1
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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2
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Sivagnanam S, Mahato P, Das P. An overview on the development of different optical sensing platforms for adenosine triphosphate (ATP) recognition. Org Biomol Chem 2023; 21:3942-3983. [PMID: 37128980 DOI: 10.1039/d3ob00209h] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Adenosine triphosphate (ATP), one of the biological anions, plays a crucial role in several biological processes including energy transduction, cellular respiration, enzyme catalysis and signaling. ATP is a bioactive phosphate molecule, recognized as an important extracellular signaling agent. Apart from serving as a universal energy currency for various cellular events, ATP is also considered a factor responsible for numerous physiological activities. It regulates cellular metabolism by breaking phosphoanhydride bonds. Several diseases have been reported widely based on the levels and behavior of ATP. The variation of ATP concentration usually causes a foreseeable impact on mitochondrial physiological function. Mitochondrial dysfunction is responsible for the occurrence of many severe diseases such as angiocardiopathy, malignant tumors and Parkinson's disease. Therefore, there is high demand for developing a sensitive, fast-responsive, nontoxic and versatile detection platform for the detection of ATP. To this end, considerable efforts have been employed by several research groups throughout the world to develop specific and sensitive detection platforms to recognize ATP. Although a repertoire of optical chemosensors (both colorimetric and fluorescent) for ATP has been developed, many of them are not arrayed appropriately. Therefore, in this present review, we focused on the design and sensing strategy of some chemosensors including metal-free, metal-based, sequential sensors, aptamer-based sensors, nanoparticle-based sensors etc. for ATP recognition via diverse binding mechanisms.
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Affiliation(s)
- Subramaniyam Sivagnanam
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu-603203, India.
| | - Prasenjit Mahato
- Department of Chemistry, Raghunathpur College, Sidho-Kanho-Birsha University, Purulia, West Bengal-723133, India
| | - Priyadip Das
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu-603203, India.
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3
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Viviano-Posadas AO, Romero-Mendoza U, Bazany-Rodríguez IJ, Velázquez-Castillo RV, Martínez-Otero D, Bautista-Renedo JM, González-Rivas N, Galindo-Murillo R, Salomón-Flores MK, Dorazco-González A. Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA. RSC Adv 2022; 12:27826-27838. [PMID: 36320280 PMCID: PMC9520314 DOI: 10.1039/d2ra05040d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 11/04/2023] Open
Abstract
The new dicationic pyridine-2,6-dicarboxamide-based compound 1 bearing two N-alkylquinolinium units was synthesized, structurally determined by single-crystal X-ray diffraction, and studied in-depth as a fluorescent receptor for nucleotides and inorganic phosphorylated anions in pure water. The addition of nucleotides to 1 at pH = 7.0 quenches its blue emission with a selective affinity towards adenosine 5'-triphosphate (ATP) and guanosine 5'-tripohosphate (GTP) over other nucleotides such CTP, UTP, ADP, AMP, dicarboxylates and inorganic anions. On the basis of the spectroscopic tools (1H, 31P NMR, UV-vis, fluorescence), MS measurements and DFT calculations, receptor 1 binds ATP with high affinity (log K = 5.04) through the simultaneous formation of strong hydrogen bonds and π-π interactions between the adenosine fragment and quinolinium ring with binding energy calculated in 8.7 kcal mol-1. High affinity for ATP/GTP is attributed to the high acidity of amides and preorganized rigid structure of 1. Receptor 1 is an order of magnitude more selective for ATP than GTP. An efficient photoinduced electron transfer quenching mechanism with simultaneous receptor-ATP complexation in both the excited and ground states is proposed. Additionally, multiple spectroscopic studies and molecular dynamics simulations showed that 1 can intercalate into DNA base pairs.
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Affiliation(s)
- Alejandro O Viviano-Posadas
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Ulises Romero-Mendoza
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Iván J Bazany-Rodríguez
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Rocío V Velázquez-Castillo
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Diego Martínez-Otero
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Joanatan M Bautista-Renedo
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Nelly González-Rivas
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah 2000 East 30 South Skaggs 306 Salt Lake City 84112 Utah USA
| | - María K Salomón-Flores
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Alejandro Dorazco-González
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
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4
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Rim Lee Y, Kwon N, Swamy KMK, Kim G, Yoon J. Rhodamine-thiourea Linked Naphthalimide Derivative to Image ATP in Mitochondria using Two Channels. Chem Asian J 2022; 17:e202200413. [PMID: 35671139 DOI: 10.1002/asia.202200413] [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: 04/19/2022] [Revised: 06/02/2022] [Indexed: 11/08/2022]
Abstract
Adenosine 5'-triphosphate (ATP), synthesized in mitochondria, is an energy molecule in all living things. ATP not only serves as an energy source for protein synthesis and muscle contraction, but also as an important indicator for various diseases, such as Parkinson's disease, cardiovascular disease, and others. Accordingly, detection and sensing of ATP, especially in mitochondria, are important. In this study, a unique ring-opening process of rhodamine was coupled to recognition of ATP via introduction of a thiourea moiety, which was further linked to a naphthalimide group. A strong fluorescent emission at ∼580 nm was accompanied by a color change from colorless to pink upon addition of ATP at pH 7.4. Fluorescent probe 1 successfully imaged mitochondrial ATP with a Pearson's coefficient of 0.8. In addition, green emission from the naphthalimide moiety at ∼530 nm was observed without any change upon addition of ATP. This emission can be considered equivalent to an internal standard to utilize probe 1 as a dual-channel probe for ATP. Furthermore, probe 1 showed negligible cytotoxicity based on MTT assays.
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Affiliation(s)
- You Rim Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Korea)
| | - Nahyun Kwon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Korea)
| | - K M K Swamy
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Korea)
| | - Gyoungmi Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Korea)
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 120-750, Korea)
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5
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Xie H, Finnegan TJ, Liyana Gunawardana VW, Xie W, Moore CE, Badjić JD. A double-decker cage for allosteric encapsulation of ATP. Chem Commun (Camb) 2022; 58:5992-5995. [PMID: 35485326 DOI: 10.1039/d2cc00927g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we describe the preparation of double-decker cage [1-H6]6+ comprising two binding pockets, each with three ammonium and three amide hydrogen bonding sites. This novel host possesses a high affinity for trapping two molecules of ATP in an allosteric fashion, with both experiments and theory suggesting the synergistic action of charged hydrogen bonds and π-π stacking in the encapsulation.
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Affiliation(s)
- Han Xie
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, USA.
| | - Tyler J Finnegan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, USA.
| | | | - William Xie
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, USA.
| | - Curtis E Moore
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, USA.
| | - Jovica D Badjić
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, USA.
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6
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Huang B, Liang B, Zhang R, Xing D. Molecule fluorescent probes for adenosine triphosphate imaging in cancer cells and in vivo. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214302] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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7
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Maity D, Hamilton AD. The helical supramolecular assembly of oligopyridylamide foldamers in aqueous media can be guided by adenosine diphosphates. Chem Commun (Camb) 2021; 57:9192-9195. [PMID: 34519293 DOI: 10.1039/d1cc02704b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A metal-free and achiral tri-pyridylamide foldamer, DM 11, containing a critical naphthalimide side chain self-assembles in a left-handed helical manner in the presence of chiral adenosine phosphates, under physiological conditions. Surprisingly, a very high degree of helicity in the foldamer assemblies was observed with ADP compared to other nucleoside phosphates, including ATP.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University, New York, NY 10003, USA.
| | - Andrew D Hamilton
- Department of Chemistry, New York University, New York, NY 10003, USA.
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8
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Erben A, Sviben I, Mihaljević B, Piantanida I, Basarić N. Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment. Molecules 2021; 26:molecules26144315. [PMID: 34299591 PMCID: PMC8306964 DOI: 10.3390/molecules26144315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.
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Affiliation(s)
- Antonija Erben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Igor Sviben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Branka Mihaljević
- Department of Material Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
- Correspondence:
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9
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Singh VR, Pandey SP, Singh PK. A polyelectrolyte based supramolecular assembly for ratiometric sensing of ATP with very high discrimination from pyrophosphate. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115314] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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11
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Mei M, Mu L, Liang S, Wang Y, She G, Shi W. A general configurational strategy to quencher-free aptasensors. Biosens Bioelectron 2021; 178:113025. [PMID: 33529860 DOI: 10.1016/j.bios.2021.113025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022]
Abstract
The aptasensor, developed from the aptamer, has aroused wide concern in recent years owing to its high sensitivity and specificity. However, the quenching unit involved in the most of the aptasensors is indispensable to the fabrication of an aptasensor, which would undoubtedly increase the complexity of the device. In this study, a facile strategy was developed for construction of the quencher-free aptasensors, in which the quenching units can be omitted, and only an aptamer strand and a fluorophore are necessary. Distinguishable from the configuration of the traditional ones, the aptasensors developed in this work rationally employed the intrinsic quenching abilities of the analytes to directly regulate the fluorescence of the fluorophore. Furthermore, the aptamer strand as a discriminatory unit efficiently captured the corresponding analytes to around the fluorophores. As a result, the fluorescence of the aptasensor can be significantly sensitive to the analytes. The generality of the current design is evidenced by the successful fabrication of seven quencher-free aptasensors for Cu2+, Ag+, Hg2+, ATP and dopamine through 6-FAM labeling aptamers of Cu2+, Ag+, Hg2+, ATP, dopamine, 5-TAMRA and ROX labeling aptamers of Cu2+. Present strategy endows an aptasensor with a simple structure, high selectivity and fine sensitivity. The configuration of the quencher-free aptasensors fabricated in this work can be readily utilized for more aptasensors.
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Affiliation(s)
- Mingliang Mei
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixuan Mu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Sen Liang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangwei She
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wensheng Shi
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Maity D. Selected peptide-based fluorescent probes for biological applications. Beilstein J Org Chem 2020; 16:2971-2982. [PMID: 33335605 PMCID: PMC7722625 DOI: 10.3762/bjoc.16.247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023] Open
Abstract
To understand the molecular interactions, present in living organisms and their environments, chemists are trying to create novel chemical tools. In this regard, peptide-based fluorescence techniques have attracted immense interest. Synthetic peptide-based fluorescent probes are advantageous over protein-based sensors, since they are synthetically accessible, more stable, and can be easily modified in a site-specific manner for selective biological applications. Peptide receptors labeled with environmentally sensitive/FRET fluorophores have allowed direct detection/monitoring of biomolecules in aqueous media and in live cells. In this review, key peptide-based approaches for different biological applications are presented.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University, New York, NY 10003, USA
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13
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Biswas R, Ghosh S, Bhaumik SK, Banerjee S. Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through "turn-on" fluorescence response. Beilstein J Org Chem 2020; 16:2728-2738. [PMID: 33224299 PMCID: PMC7670119 DOI: 10.3762/bjoc.16.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/23/2020] [Indexed: 11/23/2022] Open
Abstract
Bisimidazolium receptors, tagged with chromophoric pyrene at one end and linked to an n-alkyl chain at the other, underwent self-assembly in aqueous media depending on the length of the alkyl segment. The amphiphilic derivatives having n-decyl or longer chains, formed nano-assemblies with cyanic-green emission resulting from the stacked pyrene chromophores in the aggregates. The presence of positive surface charges on the multivalent aggregates led to ATP binding which was accompanied by a significant increase in the excimeric emission intensity. This provided a convenient way of monitoring ATP binding in a "turn-on" mode and an efficient detection of ATP was achieved in aqueous buffer and also in buffer containing 150 mM NaCl at physiological pH value. Furthermore, the multivalent aggregates demonstrated a significant selectivity in ATP detection over ADP, AMP and pyrophosphate.
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Affiliation(s)
- Rakesh Biswas
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, India
| | - Surya Ghosh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, India
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, India
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, Nadia, India
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14
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Butler SJ, Jolliffe KA. Anion Receptors for the Discrimination of ATP and ADP in Biological Media. Chempluschem 2020; 86:59-70. [DOI: 10.1002/cplu.202000567] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/29/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Stephen J. Butler
- Department of Chemistry Loughborough University Loughborough LE11 3TU United Kingdom
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15
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Biswas R, Naskar S, Ghosh S, Das M, Banerjee S. A Remarkable Fluorescence Quenching Based Amplification in ATP Detection through Signal Transduction in Self-Assembled Multivalent Aggregates. Chemistry 2020; 26:13595-13600. [PMID: 32776606 DOI: 10.1002/chem.202002648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/22/2020] [Indexed: 01/20/2023]
Abstract
Signal transduction is essential for the survival of living organisms, because it allows them to respond to the changes in external environments. In artificial systems, signal transduction has been exploited for the highly sensitive detection of analytes. Herein, a remarkable signal transduction, upon ATP binding, in the multivalent fibrillar nanoaggregates of anthracene conjugated imidazolium receptors is reported. The aggregates of one particular amphiphilic receptor sensed ATP in high pm concentrations with one ATP molecule essentially quenching the emission of thousands of receptors. A cooperative merging of the multivalent binding and signal transduction led to this superquenching and translated to an outstanding enhancement of more than a millionfold in the sensitivity of ATP detection by the nanoaggregates; in comparison to the "molecular" imidazolium receptors. Furthermore, an exceptional selectivity to ATP over other nucleotides was demonstrated.
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Affiliation(s)
- Rakesh Biswas
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Sumit Naskar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Surya Ghosh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Mousumi Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
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16
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Maity D, Kumar S, AlHussein R, Gremer L, Howarth M, Karpauskaite L, Hoyer W, Magzoub M, Hamilton AD. Sub-stoichiometric inhibition of IAPP aggregation: a peptidomimetic approach to anti-amyloid agents. RSC Chem Biol 2020; 1:225-232. [PMID: 34458762 PMCID: PMC8341728 DOI: 10.1039/d0cb00086h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Membrane-catalysed misfolding of islet amyloid polypeptide is associated with the death of β-cells in type II diabetes (T2D). Most active compounds so far reported require high doses for inhibition of membrane bound IAPP fibrillation. Here, we describe a naphthalimide-appended oligopyridylamide-based α-helical mimetic, DM 1, for targeting membrane bound IAPP. DM 1 completely inhibits the aggregation of IAPP at doses of 0.2 equivalents. DM 1 is also effective at similarly low doses for inhibition of seed-catalyzed secondary nucleation. An NMR based study demonstrates that DM 1 modulates IAPP self-assembly by stabilizing and/or perturbing the N-terminus helix conformation. DM 1 at substoichiometric doses rescues rat insulinoma cells from IAPP-mediated cytotoxicity. Most importantly, 0.2 equivalents of DM 1 disaggregate preformed oligomers and fibrils and can reverse cytotoxicity by modulating toxic preformed oligomers and fibrils of IAPP into non-toxic conformations.
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Affiliation(s)
- Debabrata Maity
- Department of Chemistry, New York University New York New York 10003 USA
| | - Sunil Kumar
- Department of Chemistry, New York University New York New York 10003 USA
| | - Ruyof AlHussein
- Department of Chemistry, New York University New York New York 10003 USA
| | - Lothar Gremer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany.,Institute of Complex Systems, Structural Biochemistry (ICS-6) Forschungszentrum Jülich 52425 Jülich Germany
| | - Madeline Howarth
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Laura Karpauskaite
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany.,Institute of Complex Systems, Structural Biochemistry (ICS-6) Forschungszentrum Jülich 52425 Jülich Germany
| | - Mazin Magzoub
- Biology Program, New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Andrew D Hamilton
- Department of Chemistry, New York University New York New York 10003 USA
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17
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Singh VR, Malegaonkar JN, Bhosale SV, Singh PK. An ATP responsive fluorescent supramolecular assembly based on a polyelectrolyte and an AIE active tetraphenylethylene derivative. Org Biomol Chem 2020; 18:8414-8423. [DOI: 10.1039/d0ob01661f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A supramolecular assembly is constructed using an anionic AIE active probe and a cationic polyelectrolyte to sense ATP fluorimetrically in solution.
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Affiliation(s)
- Vidya R. Singh
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
| | - Jotiram N. Malegaonkar
- Polymers and Functional Materials Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad – 500 007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Sidhanath V. Bhosale
- Polymers and Functional Materials Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad – 500 007
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Prabhat K. Singh
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
- Homi Bhabha National Institute
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18
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Huang LX, Guo Q, Chen Y, Verwilst P, Son S, Wu JB, Cao QY, Kim JS. Nanomolar detection of adenosine triphosphate (ATP) using a nanostructured fluorescent chemosensing ensemble. Chem Commun (Camb) 2019; 55:14135-14138. [PMID: 31687696 DOI: 10.1039/c9cc08054f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a novel nanostructured chemosensing ensemble PyNp-C13/UD, obtained by self-assembling uranine dye (UD) and an amphiphilic pyridinium salt PyNp-C13. The ensemble was developed for the fluorescence turn-on sensing of ATP in aqueous solutions and inside living cells. The assembly operates via an indicator displacement assay (IDA) method with an ultra-low detection limit of 6.8 nM.
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Affiliation(s)
- Ling-Xi Huang
- Department of Chemistry, Nanchang University, Nanchang 330031, P. R. China.
| | - Qing Guo
- Department of Chemistry, Nanchang University, Nanchang 330031, P. R. China.
| | - Yong Chen
- Institute for Advanced Study, Nanchang University, Nanchang 330031, China
| | - Peter Verwilst
- Department of Chemistry, Korea University, Seoul 02841, Korea.
| | - Subin Son
- Department of Chemistry, Korea University, Seoul 02841, Korea.
| | - Jia-Bin Wu
- Department of Chemistry, Nanchang University, Nanchang 330031, P. R. China.
| | - Qian-Yong Cao
- Department of Chemistry, Nanchang University, Nanchang 330031, P. R. China.
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea.
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19
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Li W, Gong X, Fan X, Yin S, Su D, Zhang X, Yuan L. Recent advances in molecular fluorescent probes for organic phosphate biomolecules recognition. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.07.056] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Maity D, Assaf KI, Sicking W, Hirschhäuser C, Nau WM, Schmuck C. A Selective Cucurbit[8]uril-Peptide Beacon Ensemble for the Ratiometric Fluorescence Detection of Peptides. Chemistry 2019; 25:13088-13093. [PMID: 31441544 PMCID: PMC6856807 DOI: 10.1002/chem.201901037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/14/2019] [Indexed: 11/11/2022]
Abstract
A convenient supramolecular strategy for constructing a ratiometric fluorescent chemosensing ensemble, consisting of a macrocyclic host (cucurbit[8]uril CB[8]), and a pyrene‐tagged amphiphilic peptide beacon (AP 1), is reported. AP 1 unfolds upon encapsulation of the pyrene termini into the hydrophobic CB[8] cavity. This changes pyrene excimer to monomer emission. Substrates with higher affinity for the CB[8] cavity can displace AP 1 from the ensemble. The released AP 1 folds again to form a pyrene excimer, which allows for the ratiometric fluorescence monitoring of the substrate. In this report, the ensemble capacity for ratiometric fluorescence monitoring of biological substrates, such as amino acid derivatives, specific peptides, and proteins, in aqueous media is demonstrated.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatsstrasse 7, 45117, Essen, Germany
| | - Khaleel I Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Wilhelm Sicking
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatsstrasse 7, 45117, Essen, Germany
| | - Christoph Hirschhäuser
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatsstrasse 7, 45117, Essen, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatsstrasse 7, 45117, Essen, Germany
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21
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Kumari R, Sunil D, Ningthoujam RS. Naphthalimides in fluorescent imaging of tumor hypoxia - An up-to-date review. Bioorg Chem 2019; 88:102979. [PMID: 31100616 DOI: 10.1016/j.bioorg.2019.102979] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/14/2019] [Accepted: 05/07/2019] [Indexed: 01/17/2023]
Abstract
Hypoxia is a distinctive characteristic of advanced solid malignancies that results from a disparity between oxygen supply and its consumption. The degree of hypoxia is believed to have adverse prognostic significance. Therefore detecting cellular hypoxia can potentially offer insights into the grade of tumour as well as its evolution towards a progressive malignant phenotype, which clinically translates to greater metastatic potential and treatment resistance. Fluorescence imaging to visualize hypoxia in biological systems is a minimally-invasive method. Recently there are several reports on interdisciplinary research that aims at developing functional probes that can be efficiently used for non-invasive imaging of hypoxic tumours. Upregulated levels of nitroreductase (NTR) is detected in hypoxic solid malignancies, and this characteristic feature is increasingly utilized in the development of NTR-targeted fluorescent molecules to selectively sense hypoxia in vivo. The present review summarizes various reports published on the design concepts of nitro naphthalimide-based bio-reductive fluorescent sensors that can be applied noninvasively to image hypoxia in cancer.
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Affiliation(s)
- Rashmi Kumari
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576 104, Karnataka, India
| | - Dhanya Sunil
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576 104, Karnataka, India.
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22
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Sapotta M, Hofmann A, Bialas D, Würthner F. A Water-Soluble Perylene Bisimide Cyclophane as a Molecular Probe for the Recognition of Aromatic Alkaloids. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Meike Sapotta
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Anja Hofmann
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - David Bialas
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC); Universität Würzburg; Theodor-Boveri-Weg 97074 Würzburg Germany
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23
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Sapotta M, Hofmann A, Bialas D, Würthner F. A Water-Soluble Perylene Bisimide Cyclophane as a Molecular Probe for the Recognition of Aromatic Alkaloids. Angew Chem Int Ed Engl 2019; 58:3516-3520. [DOI: 10.1002/anie.201813559] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Meike Sapotta
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Anja Hofmann
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - David Bialas
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC); Universität Würzburg; Theodor-Boveri-Weg 97074 Würzburg Germany
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24
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Zhang J, Zhang J, Yan Z, Xie J. Recent Progress in Fluorescent Probes for Adenosine Triphosphate Based on Small Organic Molecules. CHINESE J ORG CHEM 2019. [DOI: 10.6023/cjoc201905024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Maity D, Gigante A, Sánchez-Murcia PA, Sijbesma E, Li M, Bier D, Mosel S, Knauer S, Ottmann C, Schmuck C. Arginine mimetic appended peptide-based probes for fluorescence turn-on detection of 14-3-3 proteins. Org Biomol Chem 2019; 17:4359-4363. [DOI: 10.1039/c9ob00620f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of fluorescence markers for the 14-3-3 adapter protein class.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - Alba Gigante
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - Pedro A. Sánchez-Murcia
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- Währinger Str. 17 A-1090 Vienna
- Austria
| | - Eline Sijbesma
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - Mao Li
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - David Bier
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - Stefanie Mosel
- Institute for Biology
- University of Duisburg Essen
- 45141, Essen
- Germany
| | - Shirley Knauer
- Institute for Biology
- University of Duisburg Essen
- 45141, Essen
- Germany
| | - Christian Ottmann
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
| | - Carsten Schmuck
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
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26
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Agafontsev AM, Ravi A, Shumilova TA, Oshchepkov AS, Kataev EA. Molecular Receptors for Recognition and Sensing of Nucleotides. Chemistry 2018; 25:2684-2694. [PMID: 30289184 DOI: 10.1002/chem.201802978] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/05/2018] [Indexed: 12/15/2022]
Abstract
Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.
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Affiliation(s)
- Aleksandr M Agafontsev
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany.,N. N. Vorozhtsov Institute of Organic Chemistry SB RAS, 9 Lavrentiev Avenue, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova St. 1, 630090, Novosibirsk, Russia
| | - Anil Ravi
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Tatiana A Shumilova
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Aleksandr S Oshchepkov
- Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklay St. 6, Moscow, 117198, Russia
| | - Evgeny A Kataev
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
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27
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Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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28
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Kopra K, Seppälä T, Rabara D, Abreu-Blanco M, Kulmala S, Holderfield M, Härmä H. Label-Free Time-Gated Luminescent Detection Method for the Nucleotides with Varying Phosphate Content. SENSORS 2018; 18:s18113989. [PMID: 30453509 PMCID: PMC6264117 DOI: 10.3390/s18113989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 01/26/2023]
Abstract
A new label-free molecular probe for luminescent nucleotide detection in neutral aqueous solution is presented. Phosphate-containing molecules, such as nucleotides possess vital role in cell metabolism, energy economy, and various signaling processes. Thus, the monitoring of nucleotide concentration and nucleotide related enzymatic reactions is of high importance. Two component lanthanide complex formed from Tb(III) ion carrier and light harvesting antenna, readily distinguishes nucleotides containing different number of phosphates and enable direct detection of enzymatic reactions converting nucleotide triphosphate (NTP) to nucleotide di/monophosphate or the opposite. Developed sensor enables the detection of enzymatic activity with a low nanomolar sensitivity, as highlighted with K-Ras and apyrase enzymes in their hydrolysis assays performed in a high throughput screening compatible 384-well plate format.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
| | - Tanja Seppälä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
| | - Dana Rabara
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Maria Abreu-Blanco
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Sakari Kulmala
- Laboratory of Analytical Chemistry, Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Matthew Holderfield
- NCI-RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21702, USA.
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
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29
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Tomar K, Kaur G, Verma S, Ramanathan G. A self-assembled tetrapeptide that acts as a “turn-on” fluorescent sensor for Hg2+ ion. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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30
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Liu JH, Li RS, Yuan B, Wang J, Li YF, Huang CZ. Mitochondria-targeting single-layered graphene quantum dots with dual recognition sites for ATP imaging in living cells. NANOSCALE 2018; 10:17402-17408. [PMID: 30203818 DOI: 10.1039/c8nr06061d] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
As a molecular unit of intracellular energy transfer, adenosine triphosphate (ATP) is significant for maintaining the energy balance in living cells and thus monitoring cellular ATP is important to assess cellular physiological functions. However, effective monitoring of cellular ATP still faces challenges owing to the similarity of ATP to other nucleoside polyphosphates. Herein, yellow emissive single-layered graphene quantum dots (s-GQDs) with dual recognition sites including π-conjugated single sheets and positively charged sites were developed. The s-GQDs exhibit a good mitochondria targeting ability and respond only to purine nucleotides and show good selectivity in discriminating tri-, di- and monophosphate nucleotides. The good selectivity should be attributed to the concurrent effect of π-π stacking and electrostatic interactions between filmy layered positive s-GQDs and negative purine nucleotides. Owing to the mitochondria targeting ability and dual recognition sites of the s-GQDs, the mitochondrial ATP fluctuation resulting from the activation and suppression of ATP in living cells has been successfully monitored.
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Affiliation(s)
- Jia Hui Liu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
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31
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Mailhot R, Traviss‐Pollard T, Pal R, Butler SJ. Cationic Europium Complexes for Visualizing Fluctuations in Mitochondrial ATP Levels in Living Cells. Chemistry 2018; 24:10745-10755. [PMID: 29761917 PMCID: PMC6175470 DOI: 10.1002/chem.201801008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/10/2018] [Indexed: 01/02/2023]
Abstract
The ability to study cellular metabolism and enzymatic processes involving adenosine triphosphate (ATP) is impeded by the lack of imaging probes capable of signalling the concentration and distribution of intracellular ATP rapidly, with high sensitivity. We report here the first example of a luminescent lanthanide complex capable of visualizing changes in the concentration of ATP in the mitochondria of living cells. Four cationic europium(III) complexes [Eu.1-4]+ have been synthesized and their binding capabilities towards nucleoside polyphosphate anions examined in aqueous solution at physiological pH. Complexes [Eu.1]+ and [Eu.3]+ bearing hydrogen bond donor groups in the pendant arms showed excellent discrimination between ATP, ADP and monophosphate species. Complex [Eu.3]+ showed relatively strong binding to ATP (logKa =5.8), providing a rapid, long-lived luminescent signal that enabled its detection in a highly competitive aqueous medium containing biologically relevant concentrations of Mg2+ , ADP, GTP, UTP and human serum albumin. This EuIII complex responds linearly to ATP within the physiological concentration range (1-5 mm), and was used to continuously monitor the apyrase-catalyzed hydrolysis of ATP to ADP in vitro. We demonstrate that [Eu.3]+ can permeate mammalian (NIH-3T3) cells efficiently and localize to the mitochondria selectively, permitting real-time visualization of elevated mitochondrial ATP levels following treatment with a broad spectrum kinase inhibitor, staurosporine, as well as depleted ATP levels upon treatment with potassium cyanide under glucose starvation conditions.
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Affiliation(s)
- Romain Mailhot
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | | | - Robert Pal
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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32
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Fang Y, Shi W, Hu Y, Li X, Ma H. A dual-function fluorescent probe for monitoring the degrees of hypoxia in living cells via the imaging of nitroreductase and adenosine triphosphate. Chem Commun (Camb) 2018; 54:5454-5457. [PMID: 29749411 DOI: 10.1039/c8cc02209g] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new dual-function fluorescent probe is developed for detecting nitroreductase (NTR) and adenosine triphosphate (ATP) with different responses. Imaging application of the probe reveals that intracellular NTR and ATP display an adverse changing trend during a hypoxic process and ATP can serve as a new sign for cell hypoxia.
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Affiliation(s)
- Yu Fang
- Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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33
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New detection method for nucleoside triphosphates based on carbon dots: The distance-dependent singlet oxygen trapping. Anal Chim Acta 2018; 1031:145-151. [PMID: 30119732 DOI: 10.1016/j.aca.2018.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/23/2022]
Abstract
The distance-dependent based sensing mechanism, such as fluorescence resonance energy transfer (FRET) and surface plasmon resonance (SPR) absorption of gold nanoparticles, has been used widely in visual detection. In this work, we report another distance-dependent detection method for nucleoside triphosphates (NTPs) based on carbon dots (CDs) (1O2 donor) and 9, 10-diphenylanthracene-2-boronic acid (DABA, 1O2 acceptor). The CDs can generate singlet oxygen (1O2) which allows diffusion within 200 nm. Thus, the distance between CDs and DABA decreased through binding of NTPs (<200 nm), leading to absorption changes of DABA under light irradiation due to 1O2 trapping. This sensing system (CDs@DABA) has high selectivity for the detection of NTPs due to the double molecular recognition and a linear response in the 0-80 μM concentration range was accomplished with the detection limit as low as 4.35 μM.
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34
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Bojtár M, Janzsó-Berend PZ, Mester D, Hessz D, Kállay M, Kubinyi M, Bitter I. An uracil-linked hydroxyflavone probe for the recognition of ATP. Beilstein J Org Chem 2018; 14:747-755. [PMID: 29719572 PMCID: PMC5905274 DOI: 10.3762/bjoc.14.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/13/2018] [Indexed: 01/05/2023] Open
Abstract
Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4'-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy. Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum.
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Affiliation(s)
- Márton Bojtár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary
| | - Péter Zoltán Janzsó-Berend
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary
| | - Dávid Mester
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, 1521 Budapest, Hungary
| | - Dóra Hessz
- Institute of Materials and Environmental Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, 1521 Budapest, Hungary
| | - Miklós Kubinyi
- Institute of Materials and Environmental Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, P. O. Box 286, 1519 Budapest, Hungary
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, 1521 Budapest, Hungary
| | - István Bitter
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, 1521 Budapest, Hungary
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35
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Hewitt SH, Parris J, Mailhot R, Butler SJ. A continuous luminescence assay for monitoring kinase activity: signalling the ADP/ATP ratio using a discrete europium complex. Chem Commun (Camb) 2018; 53:12626-12629. [PMID: 29131206 DOI: 10.1039/c7cc05887j] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We report the application of a stable cationic europium complex [Eu.1]+ in a continuous-read luminescence assay for kinase activity. [Eu.1]+ binds reversibly to ATP and ADP in water, at neutral pH, in the presence of Mg2+ ions, providing distinctive luminescence responses that permits the kinase-catalysed conversion of ATP to ADP to be monitored in real-time.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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36
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Trévisan M, Fossépré M, Paolantoni D, Rubio-Magnieto J, Dumy P, Ulrich S, Surin M. Self-assembly and chiroptical properties in supramolecular complexes of adenosine phosphates and guanidinium-bispyrene. Chirality 2018; 30:719-729. [PMID: 29578614 DOI: 10.1002/chir.22852] [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: 11/22/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 11/10/2022]
Abstract
Supramolecular systems that respond to the hydrolysis of adenosine phosphates (APs) are attractive for biosensing and to fabricate bioinspired self-assembled materials. Here, we report on the formation of supramolecular complexes between an achiral guanidinium derivative bearing two pyrene moieties, with each of the three adenosine phosphates: AMP, ADP, and ATP. By combining results from circular dichroism spectroscopy and molecular modeling simulations, we explore the induced chirality, the dynamics of the complexes, and the interactions at play, which altogether provide insights into the supramolecular self-assembly between APs and the guanidinium-bispyrene. Finally, we identify the chiroptical signals of interest in mixtures of the guanidinium derivative with the three APs in different proportions. This study constitutes a basis to evolve toward a chiroptical detection of the hydrolysis of APs based on organic supramolecular probes.
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Affiliation(s)
- Marie Trévisan
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jenifer Rubio-Magnieto
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM, UMR 5247), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Mons, Belgium
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37
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Zhao Q, Zhang Z, Tang Y. A new conjugated polymer-based combination probe for ATP detection using a multisite-binding and FRET strategy. Chem Commun (Camb) 2018; 53:9414-9417. [PMID: 28787042 DOI: 10.1039/c7cc04293k] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new conjugated polymer-based ratiometric combination probe was constructed for adenosine triphosphate detection by taking advantage of a multisite-binding and fluorescence resonance energy transfer strategy. The method is rapid and highly selective, which can clearly discriminate ATP from persistent interferents such as ADP, AMP, other nucleoside polyphosphates and nucleobases.
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Affiliation(s)
- Qi Zhao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, P. R. China.
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38
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Faggi E, Luis SV, Alfonso I. Sensing, Transport and Other Potential Biomedical Applications of Pseudopeptides. Curr Med Chem 2018; 26:4065-4097. [PMID: 29493442 DOI: 10.2174/0929867325666180301091040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/17/2018] [Accepted: 01/20/2018] [Indexed: 11/22/2022]
Abstract
Pseudopeptides are privileged synthetic molecules built from the designed combination of peptide-like and abiotic artificial moieties. Consequently, they are benefited from the advantages of both families of chemical structures: modular synthesis, chemical and functional diversity, tailored three-dimensional structure, usually high stability in biological media and low non-specific toxicity. Accordingly, in the last years, these compounds have been used for different biomedical applications, ranging from bio-sensing, ion transport, the molecular recognition of biologically relevant species, drug delivery or gene transfection. This review highlights a selection of the most remarkable and recent advances in this field.
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Affiliation(s)
- Enrico Faggi
- Department of Biological Chemistry and Molecular Modelling, Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Cientificas, Barcelona, Spain
| | - Santiago V Luis
- Department of Inorganic and Organic Chemistry, Universitat Jaume I, Castellon, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling, Institute of Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Cientificas, Barcelona, Spain
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39
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Madhu C, Roy B, Makam P, Govindaraju T. Bicomponent β-sheet assembly of dipeptide fluorophores of opposite polarity and sensitive detection of nitro-explosives. Chem Commun (Camb) 2018; 54:2280-2283. [DOI: 10.1039/c8cc00158h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fluorescent hydrogels formed by the bicomponent β-sheet co-assembly of dipeptide–pyrene amphiphiles of opposite polarity provide a 3D microenvironment to detect toxic nitro-explosives.
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Affiliation(s)
- Chilakapati Madhu
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Bappaditya Roy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Pandeeswar Makam
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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40
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Maity D, Matković M, Li S, Ehlers M, Wu J, Piantanida I, Schmuck C. Peptide-Based Probes with an Artificial Anion-Binding Motif for Direct Fluorescence "Switch-On" Detection of Nucleic Acid in Cells. Chemistry 2017; 23:17356-17362. [PMID: 28967979 DOI: 10.1002/chem.201703813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 01/08/2023]
Abstract
This work reports two new peptide-based fluorescence probes (1 and 2) for the detection of ds-DNA at physiological pH. Probes 1 and 2 contain a fluorophore, either amino-naphthalimide or diethyl-aminocoumarin, respectively, and two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) anion-binding motif. These probes show "switch-on" fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance, they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, whereas the fluorescence of 2 is sensitive to the secondary structure of the polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies suggest that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, whereas 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | | | - Shang Li
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Martin Ehlers
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
| | - Junchen Wu
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
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42
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Tomar K, Soni S, Bhadauriya P, Parihar R, Ganesh S, Nair NN, Ramanathan G. Mercuric Ion Sensing by an Overlapping β-turn Containing Peptide. ChemistrySelect 2017. [DOI: 10.1002/slct.201701058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kalpana Tomar
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Satyendra Soni
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Pratibha Bhadauriya
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Rashmi Parihar
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Subramaniam Ganesh
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Nisanth N. Nair
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Gurunath Ramanathan
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
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Abstract
Synthetic pyrrole-based anion receptors date back to the 1990s. They have been extensively developed in the context of macrocyclic systems as expanded porphyrins and calixpyrroles, and related systems. The chemistry of open-chain pyrrolic systems is, in many respects, no less venerable. It also has more direct analogy to naturally occurring pyrrole-based anion binding motifs. However, it has not been the subject of a comprehensive review. Presented herein is a summary of efforts devoted to the creation of de novo pyrrole-based receptors, as well as the anion recognition chemistry of naturally occurring pyrrolic systems as prodigiosins and their synthetic analogues.
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