1
|
Lopina OD, Sidorenko SV, Fedorov DA, Klimanova EA. G-Quadruplexes as Sensors of Intracellular Na+/K + Ratio: Potential Role in Regulation of Transcription and Translation. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S262-S277. [PMID: 38621755 DOI: 10.1134/s0006297924140153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 04/17/2024]
Abstract
Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.
Collapse
Affiliation(s)
- Olga D Lopina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | | - Dmitry A Fedorov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | |
Collapse
|
2
|
Khatik SY, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy. Chem Sci 2023; 14:5627-5637. [PMID: 37265741 PMCID: PMC10231310 DOI: 10.1039/d3sc00519d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023] Open
Abstract
Paucity of efficient probes and small molecule ligands that can distinguish different G-quadruplex (GQ) topologies poses challenges not only in understanding their basic structure but also in targeting an individual GQ form from others. Alternatively, G-rich sequences that harbour unique chimeric structural motifs (e.g., GQ-duplex or GQ-hairpin junctions) are perceived as new therapeutic hotspots. In this context, the epidermal growth factor receptor (EGFR) gene, implicated in many cancers, contains a 30 nucleotide G-rich segment in the promoter region, which adopts in vitro two unique architectures each composed of a GQ topology (parallel and hybrid-type) juxtaposed with a hairpin domain. Here, we report the use of a novel dual-app probe, C5-trifluoromethyl benzofuran-modified 2'-deoxyuridine (TFBF-dU), in the systematic analysis of EGFR GQs and their interaction with small molecules by fluorescence and 19F NMR techniques. Notably, distinct fluorescence and 19F NMR signals exhibited by the probe enabled the quantification of the relative population of random, parallel and hybrid-type GQ structures under different conditions, which could not be obtained by conventional CD and 1H NMR techniques. Using the fluorescence component, we quantified ligand binding properties of GQs, whereas the 19F label enabled the assessment of ligand-induced changes in GQ dynamics. Studies also revealed that mutations in the hairpin domain affected GQ formation and stability, which was further functionally verified in polymerase stop assay. We anticipate that these findings and useful properties of the nucleoside probe could be utilized in designing and evaluating binders that jointly target both GQ and hairpin domains for enhanced selectivity and druggability.
Collapse
Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road Pune 411008 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road Pune 411008 India
| |
Collapse
|
3
|
Chang T, Li G, Ding Z, Li W, Zhu P, Lei W, Shangguan D. Potential G-quadruplexes within the Promoter Nuclease Hypersensitive Sites of the Heat-responsive Genes in Rice. Chembiochem 2022; 23:e202200405. [PMID: 36006168 DOI: 10.1002/cbic.202200405] [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: 07/18/2022] [Revised: 08/21/2022] [Indexed: 11/11/2022]
Abstract
G-quadruplexes (G4s) have been shown to be involved in the regulation of multiple cellular processes. Exploring putative G4-forming sequences (PQSs) in heat-responsive genes of rice and their folding structures under different conditions will help to understand the mechanism in response to heat stress. In this work, we discovered a prevalence of PQSs in nuclease hypersensitive sites within the promoters of heat-responsive genes. Moreover, 50% of the searched G3 PQSs ((G3+L1-7)3+G3+) locate in heat shock transcription factors. Circular dichroism spectroscopy, thermal difference spectroscopy, and UV melting analysis demonstrated the representative PQSs could adopt stable G4s at physiological temperature and potassium concentration. These PQSs were able to stall Klenow Fragment (KF) DNA polymerase by the formation of G4s. However, the G4s with Tm values around 50 - 60 oC could be increasingly unwound by KF with the increase of temperatures from 25 to 50 oC, implying these G4s could sense the changes in temperature by structural switch. This work offers fresh clue to understand the potential of G4-involved functions of PQSs and the molecular events in plants in the response to heat stress.
Collapse
Affiliation(s)
- Tianjun Chang
- Henan Polytechnic University, Institute of Enveiroment and Resoures, 2001 Shiji Avenue, 454003, Jiaozuo, CHINA
| | - Guangping Li
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Zhan Ding
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Weiguo Li
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Panpan Zhu
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Wei Lei
- Henan Polytechnic University, Institute of Resources and Environment, CHINA
| | - Dihua Shangguan
- Institute of Chemistry Chinese Academy of Sciences, Beijing National Laboratory for Molecular Sciences, Key Labor-atory of Analytical Chemistry for Living Biosystems, CAS Re-search/Education Center for Excellence in Molecular Sciences, CHINA
| |
Collapse
|
4
|
Kang Y, Wei C. Crescent‐shaped carbazole derivatives as light‐up fluorescence probes for G‐quadruplex DNA and live cell imaging. Chem Biodivers 2022; 19:e202101030. [DOI: 10.1002/cbdv.202101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Yongqiang Kang
- Shanxi University Institute of Molecular Science 92 Wucheng Road Taiyuan CHINA
| | - Chunying Wei
- Shanxi University Institute of Molecular Science No.92 Road Wucheng 030006 Taiyuan CHINA
| |
Collapse
|
5
|
Zhang X, Hu H, Liu W, Wang Y, Liu J, Wu P. Selective Heavy Atom Effect Forming Photosensitizing Hot Spots in Double-Stranded DNA Matrix. J Phys Chem Lett 2021; 12:9205-9212. [PMID: 34529435 DOI: 10.1021/acs.jpclett.1c02809] [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: 06/13/2023]
Abstract
Triplet exciton formation is essential for photosensitization-based photochemistry and photobiology. The heavy atom effect (HAE), in the form of either external or internal mode, is a basic mechanism for increasing the triplet exciton yield of photosensitizers. Herein, we report a new HAE mode by noncovalent cohosting of heavy atoms and photosensitizers in a double-stranded DNA (dsDNA) matrix. With dsDNA bearing several thymine (T) or cytosine (C) mismatches, heavy atoms (e.g., Hg2+ or Ag+) and dsDNA-staining dyes (photosensitizers) were spatially adjoined in close proximity, thus resulting in enhanced phosphorescence and 1O2 generation from the photosensitizers. The dsDNA-hosted HAE provides highly selective recognition for the heavy atoms, which is not applicable in either the external or the internal mode. Considering the simpleness and efficiency of the spatially adjoined HAE, as well as the functionality of DNA, the proposed HAE mode is appealing for various singlet oxygen- and phosphorescence-related applications.
Collapse
Affiliation(s)
- Xinfeng Zhang
- College of Material and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Hao Hu
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China
| | - Weiwei Liu
- College of Material and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yanying Wang
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Peng Wu
- Analytical & Testing Centre, Sichuan University, Chengdu 610064, China
| |
Collapse
|
6
|
Jin M, Li J, Chen Y, Zhao J, Zhang J, Zhang Z, Du P, Zhang L, Lu X. Near-Infrared Small Molecule as a Specific Fluorescent Probe for Ultrasensitive Recognition of Antiparallel Human Telomere G-Quadruplexes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32743-32752. [PMID: 34228441 DOI: 10.1021/acsami.1c07101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the past 10 years, many fluorescent probes have been developed to recognize G-quadruplexes (G4s) since G4s play an important role in biological systems. However, the selectivity and sensitivity of existing probes for G4s limit their further applications. Herein, we design and synthesize a new probe (TOVJ) by introducing 9-vinyljulolidine into TO. The new probe exhibits almost no fluorescence in an aqueous solution. Upon interacting with G4s, especially the antiparallel G4s, the fluorescence intensity was greatly enhanced (maximum 2742-fold) with a large Stokes shift of 198 nm and the maximum emission peak at 694 nm (near-infrared region). TOVJ showed high sensitivity and selectivity to G4s over other DNA topologies (ssDNA/dsDNA), especially to antiparallel G4s. For antiparallel human telomere G4 detection, the limits of detection of Hum24 and 22AG Na+ were as low as 164 and 231 pM, respectively. This indicates that TOVJ is a highly sensitive fluorescence sensor that can be effectively used for antiparallel human telomere G4 detection. The result of live-cell imaging showed that TOVJ could enter live cells and locate in the mitochondria.
Collapse
Affiliation(s)
- Ming Jin
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jing Li
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yang Chen
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jie Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jiahui Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhen Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Peiyao Du
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Libing Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xiaoquan Lu
- Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, People's Republic of China
| |
Collapse
|
7
|
Wickhorst PJ, Ihmels H. Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives. Chemistry 2021; 27:8580-8589. [PMID: 33855748 PMCID: PMC8252107 DOI: 10.1002/chem.202100297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/20/2022]
Abstract
The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106 M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104 M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106 M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103 M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.
Collapse
Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
| |
Collapse
|
8
|
Craciun AM, Rotaru A, Cojocaru C, Mangalagiu II, Danac R. New 2,9-disubstituted-1,10-phenanthroline derivatives with anticancer activity by selective targeting of telomeric G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119318. [PMID: 33360205 DOI: 10.1016/j.saa.2020.119318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Fifteen new 1,10-phenanthrolines disubstituted at positions 2 and 9 via amide bonds with different heterocycles have been designed and synthesized as G-quadruplex DNA stabilizers. Ten compounds were evaluated for the in vitro anticancer activity against 60 human tumor cell lines panel, four of them showing a very good inhibitory activity on several cell lines. To assess the ability of the most active compounds to interact with G-quadruplex DNA (G4-DNA), circular dichroism experiments were performed. The potency of the compounds to stabilize the G4-DNA has been shown from the thermal denaturation experiments. The mechanism of compounds binding to DNA and to G4-DNA was theoretically investigated by molecular docking studies. The experimental results demonstrated excellent capacity of the two compounds bearing two pyridin-3-yl residues (methylated and non-methylated) to act as selective G-quadruplex binders with promising anticancer activity.
Collapse
Affiliation(s)
- Anda-Mihaela Craciun
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania; "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Alexandru Rotaru
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Corneliu Cojocaru
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Ionel I Mangalagiu
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania
| | - Ramona Danac
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania.
| |
Collapse
|
9
|
Gratal PB, Quero JG, Pérez-Redondo A, Gándara Z, Gude L. PhenQE8, a Novel Ligand of the Human Telomeric Quadruplex. Int J Mol Sci 2021; 22:E749. [PMID: 33451070 PMCID: PMC7828518 DOI: 10.3390/ijms22020749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 01/02/2023] Open
Abstract
A novel quadruplex ligand based on 1,10-phenanthroline and incorporating two guanyl hydrazone functionalities, PhenQE8, is reported herein. Synthetic access was gained in a two-step procedure with an overall yield of 61%. X-ray diffraction studies revealed that PhenQE8 can adopt an extended conformation that may be optimal to favor recognition of quadruplex DNA. DNA interactions with polymorphic G-quadruplex telomeric structures were studied by different techniques, such as Fluorescence resonance energy transfer (FRET) DNA melting assays, circular dichroism and equilibrium dialysis. Our results reveal that the novel ligand PhenQE8 can efficiently recognize the hybrid quadruplex structures of the human telomeric DNA, with high binding affinity and quadruplex/duplex selectivity. Moreover, the compound shows significant cytotoxic activity against a selected panel of cultured tumor cells (PC-3, HeLa and MCF-7), whereas its cytotoxicity is considerably lower in healthy human cells (HFF-1 and RPWE-1).
Collapse
Affiliation(s)
| | | | | | - Zoila Gándara
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| |
Collapse
|
10
|
Yu QQ, Gao JJ, Lang XX, Li HY, Wang MQ. Microenvironment-Sensitive Fluorescent Ligand Binds Ascaris Telomere Antiparallel G-Quadruplex DNA with Blue-Shift and Enhanced Emission. Chembiochem 2020; 22:1042-1048. [PMID: 33140570 DOI: 10.1002/cbic.202000671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
The development of small molecules that can selectively target G-quadruplex (G4) DNAs has drawn considerable attention due to their unique physiological and pathological functions. However, only a few molecules have been found to selectively bind a particular G4 DNA structure. We have developed a fluorescence ligand Q1, a molecular scaffold with a carbazole-pyridine core bridged by a phenylboronic acid side chain, that acts as a selective ascaris telomere antiparallel G4 DNA ASC20 ligand with about 18 nm blue-shifted and enhanced fluorescence intensity. Photophysical properties revealed that Q1 was sensitive to the microenvironment and gave the best selectivity to ASC20 with an equilibrium binding constant Ka =6.04×105 M-1 . Time-resolved fluorescence studies also demonstrated that Q1 showed a longer fluorescence lifetime in the presence of ASC20. The binding characteristics of Q1 with ASC20 were shown in detail in a fluorescent intercalator displacement (FID) assay, a 2-Ap titration experiment and by molecular docking. Ligand Q1 could adopt an appropriate pose at terminal G-quartets of ASC20 through multiple interactions including π-π stacking between aromatic rings; this led to strong fluorescence enhancement. In addition, a co-staining image showed that Q1 is mainly distributed in the cytoplasm. Accordingly, this work provides insights for the development of ligands that selectively targeting a specific G4 DNA structure.
Collapse
Affiliation(s)
- Quan-Qi Yu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Juan-Juan Gao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Xue-Xian Lang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Hong-Yao Li
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| |
Collapse
|
11
|
Recent advances in fluorescent probes for G-quadruplex nucleic acids. Biochem Biophys Res Commun 2020; 531:18-24. [DOI: 10.1016/j.bbrc.2020.02.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/07/2019] [Accepted: 02/18/2020] [Indexed: 01/31/2023]
|
12
|
Singh M, Wang S, Joo H, Ye Z, Christison KM, Hekman R, Vierra C, Xue L. Use of neomycin as a structured amino-containing side chain motif for phenanthroline-based G-quadruplex ligands and telomerase inhibitors. Chem Biol Drug Des 2020; 96:1292-1304. [PMID: 32516846 DOI: 10.1111/cbdd.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/31/2020] [Indexed: 01/05/2023]
Abstract
In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by several biophysical studies. Compound 7 shows good selectivity for G-quadruplex (G4) DNA over duplex DNA. The binding of 7 with G1 is predominantly enthalpy-driven, and the binding stoichiometry of 7 with G1 is one for the tight-binding event as determined by ESI mass spectrometry. A plausible binding mode is a synergistic effect of end-stacking and groove interactions, as indicated by docking studies. Compound 7 can inhibit human telomerase activity at low micromolar concentrations, which is more potent than previously reported 5-substituted phenanthroline derivatives.
Collapse
Affiliation(s)
- Mandeep Singh
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Zhihan Ye
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | | | - Ryan Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Craig Vierra
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| |
Collapse
|
13
|
In-Gel Probing Polymorphic Structures of G-Quadruplexes Derived from c-Myc Promoter. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
14
|
Zhang L, Liu X, Lu S, Liu J, Zhong S, Wei Y, Bing T, Zhang N, Shangguan D. Thiazole Orange Styryl Derivatives as Fluorescent Probes for G-Quadruplex DNA. ACS APPLIED BIO MATERIALS 2020; 3:2643-2650. [DOI: 10.1021/acsabm.9b01243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Lingling Zhang
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Lu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Zhong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongbiao Wei
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Guangxi Medical University, No. 22, Shuangyong Road, Nanning 530021, Guangxi, PR China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
15
|
Xie X, Zuffo M, Teulade-Fichou MP, Granzhan A. Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries. Beilstein J Org Chem 2019; 15:1872-1889. [PMID: 31467609 PMCID: PMC6693400 DOI: 10.3762/bjoc.15.183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.
Collapse
Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Michela Zuffo
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| |
Collapse
|
16
|
Evaluation of the selectivity of G-quadruplex ligands in living cells with a small molecule fluorescent probe. Anal Chim Acta X 2019; 2:100017. [PMID: 33117978 PMCID: PMC7587023 DOI: 10.1016/j.acax.2019.100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/17/2019] [Indexed: 11/22/2022] Open
Abstract
G-quadruplex has been an emerging target for drug design due to its physiologically important roles in oncology. A number of quadruplex-interactive ligands have been developed by synthetic and medicinal chemists over the past decades. However, the great challenge still remains that the method for detecting the specific targeting of these ligands to the G-quadruplex structures in cells is still lacking. Herein, a detection system for directly identifying the specific targeting of a ligand to DNA G-quadruplexes in cells was constructed by using a small-molecular fluorescent probe (IMT) as a fluorescent indicator. Four typical ligands have been successfully evaluated, demonstrating the promising application of this detection system in the screening and evaluation of quadruplex-specific therapeutic agents.
Collapse
|
17
|
Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
Collapse
Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| |
Collapse
|
18
|
Chen H, Sun H, Zhang S, Yan W, Li Q, Guan A, Xiang J, Liu M, Tang Y. Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures. Chem Commun (Camb) 2019; 55:5060-5063. [DOI: 10.1039/c9cc01263j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.
Collapse
Affiliation(s)
- Hongbo Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Suge Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Wenpeng Yan
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Junfeng Xiang
- Center for Physiochemical Analysis & Measurement
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Meirong Liu
- Center for Physiochemical Analysis & Measurement
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| |
Collapse
|
19
|
Jin M, Liu X, Zhang X, Wang L, Bing T, Zhang N, Zhang Y, Shangguan D. Thiazole Orange-Modified Carbon Dots for Ratiometric Fluorescence Detection of G-Quadruplex and Double-Stranded DNA. ACS APPLIED MATERIALS & INTERFACES 2018; 10:25166-25173. [PMID: 29979027 DOI: 10.1021/acsami.8b07869] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A new carbon dot (CD)-based nanoprobe for the ratiometric fluorescence detection of DNA was constructed in this work. Thiazole orange (TO), a specific organic small molecular probe toward DNA, is covalently linked to the surface of CDs, acting as the recognition element and the fluorescence response unit. In the absence of DNA, the nanoprobe only emitted the blue fluorescence of CDs, whereas TO was almost nonfluorescent. Upon addition of DNA, a turn-on emission at 530 nm appeared and gradually enhanced along with the increasing of the target DNA, whereas the fluorescence of CDs was unchanged, which realized the ratiometric detection of the target DNA. The CD-TO nanoprobe showed good selectivity to parallel G-quadruplex (G4) and double-stranded (ds) DNA over antiparallel G4 and single-stranded DNA. Moreover, the ratiometric fluorescence nanoprobe exhibited high sensitivity for ssab (a dsDNA) and c-myc (a parallel G4) with a low detection limit of 0.90 and 3.31 nM, respectively. Additionally, the G4/hemin peroxidase activity inhibition experiment demonstrated that CD-TO bound to the G4s through the end-stacking mode.
Collapse
Affiliation(s)
- Ming Jin
- College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou 730000 , China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
| | - Yun Zhang
- College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou 730000 , China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| |
Collapse
|
20
|
Xie X, Reznichenko O, Chaput L, Martin P, Teulade-Fichou MP, Granzhan A. Topology-Selective, Fluorescent “Light-Up” Probes for G-Quadruplex DNA Based on Photoinduced Electron Transfer. Chemistry 2018; 24:12638-12651. [DOI: 10.1002/chem.201801701] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Ludovic Chaput
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
- CNRS UPR2301; Institut de Chimie des Substances Naturelles (ICSN); 91198 Gif-sur-Yvette France
| | - Pascal Martin
- ITODYS, CNRS UMR7086; Université Paris Diderot; 75205 Paris France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| |
Collapse
|
21
|
Bonaccorso C, Cesaretti A, Elisei F, Mencaroni L, Spalletti A, Fortuna CG. New Styryl Phenanthroline Derivatives as Model D-π-A-π-D Materials for Non-Linear Optics. Chemphyschem 2018; 19:1917-1929. [PMID: 29702737 DOI: 10.1002/cphc.201800391] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 11/06/2022]
Abstract
Four novel push-pull systems combining a central phenanthroline acceptor moiety and two substituted benzene rings, as a part of the conjugated π-system between the donor and the acceptor moieties, have been synthetized through a straightforward and efficient one-step procedure. The chromophores display high fluorescence and a peculiar fluorosolvatochromic behaviour. Ultrafast investigation by means of state-of-the-art femtosecond-resolved transient absorption and fluorescence up-conversion spectroscopies allowed the role of intramolecular charge transfer (ICT) states to be evidenced, also revealing the crucial role played by both, the polarity and proticity of the medium on the excited state dynamics of the chromophores. The ICT processes, responsible for the solvatochromism, also lead to interesting non-linear optical (NLO) properties: namely great two photon absorption cross-sections (hundreds of GM), investigated by the Two Photon Excited Fluorescence (TPEF) technique, and large second order hyperpolarizability coefficients, estimated through a convenient solvatochromic method.
Collapse
Affiliation(s)
- Carmela Bonaccorso
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125, Catania, Italy
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Letizia Mencaroni
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Anna Spalletti
- Department of Chemistry, Biology and Biotechnology and Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Cosimo G Fortuna
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125, Catania, Italy
| |
Collapse
|
22
|
Gu Y, Lin D, Tang Y, Fei X, Wang C, Zhang B, Zhou J. A light-up probe targeting for Bcl-2 2345 G-quadruplex DNA with carbazole TO. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:180-188. [PMID: 29032342 DOI: 10.1016/j.saa.2017.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/25/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
As its significant role, the selective recognition of G-quadruplex with specific structures and functions is important in biological and medicinal chemistry. Carbazole derivatives have been reported as a kind of fluorescent probe with many excellent optical properties. In the present study, the fluorescence of the dye (carbazole TO) increased almost 70 fold in the presence of bcl-2 2345 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10-30 fold than those in the presence of other DNAs. The binding study results by activity inhibition of G4/Hemin peroxidase experiment, NMR titration and molecular docking simulation showed the high affinity and selectivity to bcl-2 2345 G4 arises from its end-stacking interaction with G-quartet. It is said that a facile approach with excellent sensitive, good selectivity and quick response for bcl-2 2345 G-quadruplex was developed and may be used for antitumor recognition or antitumor agents.
Collapse
Affiliation(s)
- Yingchun Gu
- Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing 100190, China; School of Science, Tianjin Chengjian University, Tianjin 300384, China
| | - Dayong Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yalin Tang
- Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing 100190, China.
| | - Xuening Fei
- School of Science, Tianjin Chengjian University, Tianjin 300384, China; School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Cuihong Wang
- School of Science, Tianjin Chengjian University, Tianjin 300384, China
| | - Baolian Zhang
- School of Science, Tianjin Chengjian University, Tianjin 300384, China
| | - Jianguo Zhou
- School of Science, Tianjin Chengjian University, Tianjin 300384, China
| |
Collapse
|
23
|
Wang MQ, Liu XN, Guo ZJ, Feng C, Rui M. Synthesis of quinolinium-based probes and studies of their effects for selective G-quadruplex DNA targeting. NEW J CHEM 2018. [DOI: 10.1039/c8nj00203g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two quinolinium conjugates as G-quadruplex probes were presented. The binding properties and mechanism were investigated using both experimental and docking studies.
Collapse
Affiliation(s)
- Ming-Qi Wang
- School of Pharmacy
- Jiangsu University
- Zhenjiang
- P. R. China
| | - Xiao-Ning Liu
- School of Pharmacy
- Jiangsu University
- Zhenjiang
- P. R. China
| | - Zhong-Jian Guo
- Institute of Life Sciences
- Jiangsu University
- Zhenjiang
- P. R. China
| | - Chunlai Feng
- School of Pharmacy
- Jiangsu University
- Zhenjiang
- P. R. China
| | - Mengjie Rui
- School of Pharmacy
- Jiangsu University
- Zhenjiang
- P. R. China
| |
Collapse
|
24
|
Suseela YV, Narayanaswamy N, Pratihar S, Govindaraju T. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem Soc Rev 2018; 47:1098-1131. [DOI: 10.1039/c7cs00774d] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our review presents the recent progress on far-red fluorescent probes of canonical and non-canonical nucleic acid (NA) structures, critically discusses the design principles, applications, limitations and outline the future prospects of developing newer probes with target-specificity for different NA structures.
Collapse
Affiliation(s)
- Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| |
Collapse
|
25
|
Das RN, Chevret E, Desplat V, Rubio S, Mergny JL, Guillon J. Design, Synthesis and Biological Evaluation of New Substituted Diquinolinyl-Pyridine Ligands as Anticancer Agents by Targeting G-Quadruplex. Molecules 2017; 23:molecules23010081. [PMID: 29301210 PMCID: PMC6017375 DOI: 10.3390/molecules23010081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4) are stacked non-canonical nucleic acid structures found in specific G-rich DNA or RNA sequences in the human genome. G4 structures are liable for various biological functions; transcription, translation, cell aging as well as diseases such as cancer. These structures are therefore considered as important targets for the development of anticancer agents. Small organic heterocyclic molecules are well known to target and stabilize G4 structures. In this article, we have designed and synthesized 2,6-di-(4-carbamoyl-2-quinolyl)pyridine derivatives and their ability to stabilize G4-structures have been determined through the FRET melting assay. It has been established that these ligands are selective for G4 over duplexes and show a preference for the parallel conformation. Next, telomerase inhibition ability has been assessed using three cell lines (K562, MyLa and MV-4-11) and telomerase activity is no longer detected at 0.1 μM concentration for the most potent ligand 1c. The most promising G4 ligands were also tested for antiproliferative activity against the two human myeloid leukaemia cell lines, HL60 and K562.
Collapse
Affiliation(s)
- Rabindra Nath Das
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Edith Chevret
- Université de Bordeaux, INSERM U1053, Cutaneous Lymphoma Oncogenesis Team, 33076 Bordeaux CEDEX, France.
| | - Vanessa Desplat
- Université de Bordeaux, INSERM U1035, Cellules souches hématopoïétiques normales et leucémiques, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Sandra Rubio
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| | - Jean-Louis Mergny
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
- Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jean Guillon
- Université de Bordeaux, ARNA laboratory, INSERM U1212, UMR CNRS 5320, UFR des Sciences Pharmaceutiques, 33076 Bordeaux CEDEX, France.
| |
Collapse
|
26
|
Chang T, Li W, Ding Z, Cheng S, Liang K, Liu X, Bing T, Shangguan D. Detection of G-Quadruplex Structures Formed by G-Rich Sequences from Rice Genome and Transcriptome Using Combined Probes. Anal Chem 2017; 89:8162-8169. [DOI: 10.1021/acs.analchem.7b01992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Tianjun Chang
- Department
of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, People’s Republic of China
| | - Weiguo Li
- Department
of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, People’s Republic of China
| | - Zhan Ding
- Department
of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, People’s Republic of China
| | - Shaofei Cheng
- Department
of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, People’s Republic of China
| | - Kun Liang
- Department
of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, People’s Republic of China
| | - Xiangjun Liu
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, CAS Research/Education Center for
Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Bing
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, CAS Research/Education Center for
Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dihua Shangguan
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, CAS Research/Education Center for
Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
27
|
Zhang X, Wei Y, Bing T, Liu X, Zhang N, Wang J, He J, Jin B, Shangguan D. Development of squaraine based G-quadruplex ligands using click chemistry. Sci Rep 2017; 7:4766. [PMID: 28684846 PMCID: PMC5500484 DOI: 10.1038/s41598-017-04344-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 12/23/2022] Open
Abstract
The G-quadruplex (G4) structures of nucleic acids are considered to play an intrinsic role in gene expression. To this end, the development of new G4 ligands has attracted extensive research interests towards potential applications as G4-targeted drugs and molecular probes. To date, the majority of G4 ligands have been composed of an extended planar aromatic scaffold that interacts with the terminal G-tetrad plane via π-π interactions, and various side chains that interact with the sugar-phosphate backbone, loops or grooves of the G4 structures. The side chains act to modulate the affinity and selectivity of the G4 ligands, alongside influencing their biodistribution. Here, we present a click chemistry methodology to generate a series of squaraine-based G4 ligand derivatives based on our previously reported G4 probe (named CSTS) but with varing side chains. We find that importantly these new G4 ligand derivatives retain the G4 selectivity, optical properties and low cytotoxicity of CSTS, but exhibit different binding behaviors to G4 structures, and distinct cellular uptake efficiencies. Indeed, of these new complexes, several exhibit much higher affinity and cellular uptake than CSTS. Overall, this novel, facile and highly effective strategy has significant future potential for the high-throughput screening of G4 ligands or probes targeted towards in vivo applications.
Collapse
Affiliation(s)
- Xin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongbiao Wei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Tao Bing
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Junyan Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Junqing He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Bing Jin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of the Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
28
|
Liu W, Wang S, Dotsenko IA, Samoshin VV, Xue L. Arylsulfanyl groups - Suitable side chains for 5-substituted 1,10-phenanthroline and nickel complexes as G4 ligands and telomerase inhibitors. J Inorg Biochem 2017; 173:12-20. [PMID: 28476011 DOI: 10.1016/j.jinorgbio.2017.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/14/2017] [Accepted: 04/21/2017] [Indexed: 01/03/2023]
Abstract
Guanine-rich DNA sequences can undergo self-assembly into unique G-quadruplex structures that interfere with the binding of proteins to the same DNA region. The formation of DNA G-quadruplexes requires monovalent cations (Na+ and K+) or small molecules known as G-quadruplex (G4) ligands. Phenanthroline is a type of G4 ligand scaffold known for its coordination with metal ions to form complexes with a large aromatic surface area, which aptly stack with G-quartets. In this report, we have investigated the side chain effect on G-quadruplex recognition by evaluating a series of 5-substituted phenanthroline-based metal complexes (Phen-Ni) binding to telomeric G-quadruplex DNA. Results from biophysical methods including fluorescence and circular dichroism (CD) thermal denaturation, CD titration, and the fluorescent intercalator displacement (FID) assay suggest that several Phen-Ni complexes bind to G-quadruplex DNA with submicromolar G4DC50 values. Arylsulfanyl groups at the 5 position of 1,10-phenanthroline are the best side chains regarding binding affinity and selectivity towards G-quadruplex DNA. Most of the G-quadruplex binding Phen-Ni complexes can inhibit telomerase activity in vitro as indicated by the telomeric repeat amplification protocol (TRAP) assay and such inhibition is clearly concentration dependent. Our results here provide a guidance of utilizing 5-substituted phenanthroline derivatives as a viable and facile approach to design novel G4 ligands.
Collapse
Affiliation(s)
- Wanbo Liu
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Irina A Dotsenko
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Vyacheslav V Samoshin
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States.
| |
Collapse
|
29
|
Jiang G, Chen X, Xu L, Cao Y, Hong S, Liu M, Cao W, Pei R. Design and Synthesis of a Dimethylindole Red Trimer: A New Light-Up Red-Emitting Fluorescent Probe for G-Quadruplexes. ChemistrySelect 2017. [DOI: 10.1002/slct.201601889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Guimei Jiang
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xing Chen
- Public Health of Guangxi Medical University; Nanning 530021 China
| | - Lijun Xu
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Yi Cao
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Shanni Hong
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Min Liu
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| | - Weiguo Cao
- Department of Chemistry, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface; Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences; Suzhou 215123 China
| |
Collapse
|
30
|
Pithan PM, Decker D, Druzhinin SI, Ihmels H, Schönherr H, Voß Y. 8-Styryl-substituted coralyne derivatives as DNA binding fluorescent probes. RSC Adv 2017; 7:10660-10667. [PMID: 28496973 PMCID: PMC5361113 DOI: 10.1039/c6ra27684a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022] Open
Abstract
8-Styryl-substituted coralyne derivatives bind to duplex and quadruplex DNA and may be used for fluorimetric staining of nucleoli in cells.
Six new 8-styryl-substituted coralyne derivatives 4a–f were synthesized from coralyne (2) by a base catalysed Knoevenagel type reaction. It was shown by photometric and fluorimetric titrations of double stranded and quadruplex DNA to 4b–d as well as by fluorimetric DNA denaturation experiments that these ligands bind to DNA with different binding modes at varying ligand-DNA ratios (LDR). Specifically, the addition of DNA caused initially a hypochromic effect in absorbance and, at a particular LDR, the development of a new red shifted absorption band with a hyperchromic effect. Furthermore, 4b–d induced a significant and selective stabilization of quadruplex DNA towards unfolding (ΔTm = 31.6–32.9 °C at LDR = 5), which is even more pronounced as compared to the parent compound coralyne (2). Most notably, the addition of DNA to the dimethylamino-substituted derivative 4b leads to a new, strongly red-shifted emission band at 695 nm. Hence, this derivative is a fluorescent probe that changes its fluorescence colour from green to red in the presence of DNA and even allows the fluorimetric analysis of living cells by staining of the nucleoli.
Collapse
Affiliation(s)
- P M Pithan
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - D Decker
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - S I Druzhinin
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - H Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - H Schönherr
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Y Voß
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| |
Collapse
|
31
|
Guo Y, Chen Q, Qi Y, Xie Y, Qian H, Yao W, Pei R. Label-free ratiometric DNA detection using two kinds of interaction-responsive emission dyes. Biosens Bioelectron 2017; 87:320-324. [DOI: 10.1016/j.bios.2016.08.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/03/2016] [Accepted: 08/13/2016] [Indexed: 11/17/2022]
|
32
|
Sabale PM, Srivatsan SG. Responsive Fluorescent PNA Analogue as a Tool for Detecting G-quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome-Inactivating Proteins. Chembiochem 2016; 17:1665-73. [PMID: 27271025 DOI: 10.1002/cbic.201600192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/13/2022]
Abstract
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic-acid-based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment-sensitive 5-(benzofuran-2-yl)- and 5-(benzothiophen-2-yl)-uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene-modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn-on detection of G-quadruplex-forming promoter DNA sequences of human proto-oncogenes (c-myc and c-kit). Furthermore, the ability of benzothiophene-modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome-inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids.
Collapse
Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
| |
Collapse
|
33
|
Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
Collapse
Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| |
Collapse
|