet oxygen generated by photosensitization triggers apoptotic response, the Zn2+ complex then interacts with the exposed phosphatidylserine lipids in the external leaflet of the membrane bilayer, autonomously switching off singlet oxygen generation, and simultaneously switching on a bright emission response. This is the confirmatory signal of the cancer cell death by the action of molecular automaton and the confinement of unintended damage by excessive singlet oxygen production.
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Affiliation(s)
- Ilke S Turan
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University, 06100, Ankara, Turkey
| | - Seylan Ayan
- Department of Chemistry, Bilkent University, 06800, Ankara, Turkey
| | - Engin U Akkaya
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey. .,Department of Chemistry, Bilkent University, 06800, Ankara, Turkey.
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Dhaka G, Kaur N, Singh J. Luminescent Benzothiazole-Based Fluorophore of Anisidine Scaffoldings: a “Turn-On” Fluorescent Probe for Al3+ and Hg2+ Ions. J Fluoresc 2017; 27:1943-1948. [DOI: 10.1007/s10895-017-2148-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/18/2017] [Indexed: 01/08/2023]
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Jayabharathi J, Thanikachalam V, Ramanathan P. Phenanthrimidazole as a fluorescent sensor with logic gate operations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:886-891. [PMID: 26116998 DOI: 10.1016/j.saa.2015.06.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 06/04/2023]
Abstract
A novel sensor namely, 1-(1-(p-tolyl)-1H-phenanthro[9,10-d]imidazol-2-yl)naphthalen-2-ol was synthesised for the detection of anion as well as cation through intramolecular charge transfer mechanism. This compound was used for the selective detection of Zn(2+) ion as compared to other metal ions and the binding was evidenced from the new absorption band at 356 nm and switch on fluorescence at 453 nm. The switch on fluorescence can be explained on the basis of photoinduced electron transfer (PET) mechanism and it was demonstrated by logic gate functions.
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Affiliation(s)
- J Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India.
| | - V Thanikachalam
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
| | - P Ramanathan
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
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12
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Caruana MV, Camilleri Fava M, Magri DC. A Colorimetric and Fluorimetric Three-Input Inverted Enabled OR Logic Array by Self-Assembly of a Rhodamine Probe in Micelles. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201402236] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Kaur N, Alreja P. A novel 1,10-phenanthroline based chemosensor for differential metal ion sensing and constructing molecular logic gates. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.11.062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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14
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Xu XL, Lin FW, Xu W, Wu J, Xu ZK. Highly Sensitive INHIBIT and XOR Logic Gates Based on ICT and ACQ Emission Switching of a Porphyrin Derivative. Chemistry 2014; 21:984-7. [PMID: 25430681 DOI: 10.1002/chem.201405675] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Xiao-Ling Xu
- Department of Chemistry, Zhejiang University, Hangzhou 310027 (P.R. China)
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15
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Xu W, Ren C, Teoh CL, Peng J, Gadre SH, Rhee HW, Lee CLK, Chang YT. An Artificial Tongue Fluorescent Sensor Array for Identification and Quantitation of Various Heavy Metal Ions. Anal Chem 2014; 86:8763-9. [DOI: 10.1021/ac501953z] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Wang Xu
- Department of Chemistry & MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543
- Singapore
Peking
Oxford Research Enterprise (SPORE), Environmental Research Institute (NERI), 5A Engineering Drive 1, #02-01, Singapore 117411
| | - Changliang Ren
- Institute of Materials
Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore 117602
| | - Chai Lean Teoh
- Department of Chemistry & MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543
| | - Juanjuan Peng
- Department of Chemistry & MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543
| | | | - Hyun-Woo Rhee
- Department
of Chemistry, School of Nano-Biosceince and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | - Chi-Lik Ken Lee
- Centre for Biomedical and
Life Sciences, Technology Development Office, Singapore Polytechnic, Singapore 139651
| | - Young-Tae Chang
- Department of Chemistry & MedChem Program of Life Sciences Institute, National University of Singapore, Singapore 117543
- Singapore Bioimaging
Consortium, Agency for Science, Technology and Research (A*STAR), Singapore 138667
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16
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Pu F, Ren J, Qu X. "Plug and play" logic gates based on fluorescence switching regulated by self-assembly of nucleotide and lanthanide ions. ACS APPLIED MATERIALS & INTERFACES 2014; 6:9557-9562. [PMID: 24830828 DOI: 10.1021/am501949t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Molecular logic gates in response to chemical, biological, or optical input signals at a molecular level have received much interest over the past decade. Herein, we construct "plug and play" logic systems based on the fluorescence switching of guest molecules confined in coordination polymer nanoparticles generated from nucleotide and lanthanide ions. In the system, the addition of new modules directly enables new logic functions. PASS 0, YES, PASS 1, NOT, IMP, OR, and AND gates are successfully constructed in sequence. Moreover, different logic gates (AND, INH, and IMP) can be constructed using different guest molecules and the same input combinations. The work will be beneficial to the future logic design and expand the applications of coordination polymers.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, People's Republic of China
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Madhuprasad, Swathi N, Manjunatha JR, Das UK, Shetty AN, Trivedi DR. Dual colorimetric receptor with logic gate operations: anion induced solvatochromism. NEW J CHEM 2014. [DOI: 10.1039/c3nj01229h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Kim DS, Lynch VM, Park JS, Sessler JL. Three Distinct Equilibrium States via Self-Assembly: Simple Access to a Supramolecular Ion-Controlled NAND Logic Gate. J Am Chem Soc 2013; 135:14889-94. [DOI: 10.1021/ja4080198] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dong Sub Kim
- Department
of
Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Vincent M. Lynch
- Department
of
Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Jung Su Park
- Department of Chemistry, Sookmyung Woman’s University, Seoul 140-742, Korea
| | - Jonathan L. Sessler
- Department
of
Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
- Department of
Chemistry, Yonsei University, Seoul 120-749, Korea
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Abstract
The enzyme system was used to mimic the D-flip-flop memory unit. The reversible conversion of NAD(+) and NADH cofactors was used to encode the states of the memory unit, while a mixture of inhibitors was used as the Clock input and the substrates were used as the Data input.
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Affiliation(s)
- Kevin MacVittie
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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Mandal AK, Das P, Mahato P, Acharya S, Das A. A Taco Complex Derived from a Bis-Crown Ether Capable of Executing Molecular Logic Operation through Reversible Complexation. J Org Chem 2012; 77:6789-800. [DOI: 10.1021/jo300622b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Amal Kumar Mandal
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002,
Gujarat, India
| | - Priyadip Das
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002,
Gujarat, India
| | - Prasenjit Mahato
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002,
Gujarat, India
| | - Suhash Acharya
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002,
Gujarat, India
| | - Amitava Das
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002,
Gujarat, India
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Uahengo V, Xiong B, Zhou N, Cai P, Hu K, Cheng G. Synthesis of a Phenylhydrazone-based Colorimetric Anion Sensor with Complementary IMP/INH Logic Functions. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sakthivel S, Punniyamurthy T. Fluorescent OFF–ON polymer chemosensor bonded alternatively with 1,4-dioctyloxybenzene and (R,R)-salen for cascade Zn2+ and chiral recognition. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kaur N, Kumar S. Insights into the photophysics, protonation and Cu2+ ion coordination behaviour of anthracene-9,10-dione-based chemosensors. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.622386] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Navneet Kaur
- a Department of Chemistry , Panjab University , Chandigarh, 160 014, Punjab, India
| | - Subodh Kumar
- b Department of Chemistry , Guru Nanak Dev University , Amritsar, 143 005, Punjab, India
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Guliyev R, Ozturk S, Kostereli Z, Akkaya EU. From Virtual to Physical: Integration of Chemical Logic Gates. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104228] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Guliyev R, Ozturk S, Kostereli Z, Akkaya EU. From Virtual to Physical: Integration of Chemical Logic Gates. Angew Chem Int Ed Engl 2011; 50:9826-31. [DOI: 10.1002/anie.201104228] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Halámek J, Bocharova V, Arugula MA, Strack G, Privman V, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate. J Phys Chem B 2011; 115:9838-45. [DOI: 10.1021/jp2041372] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vera Bocharova
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Mary A. Arugula
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Guinevere Strack
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Vladimir Privman
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, and Department of Physics, Clarkson University, Potsdam, New York 13699, United States
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Remón P, Hammarson M, Li S, Kahnt A, Pischel U, Andréasson J. Molecular Implementation of Sequential and Reversible Logic Through Photochromic Energy Transfer Switching. Chemistry 2011; 17:6492-500. [DOI: 10.1002/chem.201100027] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Patricia Remón
- Center for Research in Sustainable Chemistry (CIQSO) and Department of Chemical Engineering, Physical Chemistry, and Organic Chemistry, University of Huelva, Campus de El Carmen, s/n, 21071 Huelva (Spain), Fax: (+34) 959‐21‐99‐83
| | - Martin Hammarson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Göteborg (Sweden), Fax: (+46) 31‐772‐38‐58
| | - Shiming Li
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Göteborg (Sweden), Fax: (+46) 31‐772‐38‐58
| | - Axel Kahnt
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Göteborg (Sweden), Fax: (+46) 31‐772‐38‐58
| | - Uwe Pischel
- Center for Research in Sustainable Chemistry (CIQSO) and Department of Chemical Engineering, Physical Chemistry, and Organic Chemistry, University of Huelva, Campus de El Carmen, s/n, 21071 Huelva (Spain), Fax: (+34) 959‐21‐99‐83
| | - Joakim Andréasson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, 41296 Göteborg (Sweden), Fax: (+46) 31‐772‐38‐58
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Sooksawat D, Aeungmaitrepirom W, Ngeontae W, Tuntulani T. Logic gates from ion-selective bulk optodes. NEW J CHEM 2011. [DOI: 10.1039/c0nj00620c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Puntoriero F, Nastasi F, Bura T, Ziessel R, Campagna S, Giannetto A. Molecular logics: a mixed bodipy–bipyridine dye behaving as a concealable molecular switch. NEW J CHEM 2011. [DOI: 10.1039/c0nj00770f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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33
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A Supramolecular Off-On Fluorescent Switch and IMPLICATION Logic Gate for Detection of Cationic Surfactant. J Fluoresc 2010; 21:1015-20. [DOI: 10.1007/s10895-010-0792-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
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Halámek J, Bocharova V, Chinnapareddy S, Windmiller JR, Strack G, Chuang MC, Zhou J, Santhosh P, Ramirez GV, Arugula MA, Wang J, Katz E. Multi-enzyme logic network architectures for assessing injuries: digital processing of biomarkers. MOLECULAR BIOSYSTEMS 2010; 6:2554-60. [PMID: 20953502 DOI: 10.1039/c0mb00153h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A multi-enzyme biocatalytic cascade processing simultaneously five biomarkers characteristic of traumatic brain injury (TBI) and soft tissue injury (STI) was developed. The system operates as a digital biosensor based on concerted function of 8 Boolean AND logic gates, resulting in the decision about the physiological conditions based on the logic analysis of complex patterns of the biomarkers. The system represents the first example of a multi-step/multi-enzyme biosensor with the built-in logic for the analysis of complex combinations of biochemical inputs. The approach is based on recent advances in enzyme-based biocomputing systems and the present paper demonstrates the potential applicability of biocomputing for developing novel digital biosensor networks.
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Affiliation(s)
- Jan Halámek
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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Privman V, Zhou J, Halámek J, Katz E. Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change. J Phys Chem B 2010; 114:13601-8. [DOI: 10.1021/jp107562p] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Privman
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jian Zhou
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Jan Halámek
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13676, United States
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36
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Cao C, Liu H, Zhu XQ, Cheng JP. A molecular half-adder and half-subtractor based on pyrylium. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4050-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Arugula MA, Bocharova V, Halámek J, Pita M, Katz E. Enzyme-based multiplexer and demultiplexer. J Phys Chem B 2010; 114:5222-6. [PMID: 20350002 DOI: 10.1021/jp101101b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A digital 2-to-1 multiplexer and a 1-to-2 demultiplexer were mimicked by biocatalytic reactions involving concerted operation of several enzymes. Using glucose oxidase (GOx) and laccase (Lac) as the data input signals and variable pH as the addressing signal, ferrocyanide oxidation in the output channel was selectively activated by one from two inputs, thus mimicking the multiplexer operation. A demultiplexer based on the enzyme system composed of GOx, glucose dehydrogenase (GDH) and horseradish peroxidase (HRP) allowed selective activation of different output channels (oxidation of ferrocyanide or reduction of NAD(+)) by the glucose input. The selection of the output channel was controlled by the addressing input of NAD(+). The designed systems represent important novel components of future branched enzyme networks processing biochemical signals for biosensing and bioactuating.
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Affiliation(s)
- Mary A Arugula
- Department of Chemistry and Biomolecular Science, and NanoBio Laboratory, Clarkson University, Potsdam New York 13699-5810, USA
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38
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Digital biosensors with built-in logic for biomedical applications—biosensors based on a biocomputing concept. Anal Bioanal Chem 2010; 398:1591-603. [DOI: 10.1007/s00216-010-3746-0] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/11/2010] [Accepted: 04/12/2010] [Indexed: 11/29/2022]
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Prasanna de Silva A, McClean GD, McClenaghan ND, Moody TS, Weir SM. Logische Schaltungen mit leuchtenden Molekülen. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/nadc.20010490506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Bozdemir OA, Guliyev R, Buyukcakir O, Selcuk S, Kolemen S, Gulseren G, Nalbantoglu T, Boyaci H, Akkaya EU. Selective Manipulation of ICT and PET Processes in Styryl-Bodipy Derivatives: Applications in Molecular Logic and Fluorescence Sensing of Metal Ions. J Am Chem Soc 2010; 132:8029-36. [DOI: 10.1021/ja1008163] [Citation(s) in RCA: 357] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- O. Altan Bozdemir
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Ruslan Guliyev
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Onur Buyukcakir
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Sencer Selcuk
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Safacan Kolemen
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Gulcihan Gulseren
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Tugrul Nalbantoglu
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Hande Boyaci
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
| | - Engin U. Akkaya
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey and Department of Chemistry, Bilkent University, 06800 Ankara, Turkey
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41
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Upadhyay KK, Kumar A, Mishra RK, Fyles TM, Upadhyay S, Thapliyal K. Reversible colorimetric switching of thiophene hydrazone based on complementary IMP/INH logic functions. NEW J CHEM 2010. [DOI: 10.1039/c0nj00097c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Liu XY, Han X, Zhang LP, Tung CH, Wu LZ. Molecular logic circuit based on a multi-state mononuclear platinum(ii) terpyridyl complex. Phys Chem Chem Phys 2010; 12:13026-33. [DOI: 10.1039/c0cp00100g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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44
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Pischel U, Uzunova VD, Remón P, Nau WM. Supramolecular logic with macrocyclic input and competitive reset. Chem Commun (Camb) 2010; 46:2635-7. [DOI: 10.1039/b927595a] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Andréasson J, Pischel U. Smart molecules at work--mimicking advanced logic operations. Chem Soc Rev 2009; 39:174-88. [PMID: 20023848 DOI: 10.1039/b820280j] [Citation(s) in RCA: 378] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular logic is an interdisciplinary research field, which has captured worldwide interest. This tutorial review gives a brief introduction into molecular logic and Boolean algebra. This serves as the basis for a discussion of the state-of-the-art and future challenges in the field. Representative examples from the most recent literature including adders/subtractors, multiplexers/demultiplexers, encoders/decoders, and sequential logic devices (keypad locks) are highlighted. Other horizons, such as the utility of molecular logic in bio-related applications, are discussed as well.
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Affiliation(s)
- Joakim Andréasson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
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46
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Jiang W, Han M, Zhang HY, Zhang ZJ, Liu Y. A Double Plug-Socket System Capable of Molecular Keypad Locks through Controllable Photooxidation. Chemistry 2009; 15:9938-45. [DOI: 10.1002/chem.200901206] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Qian J, Xu Y, Qian X, Zhang S. A pair of regio-isomeric compounds acting as molecular logic gates with different functions. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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48
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Melnikov D, Strack G, Pita M, Privman V, Katz E. Analog Noise Reduction in Enzymatic Logic Gates. J Phys Chem B 2009; 113:10472-9. [DOI: 10.1021/jp904585x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dmitriy Melnikov
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Guinevere Strack
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Marcos Pita
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Vladimir Privman
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699
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49
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Wagner N, Ashkenasy G. Systems chemistry: logic gates, arithmetic units, and network motifs in small networks. Chemistry 2009; 15:1765-75. [PMID: 19107891 DOI: 10.1002/chem.200801850] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mixture of molecules can be regarded as a network if all the molecular components participate in some kind of interaction with other molecules--either physical or functional interactions. Template-assisted ligation reactions that direct replication processes can serve as the functional elements that connect two members of a chemical network. In such a process, the template does not necessarily catalyze its own formation, but rather the formation of another molecule, which in turn can operate as a template for reactions within the network medium. It was postulated that even networks made up of small numbers of molecules possess a wealth of molecular information sufficient to perform rather complex behavior. To probe this assumption, we have constructed virtual arrays consisting of three replicating molecules, in which dimer templates are capable of catalyzing reactants to form additional templates. By using realistic parameters from peptides or DNA replication experiments, we simulate the construction of various functional motifs within the networks. Specifically, we have designed and implemented each of the three-element Boolean logic gates, and show how these networks are assembled from four basic "building blocks". We also show how the catalytic pathways can be wired together to perform more complex arithmetic units and network motifs, such as the half adder and half subtractor computational modules, and the coherent feed-forward loop network motifs under different sets of parameters. As in previous studies of chemical networks, some of the systems described display behavior that would be difficult to predict without the numerical simulations. Furthermore, the simulations reveal trends and characteristics that should be useful as "recipes" for future design of experimental functional motifs and for potential integration into modular circuits and molecular computation devices.
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Affiliation(s)
- Nathaniel Wagner
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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50
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Silvi S, Constable EC, Housecroft CE, Beves JE, Dunphy EL, Tomasulo M, Raymo FM, Credi A. All-optical integrated logic operations based on chemical communication between molecular switches. Chemistry 2009; 15:178-85. [PMID: 19021180 DOI: 10.1002/chem.200801645] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Molecular logic gates process physical or chemical "inputs" to generate "outputs" based on a set of logical operators. We report the design and operation of a chemical ensemble in solution that behaves as integrated AND, OR, and XNOR gates with optical input and output signals. The ensemble is composed of a reversible merocyanine-type photoacid and a ruthenium polypyridine complex that functions as a pH-controlled three-state luminescent switch. The light-triggered release of protons from the photoacid is used to control the state of the transition-metal complex. Therefore, the two molecular switching devices communicate with one another through the exchange of ionic signals. By means of such a double (optical-chemical-optical) signal-transduction mechanism, inputs of violet light modulate a luminescence output in the red/far-red region of the visible spectrum. Nondestructive reading is guaranteed because the green light used for excitation in the photoluminescence experiments does not affect the state of the gate. The reset is thermally driven and, thus, does not involve the addition of chemicals and accumulation of byproducts. Owing to its reversibility and stability, this molecular device can afford many cycles of digital operation.
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Affiliation(s)
- Serena Silvi
- Dipartimento di Chimica G. Ciamician, Università di Bologna via Selmi 2, 40126 Bologna, Italy
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