1
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. J Chem Inf Model 2024; 64:4802-4810. [PMID: 38856665 PMCID: PMC11200263 DOI: 10.1021/acs.jcim.4c00528] [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] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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2
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Saleem M, Hanif M, Rafiq M, Raza H, Ja KS, Lu C. γ-Glutamyltranspeptidase (GGT) Sensitive Fluorescence Probes for Cancer Diagnosis; Brief Review. J Fluoresc 2024; 34:977-1006. [PMID: 37505365 DOI: 10.1007/s10895-023-03353-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
Millions of deaths occur each year due to the late diagnosis of abnormal cellular growth within the body. However, the devastating impact of this can be significantly reduced if cancer metastasis is detected early through the use of enzymatic biomarkers. Among several biomarkers, γ-glutamyltranspeptidase (GGT) stands out as a member of the aminopeptidase family. It is primarily found on the surface of cancer cells such as glioma, ovarian, lung, and prostate cancer, without being overexpressed in normal cells or tissues. Recent years have witnessed significant progress in the field of cancer monitoring and imaging. Fluorescence sensing techniques have been employed, utilizing organic small molecular probes with enzyme-specific recognition sites. These probes emit a fluorescent signal upon interacting with GGT, enabling the imaging, identification, and differentiation of normal and cancerous cells, tissues, and organs. This review article presents a concise overview of recent progress in fluorescent probes developed for the selective detection of GGT, focusing on their applications in cancer imaging. It highlights the observed alterations in the fluorescence and absorption spectra of the probes before and after interaction with GGT. Additionally, the study investigates the changes in the probe molecule's structure following enzyme treatment, evaluates the sensor's detection limit, and consolidated imaging studies conducted using confocal fluorescence analysis. This comprehensive survey is expected to contribute to the advancement of sensing techniques for biomarker detection and cancer imaging, providing valuable insights for refining methodologies and inspiring future developments in this field.
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Affiliation(s)
- Muhammad Saleem
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan.
- Department of Chemistry, Thal University Bhakkar, Bhakkar, 30000, Pakistan.
| | - Muhammad Hanif
- Department of Chemistry, GC University Faisalabad, Sub Campus, Layyah, 31200, Pakistan
| | - Muhammad Rafiq
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 6300, Pakistan
| | - Hussain Raza
- Department of Biological Sciences, Kongu National University, Kongju Chungnam, Republic of Korea
| | - Kim Song Ja
- Department of Biological Sciences, Kongu National University, Kongju Chungnam, Republic of Korea
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai, 201620, China
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3
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Lucia-Tamudo J, Alcamí M, Díaz-Tendero S, Nogueira JJ. One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA. Biochemistry 2023; 62:3312-3322. [PMID: 37923303 PMCID: PMC10666269 DOI: 10.1021/acs.biochem.3c00324] [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] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
| | - Manuel Alcamí
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Sergio Díaz-Tendero
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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4
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA. Phys Chem Chem Phys 2023; 25:14578-14589. [PMID: 37191244 DOI: 10.1039/d3cp00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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5
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Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
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Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
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6
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Meher S, Gade CR, Sharma NK. Tropolone-Conjugated DNA: A Fluorescent Thymidine Analogue Exhibits Solvatochromism, Enzymatic Incorporation into DNA and HeLa Cell Internalization. Chembiochem 2023; 24:e202200732. [PMID: 36510378 DOI: 10.1002/cbic.202200732] [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: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Tropolone is a non-benzenoid aromatic scaffold with unique photophysical and metal-chelating properties. Recently, it has been conjugated with DNA, and the photophysical properties of this conjugate have been explored. Tropolonyl-deoxyuridine (tr-dU) is a synthetic fluorescent DNA nucleoside analogue that exhibits pH-dependent emissions. However, its solvent-dependent fluorescence properties are unexplored owing to its poor solubility in most organic solvents. It would be interesting to incorporate it into DNA primer enzymatically. This report describes the solvent-dependent fluorescence properties of the silyl-derivative, and enzymatic incorporation of its triphosphate analogue. For practical use, its cell-internalization and cytotoxicity are also explored. tr-dU nucleoside was found to be a potential analogue to design DNA probes and can be explored for various therapeutic applications in the future.
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Affiliation(s)
- Sagarika Meher
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Chandrasekhar Reddy Gade
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Nagendra K Sharma
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
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7
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Cui Q, Zhong Y, Shang W, Deng F, Wang B, Wu J, Wang P, Wan L, Wang K, Fang L, Dai R, Zhang H, Ledesma-Amaro R, Zhang Y, Huang J. Fluorescent Probe Combined with Photoelectric Analysis Technology for Detection of Escherichia coli. BIOSENSORS 2023; 13:150. [PMID: 36831916 PMCID: PMC9953772 DOI: 10.3390/bios13020150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Food safety is facing great challenges in preventing foodborne diseases caused by pathogenic pollution, especially in resource-limited areas. The rapid detection technique of microorganisms, such as immunological methods and molecular biological methods, plays a crucial key in timely bioanalysis and disease treatment strategies. However, it is difficult for these methods to simultaneously meet the criteria of simple operation, high specificity, and sensitivity, as well as low cost. Coconut water is known as the "water of life" in Hainan. It is a refreshing and nutritious beverage which is widely consumed due to its beneficial properties to health. Coconut water processing is an important pillar industry in Hainan. The detection of pathogenic microorganisms, such as Escherichia coli, in coconut water has become an important factor which has restricted the upgrading and development of this industry. Based on the needs of industrial development, we developed a microbial photoelectric detection system which was composed of a fluorescent probe detection reagent and a photoelectric sensor detection device. This system combined microbial enzyme targets, selective fluorescent substrate metabolism characteristics, and a photoelectric sensor signal transduction mechanism, which produce a strong signal with a high signal-to-noise ratio. The microbial detection system developed here has a simple structure, simple and convenient operation, short detecting time (≥2 h), and high sensitivity (1 CFU/mL). This system may also enable early warning and monitoring programs for other pathogenic microorganisms in order to promote the overall competitiveness of the Hainan coconut water industry.
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Affiliation(s)
- Qian Cui
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yongjie Zhong
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Wenkai Shang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Fuming Deng
- Coconut Research Center, Coconut Research Institute, Chinese Academy of Tropical Agricultural Science (CATAS), Haikou 570228, China
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Jiajia Wu
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Peng Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-Fouling Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liudang Wan
- Insititue of Biotechnology, ViewKr, Haikou 570228, China
| | - Keling Wang
- Insititue of Biotechnology, ViewKr, Haikou 570228, China
| | - Lingchen Fang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Rui Dai
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Han Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Yunuo Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Jiaomei Huang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
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8
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Zhao L, Ahmed F, Zeng Y, Xu W, Xiong H. Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes. ACS Sens 2022; 7:2833-2856. [PMID: 36112358 DOI: 10.1021/acssensors.2c00992] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na+, K+, Ag+, Tl+, Cu+/Cu2+, Hg2+, and Pb2+) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.
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Affiliation(s)
- Long Zhao
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Farid Ahmed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yating Zeng
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Weiqing Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
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9
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Bollu A, Panda SS, Sharma NK. Fluorescent DNA analog: 2-aminotroponyl-pyrrolyl-2'-deoxyuridinyl DNA oligo enhance fluorescence in DNA-duplex as compared to 2-aminotroponyl-ethynyl-2'-deoxyuridinyl DNA oligo. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:119-133. [PMID: 36002436 DOI: 10.1080/15257770.2022.2111442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The nucleobase modified fluorescent DNA and RNA analogs are synthesized by the conjugation of aromatic scaffolds through linkers, comprising mostly ethyne/ethene or fused ring residues at the pyrimidine/purine ring. These scaffolds are mainly derived from the benzenoid aromatic molecules comprising electron withdrawing/donating characters. However, non-benzenoid aromatic scaffolds such as tropolone and related derivatives are constituents of various troponoid natural products. The conjugation of nucleobases with a troponyl moiety is underutilized for the synthesis of fluorescent DNA analogs. This report describes the synthesis and photophysical studies of 2-aminotroponyl conjugated deoxyuridine nucleosides and their DNA analogs. 2-Aminotropone derivatives are conjugated at the C-5 position of uridine through an ethynyl linker/pyrrolyl ring fusion and their DNA analogs. Their photophysical studies reveal that aminotroponyl deoxyuridine analogs exhibit solvent-dependent fluorescence properties. Moreover, pyrrolyl ring-fused aminotroponyl DNA oligonucleotides enhance the fluorescence after formation of duplexation with complementary sequences of native DNA oligonucleotides. Hence, these modified nucleosides and DNA are promising fluorescent analogs which could be useful to design the sequence-specific DNA probes.
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Affiliation(s)
- Amarnath Bollu
- School of Chemical Science, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI)-Mumbai, Mumbai, India
| | - Subhashree Subhadarshini Panda
- School of Chemical Science, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI)-Mumbai, Mumbai, India
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10
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Li YX, Xie DT, Yang YX, Chen Z, Guo WY, Yang WC. Development of Small-Molecule Fluorescent Probes Targeting Enzymes. Molecules 2022; 27:molecules27144501. [PMID: 35889374 PMCID: PMC9324355 DOI: 10.3390/molecules27144501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
As biological catalysts, enzymes are vital in controlling numerous metabolic reactions. The regulation of enzymes in living cells and the amount present are indicators of the metabolic status of cell, whether in normal condition or disease. The small-molecule fluorescent probes are of interest because of their high sensitivity and selectivity, as well as their potential for automated detection. Fluorescent probes have been useful in targeting particular enzymes of interest such as proteases and caspases. However, it is difficult to develop an ideal fluorescent probe for versatile purposes. In the future, the design and synthesis of enzyme-targeting fluorescent probes will focus more on improving the selectivity, sensitivity, penetration ability and to couple the fluorescent probes with other available imaging molecules/technologies.
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Affiliation(s)
- Yuan-Xiang Li
- College of Chemistry and Materials Engineering, Huaihua University, Huaihua 418008, China; (Y.-X.L.); (D.-T.X.); (Y.-X.Y.)
| | - Dong-Tai Xie
- College of Chemistry and Materials Engineering, Huaihua University, Huaihua 418008, China; (Y.-X.L.); (D.-T.X.); (Y.-X.Y.)
| | - Ya-Xi Yang
- College of Chemistry and Materials Engineering, Huaihua University, Huaihua 418008, China; (Y.-X.L.); (D.-T.X.); (Y.-X.Y.)
| | - Zhao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China; (Z.C.); (W.-Y.G.)
| | - Wu-Yingzheng Guo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China; (Z.C.); (W.-Y.G.)
| | - Wen-Chao Yang
- College of Chemistry and Materials Engineering, Huaihua University, Huaihua 418008, China; (Y.-X.L.); (D.-T.X.); (Y.-X.Y.)
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China; (Z.C.); (W.-Y.G.)
- Correspondence: ; Tel.: +86-27-67867706; Fax: +86-27-67867141
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11
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Wang J, Jin Y, Li M, Liu S, Lo KKW, Zhao Q. Time-Resolved Luminescent Sensing and Imaging for Enzyme Catalytic Activity Based on Responsive Probes. Chem Asian J 2022; 17:e202200429. [PMID: 35819359 DOI: 10.1002/asia.202200429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Indexed: 11/07/2022]
Abstract
Enzymes, as a kind of biomacromolecules, play an important role in many physiological processes and relate directly to various diseases. Developing an efficient detection method for enzyme activity is important to achieve early diagnosis of enzyme-relevant diseases and high throughput screening of potential enzyme-relevant drugs. Time-resolved luminescence assay provide a high accuracy and signal-to-noise ratios detection methods for enzyme activity, which has been widely used in high throughput screening of enzyme-relevant drugs and diagnosis of enzyme-relevant diseases. Inspired by these advantages, various responsive probes based on metal complexes and metal-free organic compounds have been developed for time-resolved bioimaging and biosensing of enzyme activity owing to their long luminescence lifetimes, high quantum yields and photostability. In this review, we comprehensively reviewed metal complex- and metal-free organic compound-based responsive probes applied to detect enzyme activity through time-resolved imaging, including their design strategies and sensing principles. Current challenges and future prospects in this rapidly growing field are also discussed.
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Affiliation(s)
- Jiawei Wang
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Yibiao Jin
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Mingdang Li
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Shujuan Liu
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Kenneth Kam-Wing Lo
- City University of Hong Kong, Department of Chemistry, Tat Chee Avenue, Hong Kong, CHINA
| | - Qiang Zhao
- Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, 210023, Nanjing, CHINA
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12
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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13
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Abstract
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Personalized and
point-of-care (POC) diagnoses are critical for
ocular physiology and disease diagnosis. Real-time monitoring and
continuous sampling abilities of tear fluid and user-friendliness
have become the key characteristics for the applied ophthalmic techniques.
Fluorescence technologies, as one of the most popular methods that
can fulfill the requirements of clinical ophthalmic applications for
optical sensing, have been raised and applied for tear sensing and
diagnostic platforms in recent decades. Wearable sensors in this case
have been increasingly developed for ocular diagnosis. Contact lenses,
as one of the commercialized and popular tools for ocular dysfunction,
have been developed as a platform for fluorescence sensing in tears
diagnostics and real-time monitoring. Numbers of biochemical analytes
have been examined through developed fluorescent contact lens sensors,
including pH values, electrolytes, glucose, and enzymes. These sensors
have been proven for monitoring ocular conditions, enhancing and detecting
medical treatments, and tracking efficiency of related ophthalmic
surgeries at POC settings. This review summarizes the applied ophthalmic
fluorescence sensing technologies in tears for ocular diagnosis and
monitoring. In addition, the cooperation of fabricated fluorescent
sensor with mobile phone readout devices for diagnosing ocular diseases
with specific biomarkers continuously is also discussed. Further perspectives
for the developments and applications of fluorescent ocular sensing
and diagnosing technologies are also provided.
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Affiliation(s)
- Yuqi Shi
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2BU, United Kingdom
| | - Yubing Hu
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2BU, United Kingdom
| | - Nan Jiang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Ali K. Yetisen
- Department of Chemical Engineering, Imperial College London, South Kensington, London, SW7 2BU, United Kingdom
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14
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Abstract
A new fluorescent ribonucleoside alphabet (mth N) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (th N) and isothiazole[4,3-d]pyrimidine (tz N) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding mth N/mth NTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the mth N alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Shenghua Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Marcela S Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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15
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Zhang Y, Du XK, Su X, Zou X, Zhang CY. Mismatched fluorescent probes with an enhanced strand displacement reaction rate for intracellular long noncoding RNA imaging. Chem Commun (Camb) 2022; 58:1760-1763. [PMID: 35037666 DOI: 10.1039/d1cc05270e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We design mismatched fluorescent probes to directly monitor the long noncoding RNA (lncRNA) in living cells. The introduction of mismatched bases in the fluorescent probe greatly enhances the strand displacement reaction rate toward the target lncRNA. These mismatched probes can monitor the intracellular lncRNA expression level in various cell lines and discriminate cancer cells from normal cells, holding great potential in fundamental biomedical research and clinical disease diagnosis.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xue-Ke Du
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Xianwei Su
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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16
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Koboku S, Tsukada T, Oku Y, Kobayashi S, Saito Y. FRET-based dual-labeled oligonucleotide probe detects target DNA by probing a minor groove environment. Org Biomol Chem 2022; 20:1699-1706. [DOI: 10.1039/d2ob00027j] [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
A novel amino-modifier ESF nucleoside AM37zA (1) containing trifluoroacetyl (TFA)-protected amino group is designed for the functionalization of ODN probe after oligonucleotide synthesis. AM37zA (1) demonstrated remarkable solvatochromicity and ODN...
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17
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Ba S, Gao G, Li T, Zhang H. Tricking enzymes in living cells: a mechanism-based strategy for design of DNA topoisomerase biosensors. J Nanobiotechnology 2021; 19:407. [PMID: 34876137 PMCID: PMC8650243 DOI: 10.1186/s12951-021-01155-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/21/2021] [Indexed: 12/30/2022] Open
Abstract
Most activity-based molecular probes are designed to target enzymes that catalyze the breaking of chemical bonds and the conversion of a unimolecular substrate into bimolecular products. However, DNA topoisomerases are a class of enzymes that alter DNA topology without producing any molecular segments during catalysis, which hinders the development of practical methods for diagnosing these key biomarkers in living cells. Here, we established a new strategy for the effective sensing of the expression levels and catalytic activities of topoisomerases in cell-free systems and human cells. Using our newly designed biosensors, we tricked DNA topoisomerases within their catalytic cycles to switch on fluorescence and resume new rounds of catalysis. Considering that human topoisomerases have been widely recognized as biomarkers for multiple cancers and identified as promising targets for several anticancer drugs, we believe that these DNA-based biosensors and our design strategy would greatly benefit the future development of clinical tools for cancer diagnosis and treatment. ![]()
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Affiliation(s)
- Sai Ba
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Guangpeng Gao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tianhu Li
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Hao Zhang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China. .,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
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18
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Ravi Kumara GS, Seo YJ. Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein- c-myc G-quadruplex interactions. Org Biomol Chem 2021; 19:5788-5793. [PMID: 34085078 DOI: 10.1039/d1ob00863c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.
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Affiliation(s)
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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19
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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20
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Sidhu JS, Kaur N, Singh N. Trends in small organic fluorescent scaffolds for detection of oxidoreductase. Biosens Bioelectron 2021; 191:113441. [PMID: 34167075 DOI: 10.1016/j.bios.2021.113441] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/23/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022]
Abstract
Oxidoreductases are diverse class of enzymes engaged in modulating the redox homeostasis and cellular signaling cascades. Abnormal expression of oxidoreductases including thioredoxin reductase, azoreductase, cytochrome oxidoreductase, tyrosinase and monoamine oxidase leads to the initiation of numerous disorders. Thus, enzymes are the promising biomarkers of the diseased cells and their accurate detection has utmost significance for clinical diagnosis. The detection method must be extremely selective, sensitive easy to use, long self-life, mass manufacturable and disposable. Fluorescence assay approach has been developed potential substitute to conventional techniques used in enzyme's quantification. The fluorescent probes possess excellent stability, high spatiotemporal ratio and reproducibility represent applications in real sample analysis. Therefore, the enzymatic transformations have been monitored by small activatable organic fluorescent probes. These probes are generally integrated with enzyme's substrate/inhibitors to improve their binding affinity toward the enzyme's catalytic site. As the recognition unit bio catalyzed, the signaling unit produces the readout signals and provides novel insights to understand the biochemical reactions for diagnosis and development of point of care devices. Several structural modifications are required in fluorogenic scaffolds to tune the selectivity for a particular enzyme. Hence, the fluorescent probes with their structural features and enzymatic reaction mechanism of oxidoreductase are the key points discussed in this review. The basic strategies to detect each enzyme are discussed. The selectivity, sensitivity and real-time applications are critically compared. The kinetic parameters and futuristic opportunities are present, which would be enormous benefits for chemists and biologists to understand the facts to design and develop unique fluorophore molecules for clinical applications.
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Affiliation(s)
- Jagpreet Singh Sidhu
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India; Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh, 160014, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab, 140001, India.
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21
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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22
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Qin C, Hu C, Yu A, Lai G. Fe 3O 4@polydopamine and Exo III-assisted homogeneous biorecognition reaction for convenient and ultrasensitive detection of kanamycin antibiotic. Analyst 2021; 146:1414-1420. [PMID: 33404555 DOI: 10.1039/d0an02187c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Herein, we report a Fe3O4@polydopamine (PDA) nanocomposite and exonuclease III (Exo III)-assisted homogeneous fluorescence biosensing method for ultrasensitive detection of kanamycin (Kana) antibiotic. A hairpin DNA containing the Kana-aptamer sequence (HP) was first designed for the highly specific biorecognition of the target analyte. Because of the aptamer biorecognition-induced structural change of HP and the highly effective catalyzed reaction of Exo III, a large amount of fluorophore labels were released from the designed fluorescence DNA probe. During the homogeneous reaction process, the Exo III-assisted dual recycling significantly amplified the fluorescence signal output. Moreover, the excessive probes were easily adsorbed and separated by the Fe3O4@PDA nanocomposite, which decreased the background signal and increased the signal-to-noise ratio. These strategies result in the excellent analytical performance of the method, including a very low detection limit of 0.023 pg mL-1 and a very wide linear range of six orders of magnitude. In addition, this method has convenient operation, excellent selectivity, repeatability and satisfactory reliability, and does not involve the design and utilization of complicated DNA sequences. Thus, it exhibits a promising prospect for practical applications.
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Affiliation(s)
- Chuanying Qin
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Cong Hu
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
| | - Aimin Yu
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China.
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23
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Zhang H, Ba S, Lee JY, Xie J, Loh TP, Li T. Cancer Biomarker-Triggered Disintegrable DNA Nanogels for Intelligent Drug Delivery. NANO LETTERS 2020; 20:8399-8407. [PMID: 33118827 DOI: 10.1021/acs.nanolett.0c03671] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Even though various techniques have been developed thus far for targeted delivery of therapeutics, design and fabrication of cancer biomarker-triggered disintegrable nanogels, which are exclusively composed of nucleic acid macromolecules, are still challenging nowadays. Here, we describe for the first time our creation of intelligent DNA nanogels whose backbones are sorely disintegrable by flap endonuclease 1 (FEN1), an enzymatic biomarker that is highly overexpressed in most cancer cells but not in their normal counterparts. It is the catalytic actions of intracellular FEN1 on bifurcated DNA structures that lead to the cancer-specific disintegration of our DNA nanogels and controlled release of drugs in target cancer cells. Consequently, the brand-new strategies introduced in the current report could break new ground in designing drug carriers for eliminating unwanted side effects of chemotherapeutic agents and live-cell probes for cancer risk assessment, diagnosis, and prognosis.
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Affiliation(s)
- Hao Zhang
- Institute of Advanced Synthesis (IAS), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an 710072, China
- Yangtze River Delta Research Institute, Northwestern Polytechnical University (NPU), 27 Zigang Road, Taicang, Jiangsu 215400, China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jasmine Yiqin Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jianping Xie
- Department of Chemical and Biomolecular and Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Teck-Peng Loh
- Institute of Advanced Synthesis (IAS), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an 710072, China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Tianhu Li
- Institute of Advanced Synthesis (IAS), Northwestern Polytechnical University (NPU), 127 West Youyi Road, Xi'an 710072, China
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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24
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Electrochemical CYFRA21-1 DNA sensor with PCR-like sensitivity based on AgNPs and cascade polymerization. Anal Bioanal Chem 2020; 412:4155-4163. [PMID: 32306069 DOI: 10.1007/s00216-020-02652-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/20/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023]
Abstract
In this work, a new method of CYFRA21-1 DNA (tDNA) detection based on electrochemically mediated atom transfer radical polymerization (e-ATRP) and surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT) cascade polymerization and AgNP deposition is proposed. Firstly, the peptide nucleic acid (PNA) probe is captured on a gold electrode by Au-S bonds for specific recognition of tDNA. After hybridization, PNA/DNA strands provide high-density phosphate groups for the subsequent ATRP initiator by the identified carboxylate-Zr4+-phosphate chemistry. Then, a large number of monomers are successfully grafted from the DNA through the e-ATRP reaction. After that, the chain transfer agent of SI-RAFT and methacrylic acid (MAA) are connected by recognized carboxylate-Zr4+-carboxylate chemistry. Subsequently, through SI-RAFT, the resulting polymer introduces numerous aldehyde groups, which could deposit many AgNPs on tDNA through silver mirror reaction, causing significant amplification of the electrochemical signal. Under optimal conditions, this designed method exhibits a low detection limit of 0.487 aM. Moreover, the method enables us to detect DNA at the level of PCR-like and shows high selectivity and strong anti-interference ability in the presence of serum. It suggests that this new sensing signal amplification technology exhibits excellent potential of application in the early diagnosis of non-small cell lung cancer (NSCLC). Graphical abstract Electrochemical detection principle for CYFRA21-1 DNA based on e-ATRP and SI-RAFT signal amplification technology.
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25
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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26
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Liu X, Wu Y, Wu X, Zhao JX. A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity. Analyst 2020; 144:6231-6239. [PMID: 31552930 DOI: 10.1039/c9an01283d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.
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Affiliation(s)
- Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, USA.
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27
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Polysaccharide-enhanced ARGET ATRP signal amplification for ultrasensitive fluorescent detection of lung cancer CYFRA 21-1 DNA. Anal Bioanal Chem 2020; 412:2413-2421. [PMID: 32047944 DOI: 10.1007/s00216-020-02394-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/15/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022]
Abstract
An ultrasensitive fluorescence biosensor for detecting cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA of non-small cell lung carcinoma (NSCLC) is designed using polysaccharide and activator regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) signal amplification strategy. Thiolated peptide nucleic acid (PNA) is fixed on magnetic nanoparticles (MNPs) by a cross-linking agent and hybridized with CYFRA 21-1 DNA. Hyaluronic acid (HA) is linked to PNA/tDNA heteroduplexes in the form of carboxy-Zr4+-phosphate. Subsequently, multiple 2-bromo-2-methylpropionic acid (BMP) molecules are linked with HA to initiate ARGET ATRP reaction. Finally, a large number of fluorescein o-acrylate (FA) monomers are polymerized on the macro-initiators, and the fluorescence signal is significantly amplified. Under optimal conditions, this biosensor shows a significant linear correlation between the fluorescence intensity and logarithm of CYFRA 21-1 DNA concentration (0.1 fM to 0.1 nM), and the limit of detection is as low as 78 aM. Furthermore, the sensor has a good ability to detect CYFRA 21-1 DNA in serum samples and to recognize mismatched bases. It suggests that the strategy has broad application in early diagnosis by virtue of its high sensitivity and selectivity. Graphical abstract A novel and highly sensitive fluorescence biosensor for quantitatively detecting CYFRA 21-1 DNA via dual signal amplification of hyaluronic acid and ARGET ATRP reaction was developed. This proposed method has a low detection limit, wide detection range, high selectivity, and strong anti-interference.
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Advances in oligonucleotide-based detection coupled with fluorescence resonance energy transfer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Shahdeo D, Roberts A, Abbineni N, Gandhi S. Graphene based sensors. ANALYTICAL APPLICATIONS OF GRAPHENE FOR COMPREHENSIVE ANALYTICAL CHEMISTRY 2020. [PMCID: PMC7518956 DOI: 10.1016/bs.coac.2020.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The two dimensional, honeycomb structured, single carbon layered graphene has extensively been used in the field of sensor detection due to its unique physicochemical properties. These properties such as excellent electrical conductivity, high electron mobility, tunable optical properties, room temperature quantum Hall effect, large surface to volume ratio, high mechanical strength, and ease of functionalization, make it an ideal nanomaterial for sensor development. This has enabled the fabrication of a large variety of highly sensitive sensors which include colorimetric, electrochemical, potentiometric, fluorescence, etc. based sensors. These sensors in conjugation with graphene or its derivatives such as graphene quantum dots, graphene oxide, reduced graphene oxide, etc. show highly desirable properties such as high sensitivity (detecting minute amounts of target analyte), specificity (no cross reactivity while detecting the target analyte), rapid results, low cost, extended storage shelf life and robustness (stability), and easy-to-use capabilities (user-friendly). This book chapter gives a detailed overview of all the advances made in the development and fabrication of novel graphene based sensors and their application in point of care (PoC) detection of various diseases as well as health monitoring devices. The different sensors, their methods of fabrication, their sensitivity and the analytes and biomolecules used have been discussed in detail and compared.
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Taskova M, Astakhova K. Fluorescent Oligonucleotides with Bis(prop-2-yn-1-yloxy)butane-1,3-diol Scaffold Rapidly Detect Disease-Associated Nucleic Acids. Bioconjug Chem 2019; 30:3007-3012. [DOI: 10.1021/acs.bioconjchem.9b00746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Taskova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
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31
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Iwe IA, Li Z, Huang J. A dual-cycling fluorescence scheme for ultrasensitive DNA detection through signal amplification and target regeneration. Analyst 2019; 144:2649-2655. [PMID: 30843550 DOI: 10.1039/c9an00075e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, we propose an ultrasensitive fluorescence strategy for DNA detection. This method utilizes a molecular beacon (MB), a hairpin probe (HP), and an enzyme to trigger dual-cycling reactions (cycles I and II). In cycle I, the target is repeatedly used to amplify the fluorescence emission through hybridizations with the MB and cleavage reactions achieved by the enzyme. In cycle II, hybridization reactions between the HP and a segment of the MB continuously regenerate the target to trigger more cycle I reactions, leading to an enhanced fluorescent signal. The detection limit of the method is determined to be as low as 50 fM within 45 min, which is 2 to 3 orders of magnitude lower than that of the conventional fluorescence strategies. The method also shows a high selectivity over mismatched and random DNA sequences. The signal amplification mechanism of the strategy offers insights into constructing efficient and ultrasensitive biosensors for various applications.
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Affiliation(s)
- Idorenyin A Iwe
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Spatarelu CP, Zhang H, Trung Nguyen D, Han X, Liu R, Guo Q, Notbohm J, Fan J, Liu L, Chen Z. Biomechanics of Collective Cell Migration in Cancer Progression: Experimental and Computational Methods. ACS Biomater Sci Eng 2019; 5:3766-3787. [PMID: 32953985 PMCID: PMC7500334 DOI: 10.1021/acsbiomaterials.8b01428] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is associated with some biomechanical particularities such as restructuring of extracellular matrix (ECM), stress and force distribution profiles, and reorganization of the cytoskeleton. Therefore, the phenomenon could be understood by an in-depth study of cells' behavior determinants, including but not limited to mechanical cues from the environment and from fellow "travelers". This review article aims to cover the recent development of experimental and computational methods for studying the biomechanics of collective cell migration during cancer progression and invasion. We also summarized the tested hypotheses regarding the mechanism underlying collective cell migration enabled by these methods. Together, the paper enables a broad overview on the methods and tools currently available to unravel the biophysical mechanisms pertinent to cell collective migration as well as providing perspectives on future development toward eventually deciphering the key mechanisms behind the most lethal feature of cancer.
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Affiliation(s)
| | - Hao Zhang
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Dung Trung Nguyen
- Department of Engineering and Computer Science, Seattle Pacific University, Seattle, Washington 98119,
United States
| | - Xinyue Han
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ruchuan Liu
- College of Physics, Chongqing University, Chongqing 400032, China
| | - Qiaohang Guo
- School of Materials Science and Engineering, Fujian University of Technology, Fuzhou 350014,
China
| | - Jacob Notbohm
- Department of Engineering Physics, University of Wisconsin—Madison, Madison, Wisconsin 53706,
United States
| | - Jing Fan
- Department of Mechanical Engineering, City College of City University of New York, New York 10031, United
States
| | - Liyu Liu
- College of Physics, Chongqing University, Chongqing 400032, China
| | - Zi Chen
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
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Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes. Molecules 2019; 24:molecules24101863. [PMID: 31096553 PMCID: PMC6571788 DOI: 10.3390/molecules24101863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG3TTAG3-(TTA)n-G3TTAG3T (n = 1–8) (named TTA series) and AG3TTTG3-(TTA)n-G3TTTG3T (n = 1–8) (named TTT series) were examined in K+ and Na+ solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na+ solution and a hybrid G-quadruplex structure in K+ solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na+ and K+ solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops.
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Yang H, Fu F, Li W, Wei W, Zhang Y, Liu S. Telomerase and poly(ADP-ribose) polymerase-1 activity sensing based on the high fluorescence selectivity and sensitivity of TOTO-1 towards G bases in single-stranded DNA and poly(ADP-ribose). Chem Sci 2019; 10:3706-3714. [PMID: 31015914 PMCID: PMC6461019 DOI: 10.1039/c8sc05770b] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/18/2019] [Indexed: 01/12/2023] Open
Abstract
Telomerase and poly(ADP-ribose) polymerase-1 (PARP-1) are two potential cancer biomarkers and are closely related to tumor initiation and malignant progression. TOTO-1 is well-known for differentiating ss-DNA from ds-DNA because it is virtually non-fluorescent without DNA and exhibits very low fluorescence with ss-DNA, while it emits strong fluorescence with ds-DNA. In this paper, for the first time, it was found that TOTO-1 has high fluorescence selectivity and sensitivity towards the G bases in single-stranded DNA and poly(ADP-ribose) (PAR). Poly(dG) was used as the model target to explore its possible mechanism. Molecular dynamics (MD) simulation proved that intramolecular π-π stacking existed in TOTO-1 (in an aqueous solution), while intermolecular π-π stacking formed between TOTO-1 and poly(dG) in a similar way as that observed for dsDNA. Interestingly, telomerase and PARP-1 catalyzed the formation of G-rich DNA and PAR in vivo, respectively. Therefore, TOTO-1 was explored in detecting both of them, obtaining satisfactory results. To the best of our knowledge, no probe has been reported to recognize PAR. It is also the first time where telomerase is detected based on the specific recognition of G bases. Importantly, integrating multiple functions into one probe that can detect not only telomerase but also PARP-1 will significantly raise the specificity of screening cancer and decrease false positive proportion, which make TOTO-1 a promising candidate probe for clinical diagnosis and pharmaceutical screening.
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Affiliation(s)
- Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device , Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research , School of Chemistry and Chemical Engineering , Southeast University , Nanjing, 211189 , China . ; ; ; Tel: +86-25-52090613
| | - Fangjia Fu
- Institution of Theoretical and Computational Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Wei Li
- Institution of Theoretical and Computational Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device , Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research , School of Chemistry and Chemical Engineering , Southeast University , Nanjing, 211189 , China . ; ; ; Tel: +86-25-52090613
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device , Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research , School of Chemistry and Chemical Engineering , Southeast University , Nanjing, 211189 , China . ; ; ; Tel: +86-25-52090613
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device , Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research , School of Chemistry and Chemical Engineering , Southeast University , Nanjing, 211189 , China . ; ; ; Tel: +86-25-52090613
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FRET probe-based antibacterial susceptibility testing (F-AST) by detection of bacterial nucleases released by antibiotic-induced lysis. Biosens Bioelectron 2019; 130:225-229. [DOI: 10.1016/j.bios.2019.01.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/21/2022]
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Fossépré M, Trévisan ME, Cyriaque V, Wattiez R, Beljonne D, Richeter S, Clément S, Surin M. Detection of the Enzymatic Cleavage of DNA through Supramolecular Chiral Induction to a Cationic Polythiophene. ACS APPLIED BIO MATERIALS 2019; 2:2125-2136. [DOI: 10.1021/acsabm.9b00123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Marie E. Trévisan
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Sébastien Richeter
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Sébastien Clément
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
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37
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Takeda T, Yanagi M, Suzuki A, Katoh R, Saito Y. Synthesis of ethynylpyrene-modified 3-deaza-2′-deoxyguanosines as environmentally sensitive fluorescent nucleosides: Target DNA-sequence detection via changes in the fluorescence wavelength. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Fang X, Zheng Y, Duan Y, Liu Y, Zhong W. Recent Advances in Design of Fluorescence-Based Assays for High-Throughput Screening. Anal Chem 2019; 91:482-504. [PMID: 30481456 PMCID: PMC7262998 DOI: 10.1021/acs.analchem.8b05303] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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Tachallait H, Safir Filho M, Marzag H, Bougrin K, Demange L, Martin AR, Benhida R. A straightforward and versatile FeCl3 catalyzed Friedel–Crafts C-glycosylation process. Application to the synthesis of new functionalized C-nucleosides. NEW J CHEM 2019. [DOI: 10.1039/c8nj06300a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid and straightforward access to C-nucleosides using an inexpensive FeCl3 catalyst.
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Affiliation(s)
- Hamza Tachallait
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Mauro Safir Filho
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Hamid Marzag
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Luc Demange
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Anthony R. Martin
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Rachid Benhida
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
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40
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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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Kuba M, Pohl R, Hocek M. Synthesis of 2′-deoxycytidine and its triphosphate bearing tryptophan-based imidazolinone fluorophore for environment sensitive fluorescent labelling of DNA. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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42
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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43
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Xue SF, Han XY, Chen ZH, Yan Q, Lin ZY, Zhang M, Shi G. The Chemistry of Europium(III) Encountering DNA: Sprouting Unique Sequence-Dependent Performances for Multifunctional Time-Resolved Luminescent Assays. Anal Chem 2018; 90:10614-10620. [PMID: 30099873 DOI: 10.1021/acs.analchem.8b03010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Screening functional DNA that can fruitfully interact with metal ions is a long-standing hot topic in the fields of biotechnology, medicine, and DNA-based sensors. In this paper, we focus on the chemistry of europium(III) (Eu) coupled with single-stranded DNA (ssDNA), and we innovatively unveil that cytosine- and thymine-rich ssDNA oligomers (e.g., C16 and T16) can be effective antenna ligands to sensitize the luminescence of Eu. Luminescence lifetime spectroscopy, circular dichroic (CD) spectroscopy, and isothermal titration calorimetry (ITC) have been used to systematically characterize the interaction involved between Eu and ssDNA. In light of the resultant sequence-dependent performances, the long luminescence lifetime Eu/ssDNA-based label-free and versatile probes are further devised as a pattern distinction system for time-resolved luminescent (TRL) sensing applications. The interactions of metal ions and ssDNA can distinctively shift the antenna effect of ssDNA toward Eu as accessible pattern signals. As a result, as few as two Eu/ssDNA label-free TRL probes can discriminate 17 metal ions via principal component analysis (PCA). In addition, thiols can readily capture metal ions to switch the luminescence of Eu/ssDNA probes initially altered by metal ions. Hence, four Eu/ssDNA-metal ion ensembles are demonstrated to be a powerful label-free TRL sensor array for pattern differentiation of eight thiols and even chiral recognition of cysteine enantiomers with different concentrations. Moreover, the sensitive TRL detection of thiols in biofluids can be successfully realized by using our method, promising its potential practical usage. This is the first report of a ssDNA-sensitized Eu-based TRL platform for label-free yet multifunctional background-free sensing and would open a door for sprouting of more novel lanthanide ion/DNA-relevant strategies toward widespread applications.
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Affiliation(s)
- Shi-Fan Xue
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Xin-Yue Han
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Han Chen
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Qing Yan
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Zi-Yang Lin
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , China
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Bag SS, Gogoi H. Design of "Click" Fluorescent Labeled 2'-deoxyuridines via C5-[4-(2-Propynyl(methyl)amino)]phenyl Acetylene as a Universal Linker: Synthesis, Photophysical Properties, and Interaction with BSA. J Org Chem 2018; 83:7606-7621. [PMID: 29877080 DOI: 10.1021/acs.joc.7b03097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microenvironment-sensitive fluorescent nucleosides present attractive advantages over single-emitting dyes for sensing inter-biomolecular interactions involving DNA. Herein, we report the rational design and synthesis of triazolyl push-pull fluorophore-labeled uridines via the intermediacy of C5-[4-(2-propynyl(methyl)amino)]phenyl acetylene as a universal linker. The synthesized nucleosides showed interesting solvatochromic characteristic and/or intramolecular charge transfer (ICT) features. A few of them also exhibited dual-emitting characteristics evidencing our designing concept. The HOMO-LUMO distribution showed that the emissive states of these nucleosides were characterized with more significant electron redistribution between the C5-[4-(2-propynyl(methyl)amino)]phenyl triazolyl donor moiety and the aromatic chromophores linked to it, leading to modulated emission property. The solvent polarity sensitivity of these nucleosides was also tested. The synthesized triazolyl benzonitrile (10C), naphthyl (10E), and pyrenyl (10G) nucleosides were found to exhibit interesting ICT and dual (LE/ICT) emission properties. The dual-emitting pyrenyl nucleoside maintained a good ratiometric response in the BSA protein microenvironment, enabling the switch-on ratiometric sensing of BSA as the only protein biomolecule. Thus, it is expected that the new fluorescent nucleoside analogues would be useful in designing DNA probes for nucleic acid analysis or studying DNA-protein interactions via a drastic change in fluorescence response due to a change in micropolarity.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
| | - Hiranya Gogoi
- Bioorganic Chemistry Laboratory, Department of Chemistry , Indian Institute of Technology Guwahati 781039 , India
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45
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Mukhametshina AR, Fedorenko SV, Petrov AM, Zakyrjanova GF, Petrov KA, Nurullin LF, Nizameev IR, Mustafina AR, Sinyashin OG. Targeted Nanoparticles for Selective Marking of Neuromuscular Junctions and ex Vivo Monitoring of Endogenous Acetylcholine Hydrolysis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:14948-14955. [PMID: 29652477 DOI: 10.1021/acsami.8b04471] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The present work for the first time introduces nanosensors for luminescent monitoring of acetylcholinesterase (AChE)-catalyzed hydrolysis of endogenous acetylcholine (ACh) released in neuromuscular junctions of isolated muscles. The sensing function results from the quenching of Tb(III)-centered luminescence due to proton-induced degradation of luminescent Tb(III) complexes doped into silica nanoparticles (SNs, 23 nm), when acetic acid is produced from the enzymatic hydrolysis of ACh. The targeting of the silica nanoparticles by α-bungarotoxin was used for selective staining of the synaptic space in the isolated muscles by the nanosensors. The targeting procedure was optimized for the high sensing sensitivity. The measuring of the Tb(III)-centered luminescence intensity of the targeted SNs by fluorescent microscopy enables us to sense a release of endogenous ACh in neuromuscular junctions of the isolated muscles under their stimulation by a high-frequency train (20 Hz, for 3 min). The ability of the targeted SNs to sense an inhibiting effect of paraoxon on enzymatic activity of AChE in ex vivo conditions provides a way of mimicking external stimuli effects on enzymatic processes in the isolated muscles.
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Affiliation(s)
- Alsu R Mukhametshina
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
| | - Svetlana V Fedorenko
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
| | - Alexey M Petrov
- Kazan State Medial University , Butlerov Str. 49 , 420012 Kazan , Russian Federation
- Kazan Institute of Biochemistry and Biophysics , Federal Research Center "Kazan Scientific Center of RAS" , P.O. Box 30 , 420111 Kazan , Russian Federation
| | - Guzel F Zakyrjanova
- Kazan Institute of Biochemistry and Biophysics , Federal Research Center "Kazan Scientific Center of RAS" , P.O. Box 30 , 420111 Kazan , Russian Federation
| | - Konstantin A Petrov
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
| | - Leniz F Nurullin
- Kazan Institute of Biochemistry and Biophysics , Federal Research Center "Kazan Scientific Center of RAS" , P.O. Box 30 , 420111 Kazan , Russian Federation
| | - Irek R Nizameev
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
| | - Asiya R Mustafina
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
| | - Oleg G Sinyashin
- Arbuzov Institute of Organic and Physical Chemistry , FRC Kazan Scientific Center of RAS , Arbuzov Str. 8 , 420088 Kazan , Russian Federation
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46
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Kanamori T, Takamura A, Tago N, Masaki Y, Ohkubo A, Sekine M, Seio K. Fluorescence enhancement of oligodeoxynucleotides modified with green fluorescent protein chromophore mimics upon triplex formation. Org Biomol Chem 2018; 15:1190-1197. [PMID: 28084483 DOI: 10.1039/c6ob01278g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP)-based molecular-rotor chromophores were attached to the 5-positions of deoxyuridines, and subsequently, incorporated into the middle positions of oligodeoxynucleotides. These oligonucleotides were designed to form triplex DNA in order to encapsulate the GFP chromophores, mimicking GFP structures. Upon triplex formation, the embedded GFP chromophores exhibited fluorescence enhancement, suggesting the potential application of these fluorescent probes for the detection of nucleic acids.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Takamura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Nobuhiro Tago
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
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47
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Xu C, Qian Y, Qi ZQ, Lu CG, Cui YP. A conjugated BODIPY–triphenylamine multi-aldoxime: Sonogashira coupling, ratiometric chemodosimeter and rapid detection of hypochlorite with two-photon excited fluorescence. NEW J CHEM 2018. [DOI: 10.1039/c8nj00368h] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The chemodosimeter is an off–on TPEF probe for detecting NaOCl selectively with red emission.
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Affiliation(s)
- Chao Xu
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Ying Qian
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- China
| | - Zheng-qing Qi
- Advanced Photonics Center
- Southeast University
- Nanjing
- China
| | - Chang-gui Lu
- Advanced Photonics Center
- Southeast University
- Nanjing
- China
| | - Yi-ping Cui
- Advanced Photonics Center
- Southeast University
- Nanjing
- China
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48
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Hu W, Zhao H, Jing J, Zhang X. A label-free ratiometric fluorescence strategy for 3′–5′ exonuclease detection. NEW J CHEM 2018. [DOI: 10.1039/c8nj03242d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A label-free ratiometric fluorescent biosensor for detection of exonuclease was proposed through utilizing two individual DNA conformation-specific dyes (DAPI and NMM).
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Affiliation(s)
- Wei Hu
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Hengzhi Zhao
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Jing Jing
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
| | - Xiaoling Zhang
- Key Laboratory of Cluster Science of Ministry of Education
- Beijing Key Laboratory of Photo-electronic/Electro-photonic Conversion Materials
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
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49
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Yanagi M, Suzuki A, Hudson RHE, Saito Y. A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2′-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift. Org Biomol Chem 2018; 16:1496-1507. [DOI: 10.1039/c8ob00062j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first example of a fluorescent adenosine analogue possessing simultaneous major- and minor-groove substitution selectively reports base-pairing to thymidine.
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Affiliation(s)
- Masaki Yanagi
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Azusa Suzuki
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
| | - Robert H. E. Hudson
- Department of Chemistry
- The University of Western Ontario
- London
- Canada N6A 5B7
| | - Yoshio Saito
- Department of Chemical Biology and Applied Chemistry
- College of Engineering
- Nihon University
- Koriyama
- Japan
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50
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Almeida-Marrero V, van de Winckel E, Anaya-Plaza E, Torres T, de la Escosura A. Porphyrinoid biohybrid materials as an emerging toolbox for biomedical light management. Chem Soc Rev 2018; 47:7369-7400. [DOI: 10.1039/c7cs00554g] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present article reviews the most important developing strategies in light-induced nanomedicine, based on the combination of porphyrinoid photosensitizers with a wide variety of biomolecules and biomolecular assemblies.
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Affiliation(s)
| | | | - Eduardo Anaya-Plaza
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
| | - Tomás Torres
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
- Institute for Advanced Research in Chemistry (IAdChem)
| | - Andrés de la Escosura
- Departamento de Química Orgánica
- Universidad Autónoma de Madrid
- Cantoblanco 28049
- Spain
- Institute for Advanced Research in Chemistry (IAdChem)
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