1
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Zeng Y, Mao Y, Chen Y, Wang Y, Xu S. DNA methylation induces subtle mechanical alteration but significant chiral selectivity. Chem Commun (Camb) 2023; 59:14855-14858. [PMID: 38015496 PMCID: PMC10794036 DOI: 10.1039/d3cc05211g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
DNA methylation is a major epigenetic modification that is closely related to human health. Many experimental techniques as well as theoretical methods have been used to detect the modified nucleotides and identify their effects on molecular binding. It remains challenging to resolve the effect of few methylations of nucleic acids. Using super-resolution force spectroscopy, we firstly revealed that single cytosine methylation increases the mechanical stability of the DNA duplex by 1.9 ± 0.3 pN. Methylation also induces significant chiral selectivity towards drug molecules such as d,l-tetrahydropalmatine. Our results precisely quantify the mechanical effect of methylation and suggest that drug design should take methylation into consideration for enhanced selectivity.
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Affiliation(s)
- Yi Zeng
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yujia Mao
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yanjun Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, TX 77204, USA.
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
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2
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Hong T, Zhou W, Tan S, Cai Z. A cooperation tale of biomolecules and nanomaterials in nanoscale chiral sensing and separation. NANOSCALE HORIZONS 2023; 8:1485-1508. [PMID: 37656443 DOI: 10.1039/d3nh00133d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The cooperative relationship between biomolecules and nanomaterials makes up a beautiful tale about nanoscale chiral sensing and separation. Biomolecules are considered a fabulous chirality 'donor' to develop chiral sensors and separation systems. Nature has endowed biomolecules with mysterious chirality. Various nanomaterials with specific physicochemical attributes can realize the transmission and amplification of this chirality. We focus on highlighting the advantages of combining biomolecules and nanomaterials in nanoscale chirality. To enhance the sensors' detection sensitivity, novel cooperation approaches between nanomaterials and biomolecules have attracted tremendous attention. Moreover, innovative biomolecule-based nanocomposites possess great importance in developing chiral separation systems with improved assay performance. This review describes the formation of a network based on nanomaterials and biomolecules mainly including DNA, proteins, peptides, amino acids, and polysaccharides. We hope this tale will record the perpetual relation between biomolecules and nanomaterials in nanoscale chirality.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
- Academician Workstation, Changsha Medical University, Changsha 410219, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
- Jiangsu Dawning Pharmaceutical Co., Ltd, Changzhou, Jiangsu 213100, China
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
- Jiangsu Dawning Pharmaceutical Co., Ltd, Changzhou, Jiangsu 213100, China
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3
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Debia NP, Muller JM, Gonçalves PFB, Rodembusch FS, Lüdtke DS. Effective enantioselective recognition by steady-state fluorescence spectroscopy: Towards a paradigm shift to optical sensors with unusual chemical architecture. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122526. [PMID: 36868019 DOI: 10.1016/j.saa.2023.122526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
A series of amino acid-derived 1,2,3-triazoles presenting the amino acid residue and the benzazole fluorophore connected by a triazole-4-carboxylate spacer was studied for enantioselective recognition using only steady-state fluorescence spectroscopy in solution. In this investigation, the optical sensing was performed with D-(-) and L-(+)-Arabinose and (R)-(-) and (S)-(+)-Mandelic acid as chiral analytes. The optical sensors showed specific interactions with each pair of enantiomers, allowing photophysical responses, which were used for their enantioselective recognition. DFT calculations confirm the specific interaction between the fluorophores and the analytes corroborating the observed high enantioselectivity of these compounds with the studied enantiomers. Finally, this study investigated nontrivial sensors for chiral molecules by a mechanism different than turn-on fluorescence and has the potential to broad chiral compounds with fluorophoric units as optical sensors for enantioselective sensing.
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Affiliation(s)
- Natalí P Debia
- Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Jenifer M Muller
- Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Paulo F B Gonçalves
- Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Fabiano S Rodembusch
- Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil.
| | - Diogo S Lüdtke
- Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil.
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4
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Daneshvar Tarigh G. Enantioseparation/Recognition based on nano techniques/materials. J Sep Sci 2023:e2201065. [PMID: 37043692 DOI: 10.1002/jssc.202201065] [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: 12/31/2022] [Revised: 03/15/2023] [Accepted: 03/18/2023] [Indexed: 04/14/2023]
Abstract
Enantiomers show different behaviors in interaction with the chiral environment. Due to their identical chemical structure and their wide application in various industries, such as agriculture, medicine, pesticide, food, and so forth, their separation is of great importance. Today, the term "nano" is frequently encountered in all fields. Technology and measuring devices are moving towards miniaturization, and the usage of nanomaterials in all sectors is expanding substantially. Given that scientists have recently attempted to apply miniaturized techniques known as nano-liquid chromatography/capillary-liquid chromatography, which were originally accomplished in 1988, as well as the widespread usage of nanomaterials for chiral resolution (back in 1989), this comprehensive study was developed. Searching the terms "nano" and "enantiomer separation" on scientific websites such as Scopus, Google Scholar, and Web of Science yields articles that either use miniaturized instruments or apply nanomaterials as chiral selectors with a variety of chemical and electrochemical detection techniques, which are discussed in this article.
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Affiliation(s)
- Ghazale Daneshvar Tarigh
- Department of Analytical Chemistry, University College of Science, University of Tehran, Tehran, Iran
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5
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Huang C, Tian HQ, Li RF, Xiong Y, Jiang T, Chen DM, Zhu BX. Coordination-Driven Self-Assembly of Complexes Constructed from Two Helical Ligands: Synthesis, Structures, and Selective Gas Adsorption Properties. Inorg Chem 2022; 61:19512-19523. [DOI: 10.1021/acs.inorgchem.2c03448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Chao Huang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Hua-Qing Tian
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Rong-Feng Li
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Ying Xiong
- School of Chemistry and Materials, Guizhou Normal University, Guiyang 550025, China
| | - Tao Jiang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Dong-Mei Chen
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Bi-Xue Zhu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
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6
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Wang DM, Jia J, Huang RF, Zhang X. A base-repair based electrochemiluminescent genotoxicity sensor that detects abasic sites in double-stranded DNA films. Chem Commun (Camb) 2021; 56:12558-12561. [PMID: 32940265 DOI: 10.1039/d0cc05186a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A novel genotoxicity sensor was developed based on the base repair process associated with the electrochemiluminescence (ECL) detection of abasic sites in a double-stranded DNA monolayer. This is the first time that an ECL sensor with the ability to identify the removed nucleobases in a DNA duplex has been studied. The successful detection of abasic sites created by DNA glycosylase indicates its further applications for examining some other specific types of DNA damage.
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Affiliation(s)
- Dong-Mei Wang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Jia Jia
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Rong-Fu Huang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China.
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7
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Wei YF, Wang Y, Wei XR, Sun R, Xu YJ, Ge JF. Adenine-based small molecule fluorescent probe for imaging mitochondrial nucleic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117865. [PMID: 31813730 DOI: 10.1016/j.saa.2019.117865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
A small molecule fluorescent probe (probe 1) based on adenine-coumarin derivative was designed and synthesized in this paper. Probe 1 exhibited a significant fluorescence-enhancing response to nucleic acids at 495 nm (for DNA) and 487 nm (for RNA). The fluorescence enhancement of probe 1 for DNA and RNA was 5.68 and 9.73 times respectively, the fluorescence quantum yield was changed from 2.5% to 11.7% and 22.5% accordingly. Meanwhile, an excellent linear relationship of fluorescence intensity at 495 nm or 487 nm versus the nucleic acid concentration (1 μM for probe 1, 0-350 μg/mL for DNA and 0-300 μg/mL for RNA) was obtained. Co-staining and nucleic acid digestion experiments showed that probe 1 could selectively image nucleic acids in mitochondria and nucleoli in HeLa cells.
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Affiliation(s)
- Yu-Fang Wei
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Yue Wang
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Xue-Rui Wei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
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8
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Kong RM, Ma L, Han X, Ma C, Qu F, Xia L. Hg 2+-mediated stabilization of G-triplex based molecular beacon for label-free fluorescence detection of Hg 2+, reduced glutathione, and glutathione reductase activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117855. [PMID: 31784222 DOI: 10.1016/j.saa.2019.117855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
G-triplexes have been reported recently with the similar function to G-quadruplex that can combine with thioflavin T (ThT) and emit strong fluorescence but easier to be controlled and excited. In this work, we report an Hg2+-mediated stabilization of G-triplex based functional molecular beacon (G3TMB) sensing system for the label-free detection of Hg2+, reduced glutathione (GSH), and glutathione reductase (GR) activity. In the presence of Hg2+, the extended G-triplex sequence containing the "T" bases can form a stable hairpin structure due to the strong interactions of "T-Hg2+-T", resulting in the locking of G-tracts in the stem of the G3TMB effectively. However, the hairpin structure of the G3TMB can be opened by the introduction of GSH through the stronger "GSH-Hg2+" interaction. Therefore, by employing the fact that GR can catalyze the reduction of oxidized glutathione (GSSG) into GSH, this concept can be applied to fluorescence "off-on" detection of GR activity, with a linear range of 0.02-30 mU/mL and detection limit of 0.01 mU/mL. This work may expand a new perspective of G-triplex based functional molecular beacon as the label-free fluorescent probes in the detection of small biomolecule and enzyme activity.
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Affiliation(s)
- Rong-Mei Kong
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China.
| | - Lin Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Xue Han
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Chunran Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Lian Xia
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
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9
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Oukacine F, Ravelet C, Peyrin E. Enantiomeric sensing and separation by nucleic acids. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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11
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Feng B, Wang K, Yang Y, Wang G, Zhang H, Liu Y, Jiang K. Ultrasensitive recognition of AP sites in DNA at the single-cell level: one molecular rotor sequentially self-regulated to form multiple different stable conformations. Chem Sci 2019; 10:10373-10380. [PMID: 32110326 PMCID: PMC6988597 DOI: 10.1039/c9sc04140k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 01/22/2023] Open
Abstract
The AP site is a primary form of DNA damage. Its presence alters the genetic structure and eventually causes malignant diseases. AP sites generally present a high-speed dynamic change in the DNA sequence. Thus, precisely recognizing AP sites is difficult, especially at the single-cell level. To address this issue, we provide a broad-spectrum strategy to design a group of molecular rotors, that is, a series of nonfluorescent 2-(4-vinylbenzylidene)malononitrile derivatives (BMN-Fluors), which constantly display molecular rotation in a free state. Interestingly, after activating the relevant specific-recognition reaction (i.e., hydrolysis reaction of benzylidenemalononitrile) only in the AP-site cavity within a short time (approximately 300 s), each of these molecules can be fixed into this cavity and can sequentially self-regulate to form different stable conformations in accordance with the cavity size. The different stable conformations possess various HOMO-LUMO energy gaps in their excited state. This condition enables the AP site to emit different fluorescence signals at various wavelengths. Given the different self-regulation abilities of the conformations, the series of molecules, BMN-Fluors, can emit different types of signals, including an "OFF-ON" single-channel signal, a "ratio" double-channel signal, and even a precise multichannel signal. Among the BMN-Fluors derivatives, d1-BMN can sequentially self-regulate to form five stable conformations, thereby resulting in the emission of a five-channel signal for different AP sites in situ. Thus, d1-BMN can be used as a probe to ultrasensitively recognize the AP site with precise fluorescent signals at the single-cell level. This design strategy can be generalized to develop additional single-channel to multichannel signal probes to recognize other specific sites in DNA sequences in living organisms.
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Affiliation(s)
- Beidou Feng
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kui Wang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yonggang Yang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Ge Wang
- Xinxiang Medical University , Xinxiang 453000 , P. R. China
| | - Hua Zhang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yufang Liu
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kai Jiang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
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12
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Feng B, Wang K, Liu J, Mao G, Cui J, Xuan X, Jiang K, Zhang H. Ultrasensitive Apurinic/Apyrimidinic Site-Specific Ratio Fluorescent Rotor for Real-Time Highly Selective Evaluation of mtDNA Oxidative Damage in Living Cells. Anal Chem 2019; 91:13962-13969. [PMID: 31580062 DOI: 10.1021/acs.analchem.9b03494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The unrepaired apurinic/apyrimidinic site (AP site) in mitochondrial DNA (mtDNA) promotes misincorporation of nucleotides and further causes serious damage for the living organism. Thus, accurate quantitative detection of AP sites in mtDNA in a rapid, highly sensitive, and highly selective fashion is important for the real-time evaluation of mtDNA oxidative damage. In this study, a targeting mtDNA ultrasensitive AP site-specific fluorescent rotor (BTBM-CN2) was designed by the strategy of molecular conformation torsion adjustment ratio fluorescent signal. The specific recognition reaction is activated when it encountered AP sites in mtDNA within 20 s, and BTBM-CN2 presented a "turn-on" red fluorescence signal at 598 nm. Then, about 100 s later, BTBM-CN2 emitted a new green fluorescence signal at 480 nm, which is mainly due to the activation of the rate-limiting reaction. With increasing numbers of AP sites (1-40 in 1 × 105 bp of mtDNA), the fluorescence emission at 598 nm decreased gradually, and the new emission at 480 nm increased. Intracellular experiments indicated that BTBM-CN2 could detect AP sites in mtDNA in a rapid and quantitative fashion with high selectivity and ultrasensitivity. On the basis of the emergence of the fluorescence signal at 480 nm and its signal strength, the cell whose mtDNA was damaged could be screened by flow cytometry and its degree of damage could be evaluated in real time by comet assay. Hence, the rotor may have potential applications varying from accurate and ultrasensitive detection of AP sites to the real-time evaluation of the oxidative damage in living cells.
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Huang D, Yang C, Yao Y, Li J, Guo C, Chen J, Zhang Y, Yang S, Yang Q, Tang Y. Versatile and Homogeneous DNA Tetraplex Platform for Constructing Label‐Free Logic Devices: From Design to Application. Chemistry 2019; 25:6996-7003. [PMID: 30933378 DOI: 10.1002/chem.201900734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Huang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chunrong Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Ye Yao
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jicheng Li
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Chen Guo
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Jianchi Chen
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yi Zhang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Shu Yang
- Department West China School of PharmacySichuan University Chengdu 610064 P.R. China
| | - Qianfan Yang
- College of ChemistrySichuan University Chengdu 610064 P.R. China
| | - Yalin Tang
- National Laboratory for Molecular SciencesCentre for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable, and Stable SpeciesInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P.R. China
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14
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Sato Y, Yajima S, Taguchi A, Baba K, Nakagomi M, Aiba Y, Nishizawa S. Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA. Chem Commun (Camb) 2019; 55:3183-3186. [DOI: 10.1039/c9cc00414a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report that TO-PRO-3 functions as a deep-red fluorescent indicator for the internal loop structure of the bacterial (Escherichia coli) A-site, which enables the assessment of A-site binding capability of various test compounds including blue and even-green-emitting compounds.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Sayaka Yajima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Akifumi Taguchi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kyosuke Baba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mayu Nakagomi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yuri Aiba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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15
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Target-switched triplex nanotweezer and synergic fluorophore translocation for highly selective melamine assay. Mikrochim Acta 2018; 186:42. [PMID: 30569196 DOI: 10.1007/s00604-018-3134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
Abstract
This paper describes a triplex DNA nanotweezer to specifically capture melamine (MEL). The triplex-forming oligonucleotide (TFO) arm can be switched from the open state to the closed state once MEL binds to the abasic site (AP site) in duplex via the bifacial hydrogen bonding with thymines. Following this nanotweezer operation, the AP site-bound fluorophore is translocated to the terminal triplet to subsequently light up the nanotweezer. The TFO arm is found to be pivotal for permitting the AP site binding. The synergic processes of target competition and fluorophore translocation support a high selectivity for the MEL assay even against the inherent adenosine and the MEL hydrolysis products. Chelerythrine is employed as the fluorescent probe. The detection limit of MEL was estimated to be about 140 nM assuming a signal-to-noise ratio of 3. It was applied to the determination of MEL in spiked milk samples without any separation procedure. Conceivably, this method opens a new avenue towards highly selective triplex-based sensors by making use of other commercially available DNA modifications for recognizing other analytes. Graphical abstract Schematic presentation of a triplex nanotweezer with an open-to-close conversion upon the abasic site binding of melamine. The assay is based on a synergic fluorophore translocation. The corresponding duplex otherwise shows no binding with melamine. Chelerythrine (CHE) with a yellow-green emission peaking at 544 nm is employed as the fluorescent probe.
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