1
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Shu JJ, Tan ZH, Wang QW, Yong KY. Programmable Biomolecule-Mediated Processors. J Am Chem Soc 2023; 145:25033-25042. [PMID: 37864571 PMCID: PMC10682996 DOI: 10.1021/jacs.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.
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Affiliation(s)
- Jian-Jun Shu
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Zi Hian Tan
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Qi-Wen Wang
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Kian-Yan Yong
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
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2
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Georgiev NI, Bakov VV, Bojinov VB. A Tutorial Review on the Fluorescent Probes as a Molecular Logic Circuit-Digital Comparator. Molecules 2023; 28:6327. [PMID: 37687156 PMCID: PMC10489932 DOI: 10.3390/molecules28176327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The rapid progress in the field of fluorescent probes and fluorescent sensing material extended this research area toward more complex molecular logic gates capable of carrying out a variety of sensing functions simultaneously. These molecules are able to calculate a composite result in which the analysis is not performed by a man but by the molecular device itself. Since the first report by de Silva of AND molecular logic gate, all possible logic gates have been achieved at the molecular level, and currently, utilization of more complicated molecular logic circuits is a major task in this field. Comparison between two digits is the simplest logic operation, which could be realized with the simplest logic circuit. That is why the right understanding of the applied principles during the implementation of molecular digital comparators could play a critical role in obtaining logic circuits that are more complicated. Herein, all possible ways for the construction of comparators on the molecular level were discussed, and recent achievements connected with these devices were presented.
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Affiliation(s)
- Nikolai I. Georgiev
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridsky Str., 1756 Sofia, Bulgaria;
| | - Ventsislav V. Bakov
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridsky Str., 1756 Sofia, Bulgaria;
| | - Vladimir B. Bojinov
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridsky Str., 1756 Sofia, Bulgaria;
- Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria
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3
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Georgiev NI, Krasteva PV, Bakov VV, Bojinov VB. A Highly Water-Soluble and Solid State Emissive 1,8-Naphthalimide as a Fluorescent PET Probe for Determination of pHs, Acid/Base Vapors, and Water Content in Organic Solvents. Molecules 2022; 27:molecules27134229. [PMID: 35807479 PMCID: PMC9268048 DOI: 10.3390/molecules27134229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 12/25/2022] Open
Abstract
A new highly water-soluble 1,8-naphthalimide fluorophore designed on the “fluorophore-spacer-receptor1-receptor2” model has been synthesized. Due to the unusually high solubility in water, the novel compound proved to be a selective PET-based probe for the determination of pHs in aqueous solutions and rapid detection of water content in organic solvents. Based on the pH dependence of the probe and its high water solubility, the INH logic gate was achieved using NaOH and water as chemical inputs, where NaOH is the disabler and the water is an enabler. In addition, the probe showed effective fluorescence “off-on” reversibility on glass support after exposure to acid and base vapors, which defines it as a promising platform for rapid detection of acid/base vapors in the solid-state, thus extending the molecular sensing concept from solution to the solid support.
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Affiliation(s)
- Nikolai I. Georgiev
- Correspondence: (N.I.G.); (V.B.B.); Tel.: +35-(92)-8163207 (N.I.G.); +35-(92)-8163206 (V.B.B.)
| | | | | | - Vladimir B. Bojinov
- Correspondence: (N.I.G.); (V.B.B.); Tel.: +35-(92)-8163207 (N.I.G.); +35-(92)-8163206 (V.B.B.)
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4
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Larsen CB. Temperature and solvent-dependent photoluminescence quenching in [Ru(bpy) 2(bpy-cc-AQ)] 2. Phys Chem Chem Phys 2021; 23:3574-3580. [PMID: 33514966 DOI: 10.1039/d0cp05044j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
I have herein investigated the solvent-dependent photoluminescence quenching mechanism of [Ru(bpy)2(bpy-cc-AQ)]2+ using variable temperature emission spectroscopies. The photophysics of this complex are dominated by an excited-state thermal equilibrium between a photoluminescent 3MLCT state and a charge-separated state that lies higher in energy relative to the 3MLCT state in low polarity solvents and approximately isoenergetic in high polarity solvents. Furthermore, an unusual photoluminescence temperature-dependence in high polarity solvents is shown to arise from competition between enthalpic factors favouring the charge-separated state and entropic factors favouring the photoluminescent 3MLCT state, analogous to the molecular light-switch effect of [Ru(bpy)2(dppz)]2+. The solvent-dependent photoluminescence quenching of [Ru(bpy)2(bpy-cc-AQ)]2+ is attributed to two key solvent-dependent factors: (1) the excited-state equilibrium position and (2) the rate of charge-recombination from the charge-separated state.
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Affiliation(s)
- Christopher B Larsen
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
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5
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Singh P. Molecular switches and dual channel detection of Cd 2+ and Fe 3+ ions based on a multipodand system. LUMINESCENCE 2021; 36:802-811. [PMID: 33386700 DOI: 10.1002/bio.4005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/20/2020] [Accepted: 12/29/2020] [Indexed: 11/05/2022]
Abstract
Multipodand conjugates were designed and synthesized and incorporated 5-chloro-8-hydroxyquinoline for efficient performance and fine tuning to behave as molecular switches by the addition of metals ions, protonation, and their combination in CH3 CN and CH3 CN-H2 O. Dipodand 3 and tetrapodand 4 showed a switching 'ON' of fluorescence (λem = 435-445) with Zn2+ and Cd2+ (OR logic) and switching 'OFF' of fluorescence (λem = 402) in the presence of Cu2+ , Co2+ and Ni2+ (NOR logic). 4 showed switching 'OFF' of fluorescence at 402 nm at low concentrations of Ag+ , Pb2+ , Hg2+ and Fe3+ and, on further accumulation of these metal ions, excimer bands at 432 nm (Ag+ ) and 510 nm (Pb2+ , Hg2+ and Fe3+ ) provided the opportunity for 'ON-OFF-ON' switching. In contrast, 3 showed no change with Ag+ , while Pb2+ caused only 'ON-OFF' switching and Hg2+ and Fe3+ ions caused similar 'ON-OFF-ON' switching. The H+ -induced 'ON-OFF-ON' molecular switch was combined with Cu2+ that persuaded NOR logic to mimic inhibit (INH) logic. The compound also exhibited a H+ /Cu2+ -induced 'OFF-ON-OFF' type of signalling pattern. These proton-induced multiple outputs provide opportunities for YES, NOT logic gates. 3 showed selective 'ON-OFF' behaviour with Fe3+ ions and 'OFF-ON' behaviour with Cd2+ ions in 20% HEPES buffer-CH3 CN.
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Affiliation(s)
- Prabhpreet Singh
- Department of Chemistry, UGC Centre for Advanced Studies-II, Guru Nanak Dev University, Amritsar, India
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6
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When Molecular Magnetism Meets Supramolecular Chemistry: Multifunctional and Multiresponsive Dicopper(II) Metallacyclophanes as Proof-of-Concept for Single-Molecule Spintronics and Quantum Computing Technologies? MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Molecular magnetism has made a long journey, from the fundamental studies on through-ligand electron exchange magnetic interactions in dinuclear metal complexes with extended organic bridges to the more recent exploration of their electron spin transport and quantum coherence properties. Such a field has witnessed a renaissance of dinuclear metallacyclic systems as new experimental and theoretical models for single-molecule spintronics and quantum computing, due to the intercrossing between molecular magnetism and metallosupramolecular chemistry. The present review reports a state-of-the-art overview as well as future perspectives on the use of oxamato-based dicopper(II) metallacyclophanes as promising candidates to make multifunctional and multiresponsive, single-molecule magnetic (nano)devices for the physical implementation of quantum information processing (QIP). They incorporate molecular magnetic couplers, transformers, and wires, controlling and facilitating the spin communication, as well as molecular magnetic rectifiers, transistors, and switches, exhibiting a bistable (ON/OFF) spin behavior under external stimuli (chemical, electronic, or photonic). Special focus is placed on the extensive research work done by Professor Francesc Lloret, an outstanding chemist, excellent teacher, best friend, and colleague, in recognition of his invaluable contributions to molecular magnetism on the occasion of his 65th birthday.
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7
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Barnoy EA, Popovtzer R, Fixler D. Fluorescence for biological logic gates. JOURNAL OF BIOPHOTONICS 2020; 13:e202000158. [PMID: 32537894 DOI: 10.1002/jbio.202000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 05/03/2023]
Abstract
Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.
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Affiliation(s)
- Eran A Barnoy
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Rachela Popovtzer
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dror Fixler
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
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8
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Larsen CB, Farrow GA, Smith LD, Appleby MV, Chekulaev D, Weinstein JA, Wenger OS. Solvent-Mediated Activation/Deactivation of Photoinduced Electron-Transfer in a Molecular Dyad. Inorg Chem 2020; 59:10430-10438. [DOI: 10.1021/acs.inorgchem.0c00679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher B. Larsen
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel CH-4056, Switzerland
| | - George A. Farrow
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Liam D. Smith
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Martin V. Appleby
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Dimitri Chekulaev
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Julia A. Weinstein
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Oliver S. Wenger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel CH-4056, Switzerland
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9
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Yu Y, Xu S, Gao Y, Jiang M, Zhang J, Li X, Zhang X, Chen B. Multiple logic operations based on chemically triggered upconversion fluorescence switching. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118047. [PMID: 31954362 DOI: 10.1016/j.saa.2020.118047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/01/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
The development of upconversion nanoparticles based logic systems, especially integrated logic systems is still a challenge until now. In this work, an upconversion nanocomposite system is developed and studied for the sensing abilities toward hydrion, hydroxyl ions, metal ions and anions (S2-, I-) by taking the advantages of turn-on and turn-off upconversion fluorescence switching response. Triggering by different kinds of ions, the upconversion system can act as a fluorescence switch due to the specific recognition abilities of Rhodamine 6G functionalized PEI for specific ions and the energy transfer process from upconversion nanoparticles to recognition molecules. Based on these results, multiple molecular logic gates, including single-input logic operation (YES, NOT), double-inputs logic operation (OR, AND, NOR, INHIBIT) and multiple-input integrative logic operation (INHIBIT+OR) are developed by employing hydrion, hydroxyl ions, metal ions and anions as inputs and the changes in the upconversion fluorescence intensity as output. The multiple logic operations are of great significance for the applications in biomedicine and molecular calculation.
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Affiliation(s)
- Yang Yu
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Sai Xu
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China.
| | - Yuefeng Gao
- College of Marine Engineering, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Muhan Jiang
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Jinsu Zhang
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Xiangping Li
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Xizhen Zhang
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China
| | - Baojiu Chen
- School of Science, Dalian Maritime University, Dalian 116026, People's Republic of China.
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10
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Yao CY, Uchiyama S, de Silva AP. A Personal Journey across Fluorescent Sensing and Logic Associated with Polymers of Various Kinds. Polymers (Basel) 2019; 11:E1351. [PMID: 31416199 PMCID: PMC6723954 DOI: 10.3390/polym11081351] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/05/2023] Open
Abstract
Our experiences concerning fluorescent molecular sensing and logic devices and their intersections with polymer science are the foci of this brief review. Proton-, metal ion- and polarity-responsive cases of these devices are placed in polymeric micro- or nano-environments, some of which involve phase separation. This leads to mapping of chemical species on the nanoscale. These devices also take advantage of thermal properties of some polymers in water in order to reincarnate themselves as thermometers. When the phase separation leads to particles, the latter can be labelled with identification tags based on molecular logic. Such particles also give rise to reusable sensors, although molecular-scale resolution is sacrificed in the process. Polymeric nano-environments also help to organize rather complex molecular logic systems from their simple components. Overall, our little experiences suggest that researchers in sensing and logic would benefit if they assimilate polymer concepts.
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Affiliation(s)
- Chao-Yi Yao
- School of Chemistry and Chemical Engineering, Queen's University, BT9 5AG Belfast, Northern Ireland.
| | - Seiichi Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan.
| | - A Prasanna de Silva
- School of Chemistry and Chemical Engineering, Queen's University, BT9 5AG Belfast, Northern Ireland.
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11
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Fan D, Wang J, Wang E, Dong S. A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library. Chem Sci 2019; 10:7290-7298. [PMID: 31588299 PMCID: PMC6686727 DOI: 10.1039/c9sc01865d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 06/12/2019] [Indexed: 12/27/2022] Open
Abstract
Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Chinese Academy of Sciences , Beijing , 100039 , China
| | - Juan Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , China . ;
- University of Science and Technology of China , Hefei , Anhui 230026 , China
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12
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Varadaraju C, Paulraj MS, Tamilselvan G, Muthu Vijayan Enoch IV, Srinivasadesikan V, Shyi-Long L. Evaluation of metal ion sensing behaviour of fluorescent probe along with its precursors: PET-CHEF mechanism, molecular logic gate behaviour and DFT studies. J INCL PHENOM MACRO 2019. [DOI: 10.1007/s10847-019-00919-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Suo Z, Chen J, Hou X, Hu Z, Xing F, Feng L. Growing prospects of DNA nanomaterials in novel biomedical applications. RSC Adv 2019; 9:16479-16491. [PMID: 35516377 PMCID: PMC9064466 DOI: 10.1039/c9ra01261c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.
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Affiliation(s)
- Zhiguang Suo
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Jingqi Chen
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Xialing Hou
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Ziheng Hu
- Materials Genome Institute, Shanghai University Shanghai 200444 China
| | - Feifei Xing
- Department of Chemistry, College of Science, Shanghai University Shanghai 200444 China
| | - Lingyan Feng
- Materials Genome Institute, Shanghai University Shanghai 200444 China
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14
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Zhang C, Ge L, Zhang X, Wei W, Zhao J, Zhang Z, Wang Z, You X. A Uniform Molecular Low-Density Parity Check Decoder. ACS Synth Biol 2019; 8:82-90. [PMID: 30513194 DOI: 10.1021/acssynbio.8b00304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Error correction codes, such as low-density parity check (LDPC) codes, are required to be larger scale to meet the increasing demands for reliable and massive data transmission. However, the construction of such a large-scale decoder will result in high complexity and hinder its silicon implementation. Thanks to the advantages of natural computing in high parallelism and low power, we propose a method to synthesize a uniform molecular LDPC decoder by implementing the belief-propagation algorithm with chemical reaction networks (CRNs). This method enables us to flexibly design the LDPC decoder with arbitrary code length, code rate, and node degrees. Compared with existing methods, our proposal reduces the number of reactions to update the variable nodes by 42.86% and the check nodes by 47.37%. Numerical results are presented to show the feasibility and validity of our proposal.
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15
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Bhat MP, Kigga M, Govindappa H, Patil P, Jung HY, Yu J, Kurkuri M. A reversible fluoride chemosensor for the development of multi-input molecular logic gates. NEW J CHEM 2019. [DOI: 10.1039/c9nj03399h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A reversible chemosensor for the development of a multi-input molecular logic gate was shown.
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Affiliation(s)
- Mahesh P. Bhat
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru-562112
- India
| | - Madhuprasad Kigga
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru-562112
- India
| | - Harshith Govindappa
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru-562112
- India
| | - Pravin Patil
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru-562112
- India
| | - Ho-Young Jung
- Department of Environment and Energy Engineering
- Chonnam National University
- Gwangju 61186
- Republic of Korea
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale Biophotonics (CNBP)
- Institute of Photonics and Advanced Sensing (IPAS)
- School of Physical Sciences
- University of Adelaide
- Adelaide
| | - Mahaveer Kurkuri
- Centre for Nano and Material Sciences
- Jain University
- Jain Global Campus
- Bengaluru-562112
- India
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16
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Kawano R. Nanopore Decoding of Oligonucleotides in DNA Computing. Biotechnol J 2018; 13:e1800091. [PMID: 30076732 DOI: 10.1002/biot.201800091] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/24/2018] [Indexed: 12/17/2022]
Abstract
In conventional DNA-computation methods involving logic gate operations, the output molecules are detected and decoded mainly by gel electrophoresis or fluorescence measurements. To employ rapid and label-free decoding, nanopore technology, an emerging methodology for single-molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations. This review describes recent approaches to decoding DNA computation using label-free and electrical nanopore measurements. Several attempts have been successful in DNA decoding with the nanopore either through enzymatic reactions or in water-in-oil droplets. Additionally, DNA computing combined with nanopore decoding has clinical applications, including microRNA detection for early diagnosis of cancers. Because this decoding methodology is still in development and not yet widely accepted, this review aims to inform the scientific community regarding usefulness.
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Affiliation(s)
- Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Harumicho, Fuchu, Tokyo 183-8538, Japan
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17
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Alreja P, Kaur N. Probing anion and cation with novel salicylidene Schiff base receptor appended with 1, 10-phenanthroline: Mimicking INHIBIT molecular logic gate. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Howlader P, Mondal B, Purba PC, Zangrando E, Mukherjee PS. Self-Assembled Pd(II) Barrels as Containers for Transient Merocyanine Form and Reverse Thermochromism of Spiropyran. J Am Chem Soc 2018; 140:7952-7960. [DOI: 10.1021/jacs.8b03946] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Prodip Howlader
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bijnaneswar Mondal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Prioti Choudhury Purba
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ennio Zangrando
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste 34127, Italy
| | - Partha Sarathi Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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19
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Singh P, Singh H, Sharma R, Dhawan S, Singh P, Bhargava G, Kumar S. Fluorometric differential detection of Zn2+ and Cu2+ by picolylamine appended pyrimidinone-based receptor: Application in mimicking TRANSFER and INH logic gate. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Hamdi I, Buntinx G, Perrier A, Devos O, Jaïdane N, Delbaere S, Tiwari AK, Dubois J, Takeshita M, Wada Y, Aloïse S. New insights into the photoswitching mechanisms of normal dithienylethenes. Phys Chem Chem Phys 2018; 18:28091-28100. [PMID: 27711399 DOI: 10.1039/c6cp03471c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The photoswitching and competitive processes of the referent photochromic diarylethene derivative 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (DTE) and a novel bridged analog DTE-m5 have been investigated by state-of-the-art TD-DFT calculations and ultrafast spectroscopy supported by advanced chemometric data treatments. Focusing on DTE, the overall deactivation pathway of both antiparallel (AP) and parallel (P) conformers of the open form (OF) (1 : 1 in solution) has been resolved and rationalized starting from the Franck-Condon (FC) region to the ground state recovery. For the photo-excited P conformer, after ultrafast relaxation (∼200 fs) towards the S1 relaxed state, an expected ISC occurred (55 ps) to produce a triplet state, 3P, the latter relaxing within 2.5 μs. Concerning the AP conformer, the photocyclization reaction is reported to proceed immediately (100 fs) starting from the FC region while the relaxed singlet state is populated in parallel. For the first time, we discovered that the latter state evolves through an unexpected ISC process (1 ps) giving rise to a second triplet state,3AP. For DTE-m5, by slightly constraining the molecule with the bridge, this triplet becomes reactive and participates in the formation of 10% of closed form (CF) probably through an adiabatic mechanism. Concerning the photoreversion, in accordance with the literature, we report on a two-step process, a 190 fs vibrational relaxation followed by a 6 ps ring-opening reaction. For the overall species at the singlet or triplet manifold, the use of advanced MCR-ALS allows us to obtain specific spectral signatures. This study is therefore a new step within the comprehension of DTE photochemistry.
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Affiliation(s)
- I Hamdi
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, 1060 Tunis, Tunisia
| | - G Buntinx
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
| | - A Perrier
- Université Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas Mann, 75205 Paris Cedex 13, France and Chimie Paris Tech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France
| | - O Devos
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
| | - N Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, 1060 Tunis, Tunisia
| | - S Delbaere
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
| | - A K Tiwari
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
| | - J Dubois
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
| | - M Takeshita
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo 1, Saga 840-8502, Japan
| | - Y Wada
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo 1, Saga 840-8502, Japan
| | - S Aloïse
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France.
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21
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Gupta AS, Kumar G, Paul K, Luxami V. BINOL-based differential chromo-fluorescent sensor and its application in miniaturized 1-2/4-2 bit encoders and decoders. NEW J CHEM 2018. [DOI: 10.1039/c7nj03653a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A BINOL (1,1′-bi-2-naphthol)-based probe 1 with a diamide group has been synthesized and investigated for its photophysical behavior towards various cations and anions.
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Affiliation(s)
- Akul Sen Gupta
- School of Chemistry and Biochemistry, Thapar University
- Patiala-147004
- India
| | - Gulshan Kumar
- School of Chemistry and Biochemistry, Thapar University
- Patiala-147004
- India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry, Thapar University
- Patiala-147004
- India
| | - Vijay Luxami
- School of Chemistry and Biochemistry, Thapar University
- Patiala-147004
- India
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22
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McKinney BOF, Daly B, Yao C, Schroeder M, de Silva AP. Consolidating Molecular Logic with New Solid-Bound YES and PASS 1 Gates and Their Combinations. Chemphyschem 2017; 18:1760-1766. [DOI: 10.1002/cphc.201700120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Indexed: 01/05/2023]
Affiliation(s)
| | - Brian Daly
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Chaoyi Yao
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - Marc Schroeder
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
| | - A. Prasanna de Silva
- School of Chemistry and Chemical Engineering; Queen's University; Belfast BT9 5AG UK
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23
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Baroncini M, Semeraro M, Credi A. Unconventional Nonlinear Input-Output Response in a Luminescent Molecular Switch by Inner Filtering Effects. Chemphyschem 2017; 18:1755-1759. [DOI: 10.1002/cphc.201700046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Massimo Baroncini
- Dipartimento di Scienze e Tecnologie Agro-alimentari; Alma Mater Studiorum; Università di Bologna; Viale Fanin 50 40127 Bologna Italy
| | - Monica Semeraro
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Alberto Credi
- Dipartimento di Scienze e Tecnologie Agro-alimentari; Alma Mater Studiorum; Università di Bologna; Viale Fanin 50 40127 Bologna Italy
- Istituto ISOF-CNR; Via Gobetti 101 40129 Bologna Italy
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24
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Cheng N, Zhu P, Xu Y, Huang K, Luo Y, Yang Z, Xu W. High-sensitivity assay for Hg (II) and Ag (I) ion detection: A new class of droplet digital PCR logic gates for an intelligent DNA calculator. Biosens Bioelectron 2016; 84:1-6. [DOI: 10.1016/j.bios.2016.04.084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 12/21/2022]
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25
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Kaur P, Singh R, Kaur V, Talwar D. A chromogenic “off–on” azomethine sensor possessing ONNNO receptor site for iron species and its application in the fabrication of INHIBIT type molecular logic gate. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. Chem Commun (Camb) 2016; 52:179-82. [DOI: 10.1039/c5cc08242k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Liya Ji
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
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27
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Castellano M, Ruiz-García R, Cano J, Ferrando-Soria J, Pardo E, Fortea-Pérez FR, Stiriba SE, Barros WP, Stumpf HO, Cañadillas-Delgado L, Pasán J, Ruiz-Pérez C, de Munno G, Armentano D, Journaux Y, Lloret F, Julve M. Metallosupramolecular approach toward multifunctional magnetic devices for molecular spintronics. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.05.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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28
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Zhang Y, Liu W, Zhang W, Yu S, Yue X, Zhu W, Zhang D, Wang Y, Wang J. DNA-mediated gold nanoparticle signal transducers for combinatorial logic operations and heavy metal ions sensing. Biosens Bioelectron 2015; 72:218-24. [DOI: 10.1016/j.bios.2015.05.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 04/29/2015] [Accepted: 05/07/2015] [Indexed: 01/25/2023]
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29
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Shi W, Fu Y, Li Z, Wei M. Multiple and configurable optical logic systems based on layered double hydroxides and chromophore assemblies. Chem Commun (Camb) 2015; 51:711-3. [PMID: 25418921 DOI: 10.1039/c4cc08069f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple and configurable fluorescence logic gates were fabricated via self-assembly of layered double hydroxides and various chromophores. These logic gates were operated by observation of different emissions with the same excitation wavelength, which achieve YES, NOT, AND, INH and INHIBIT logic operations, respectively.
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Affiliation(s)
- Wenying Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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30
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Ling J, Daly B, Silverson VAD, de Silva AP. Taking baby steps in molecular logic-based computation. Chem Commun (Camb) 2015; 51:8403-9. [DOI: 10.1039/c4cc10000j] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Constructs of fluorophores, receptors, spacers, 1O2 sensitizers, enzymes and oligonucleotides play their part in advancing the field of molecular logic-based computation.
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Affiliation(s)
- Jue Ling
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast BT9 5AG
- UK
| | - Brian Daly
- School of Chemistry and Chemical Engineering
- Queen's University
- Belfast BT9 5AG
- UK
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31
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Totsingan F, Marchelli R, Corradini R. Molecular computing by PNA:PNA duplex formation. ARTIFICIAL DNA, PNA & XNA 2014; 2:16-22. [PMID: 21686248 DOI: 10.4161/adna.2.1.15459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/09/2011] [Accepted: 03/14/2011] [Indexed: 11/19/2022]
Abstract
Molecular computing is potentially one of the most powerful tools for the development of massive parallel computing protocols. In the present paper, a first example of the use of PNA:PNA interactions in molecular computing is described. A series of short PNA sequences have been designed with a four base stretch coding for variables and solutions. Hybridization of the components in different combinations was tested both in solution and in a microarray format. A series of PNA representing the solutions were spotted on a microarray surface in order to simulate the hardware. A series of PNA representing the variables, labeled with TAMRA, were used to interrogate the device enabling to solve non-deterministic logic operations. The system was shown to be able to solve a two-variable equation with a high signal to noise ratio. This paper intends to provide a proof of principle that PNA, on account of their stability and specificity of binding, are most suitable for constructing organic-type computers.
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32
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Chen L, Zhu Y, Yang D, Zou R, Wu J, Tian H. Synthesis and antibacterial activities of antibacterial peptides with a spiropyran fluorescence probe. Sci Rep 2014; 4:6860. [PMID: 25358905 PMCID: PMC4215325 DOI: 10.1038/srep06860] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/13/2014] [Indexed: 11/21/2022] Open
Abstract
In this report, antibacterial peptides 1-3 were prepared with a spiropyran fluorescence probe. The probe exhibits a change in fluorescence when isomerized from a colorless spiro-form (spiropyran, Sp) to a colored open-form (merocyanine, Mc) under different chemical environments, which can be used to study the mechanism of antimicrobial activity. Peptides 1-3 exhibit a marked decrease in antimicrobial activity with increasing alkyl chain length. This is likely due to the Sp-Mc isomers in different polar environments forming different aggregate sizes in TBS, as demonstrated by time-dependent dynamic light scattering (DLS). Moreover, peptides 1-3 exhibited low cytotoxicity and hemolytic activity. These probe-modified peptides may provide a novel approach to study the effect of structural changes on antibacterial activity, thus facilitating the design of new antimicrobial agents to combat bacterial infection.
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Affiliation(s)
- Lei Chen
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
| | - Yu Zhu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
| | - Danling Yang
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
| | - Rongfeng Zou
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
| | - He Tian
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237 (P. R. China)
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33
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Avellini T, Baroncini M, Ragazzon G, Silvi S, Venturi M, Credi A. Photochemically Controlled Molecular Machines with Sequential Logic Operation. Isr J Chem 2014. [DOI: 10.1002/ijch.201400039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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34
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Credi A, Silvi S, Venturi M. Light-Operated Machines Based on Threaded Molecular Structures. MOLECULAR MACHINES AND MOTORS 2014; 354:1-34. [DOI: 10.1007/128_2013_509] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Cao J, Ma X, Min M, Cao T, Wu S, Tian H. INHIBIT logic operations based on light-driven β-cyclodextrin pseudo[1]rotaxane with room temperature phosphorescence addresses. Chem Commun (Camb) 2014; 50:3224-6. [DOI: 10.1039/c3cc49820d] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INHIBIT logic gates based on light-driven β-cyclodextrin pseudo[1]rotaxane were fabricated conveniently utilizing reversible ICD and RTP as output addresses respectively.
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Affiliation(s)
- Jingjing Cao
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Xiang Ma
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Mingri Min
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Tiantian Cao
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Shuaifan Wu
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - He Tian
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
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36
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Chen L, Wu J, Schmuck C, Tian H. A switchable peptide sensor for real-time lysosomal tracking. Chem Commun (Camb) 2014; 50:6443-6. [DOI: 10.1039/c4cc00670d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A bis-spiropyran functionalized peptide1, which exhibits good cell-permeability, biocompatibility and low cytotoxicity, has been developed for lysosomal tracking.
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Affiliation(s)
- Lei Chen
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Junchen Wu
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
| | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- 45117 Essen, Germany
| | - He Tian
- Key Labs for Advanced Materials and Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai 200237, China
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37
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Erbas-Cakmak S, Akkaya EU. Cascading of Molecular Logic Gates for Advanced Functions: A Self-Reporting, Activatable Photosensitizer. Angew Chem Int Ed Engl 2013; 52:11364-8. [DOI: 10.1002/anie.201306177] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 11/10/2022]
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38
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Erbas-Cakmak S, Akkaya EU. Cascading of Molecular Logic Gates for Advanced Functions: A Self-Reporting, Activatable Photosensitizer. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306177] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Demchenko AP. Nanoparticles and nanocomposites for fluorescence sensing and imaging. Methods Appl Fluoresc 2013; 1:022001. [DOI: 10.1088/2050-6120/1/2/022001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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40
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Frey J, Kodis G, Straight SD, Moore TA, Moore AL, Gust D. Photonic Modulation of Electron Transfer with Switchable Phase Inversion. J Phys Chem A 2013; 117:607-15. [DOI: 10.1021/jp3106887] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julien Frey
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Gerdenis Kodis
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Stephen D. Straight
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Thomas A. Moore
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Ana L. Moore
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
| | - Devens Gust
- Department of Chemistry
and Biochemistry, Arizona State University, Tempe, Arizona 85287, United
States
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41
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Erbas-Cakmak S, Bozdemir OA, Cakmak Y, Akkaya EU. Proof of principle for a molecular 1 : 2 demultiplexer to function as an autonomously switching theranostic device. Chem Sci 2013. [DOI: 10.1039/c2sc21499g] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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42
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Kumar M, Reja SI, Bhalla V. A Charge Transfer Amplified Fluorescent Hg2+ Complex for Detection of Picric Acid and Construction of Logic Functions. Org Lett 2012. [DOI: 10.1021/ol3029753] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manoj Kumar
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies-1, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Shahi Imam Reja
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies-1, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Vandana Bhalla
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies-1, Guru Nanak Dev University, Amritsar-143005, Punjab, India
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43
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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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44
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Pischel U, Andréasson J, Gust D, Pais VF. Information Processing with Molecules-Quo Vadis? Chemphyschem 2012; 14:28-46. [DOI: 10.1002/cphc.201200157] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/16/2012] [Indexed: 11/11/2022]
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45
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Chaplin JC, Russell NA, Krasnogor N. Implementing conventional logic unconventionally: photochromic molecular populations as registers and logic gates. Biosystems 2012; 109:35-51. [PMID: 22240019 DOI: 10.1016/j.biosystems.2011.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/24/2011] [Accepted: 12/27/2011] [Indexed: 11/28/2022]
Abstract
In this paper we detail experimental methods to implement registers, logic gates and logic circuits using populations of photochromic molecules exposed to sequences of light pulses. Photochromic molecules are molecules with two or more stable states that can be switched reversibly between states by illuminating with appropriate wavelengths of radiation. Registers are implemented by using the concentration of molecules in each state in a given sample to represent an integer value. The register's value can then be read using the intensity of a fluorescence signal from the sample. Logic gates have been implemented using a register with inputs in the form of light pulses to implement 1-input/1-output and 2-input/1-output logic gates. A proof of concept logic circuit is also demonstrated; coupled with the software workflow describe the transition from a circuit design to the corresponding sequence of light pulses.
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Affiliation(s)
- J C Chaplin
- Interdisciplinary Computing and Complex Systems Research Group, School of Computer Science, University of Nottingham, Jubilee Campus, UK.
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Deniz E, Battal M, Cusido J, Sortino S, Raymo FM. Insights into the isomerization of photochromic oxazines from the excitation dynamics of BODIPY–oxazine dyads. Phys Chem Chem Phys 2012; 14:10300-7. [DOI: 10.1039/c2cp41089c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Luxami V, Kumar S. ESIPT based dual fluorescent sensor and concentration dependent reconfigurable boolean operators. RSC Adv 2012. [DOI: 10.1039/c2ra21170j] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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Credi A, Semeraro M, Silvi S, Venturi M. Redox control of molecular motion in switchable artificial nanoscale devices. Antioxid Redox Signal 2011; 14:1119-65. [PMID: 20568952 DOI: 10.1089/ars.2010.3223] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The design, synthesis, and operation of molecular-scale systems that exhibit controllable motions of their component parts is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The development of this kind of species constitutes the premise to the construction of molecular machines and motors, which in a not-too-distant future could find applications in fields such as materials science, information technology, energy conversion, diagnostics, and medicine. In the past 25 years the development of supramolecular chemistry has enabled the construction of an interesting variety of artificial molecular machines. These devices operate via electronic and molecular rearrangements and, like the macroscopic counterparts, they need energy to work as well as signals to communicate with the operator. Here we outline the design principles at the basis of redox switching of molecular motion in artificial nanodevices. Redox processes, chemically, electrically, or photochemically induced, can indeed supply the energy to bring about molecular motions. Moreover, in the case of electrically and photochemically induced processes, electrochemical and photochemical techniques can be used to read the state of the system, and thus to control and monitor the operation of the device. Some selected examples are also reported to describe the most representative achievements in this research area.
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Affiliation(s)
- Alberto Credi
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Bologna, Italy.
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50
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Deniz E, Impellizzeri S, Sortino S, Raymo FM. A photoswitchable bichromophoric oxazine with fast switching speeds and excellent fatigue resistance. CAN J CHEM 2011. [DOI: 10.1139/v10-070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In search of strategies to regulate the photochemical and photophysical properties of photochromic oxazines, we designed a multichromophoric compound incorporating 3H-indole, benzooxazine, and 2-(4-dimethylaminophenyl)ethynyl fragments. We synthesized this molecule in two steps in an overall yield of 51%, starting from commercial precursors. The ultraviolet irradiation of this photochrome opens a [1,3]oxazine ring in less than 6 ns to generate a zwitterionic isomer with a quantum yield of 0.10. In particular, the photoinduced ring opening generates a 4-nitrophenolate anion and a 3H-indolium cation. Additionally, this process brings the 2-(4-dimethylaminophenyl)ethynyl appendage into conjugation with the 3H-indolium cation. As a result, two distinct bands for the anionic and cationic fragments of the photogenerated zwitterion appear in the visible region of the absorption spectrum. The photogenerated isomer has a lifetime of 2 µs and switches back to the original form with first-order kinetics. Furthermore, this bichromophoric photochrome tolerates hundreds of switching cycles with no sign of degradation and can be operated within rigid polymer matrices. Thus, this particular structural design can lead to the development of a new family of bichromophoric photochromes and photoresponsive materials with microsecond switching times and excellent fatigue resistances.
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Affiliation(s)
- Erhan Deniz
- University of Miami Department of Chemistry, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
- Dipartimento di Scienze Chimiche, Università di Catania, viale Andrea Doria 8, Catania, I-95125, Italy
| | - Stefania Impellizzeri
- University of Miami Department of Chemistry, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
- Dipartimento di Scienze Chimiche, Università di Catania, viale Andrea Doria 8, Catania, I-95125, Italy
| | - Salvatore Sortino
- University of Miami Department of Chemistry, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
- Dipartimento di Scienze Chimiche, Università di Catania, viale Andrea Doria 8, Catania, I-95125, Italy
| | - Françisco M. Raymo
- University of Miami Department of Chemistry, 1301 Memorial Drive, Coral Gables, FL 33146-0431, USA
- Dipartimento di Scienze Chimiche, Università di Catania, viale Andrea Doria 8, Catania, I-95125, Italy
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