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Roy L, Roy A, Bose D, Banerjee N, Chatterjee S. Unraveling the structural aspects of the G-quadruplex in SMO promoter and elucidating its contribution in transcriptional regulation. J Biomol Struct Dyn 2023:1-16. [PMID: 37878583 DOI: 10.1080/07391102.2023.2268200] [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: 07/24/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023]
Abstract
We located a 25 nt G-rich sequence in the promoter region of SMO oncogene. We performed an array of biophysical and biochemical assays and confirmed the formation of a parallel G quadruplex (SMO1-GQ) by the identified sequence. SMO1-GQ is highly conserved in primates. For a comprehensive characterization of the SMO quadruplex structure, we have performed spectroscopic and in silico analysis with established GQ binder small molecules TMPyP4 and BRACO-19. We observed comparatively higher stable interaction of BRACO-19 with SMO1-GQ. Structure-based, rational drug design against SMO1-GQ to target SMO oncogene requires a detailed molecular anatomy of the G-quadruplex. We structurally characterised the SMO1-GQ using DMS footprinting assay and molecular modelling, docking, and MD simulation to identify the probable atomic regions that interact with either of the small molecules. We further investigated SMO1-GQ in vivo by performing chromatin immunoprecipitation (ChIP) assay. ChIP data revealed that this gene element functions as a scaffold for a number of transcription factors: specificity protein (Sp1), nucleolin (NCL), non-metastatic cell 2 (NM23-H2), cellular nucleic acid binding protein (CNBP), and heterogeneous nuclear ribonucleoprotein K (hnRNPK) which reflects the SMO1-P1 G-quadruplex to be the master regulator of SMO1 transcriptional activity. The strong binding interaction detected between SMO1-GQ and BRACO-19 contemplates the potential of the G quadruplex as a promising anti-cancer druggable target to downregulate SMO1 oncogene driven cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laboni Roy
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Ananya Roy
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Debopriya Bose
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Science, Bose Institute, Kolkata, West Bengal, India
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2
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Berrones Reyes J, Sherin PS, Sarkar A, Kuimova MK, Vilar R. Platinum(II)-Based Optical Probes for Imaging Quadruplex DNA Structures via Phosphorescence Lifetime Imaging Microscopy. Angew Chem Int Ed Engl 2023; 62:e202310402. [PMID: 37642538 PMCID: PMC10952808 DOI: 10.1002/anie.202310402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 08/31/2023]
Abstract
G-quadruplex DNA is a non-canonical structure that forms in guanine-rich regions of the genome. There is increasing evidence showing that G-quadruplexes have important biological functions, and therefore molecular tools to visualise these structures are important. Herein we report on a series of new cyclometallated platinum(II) complexes which, upon binding to G-quadruplex DNA, display an increase in their phosphorescence, acting as switch-on probes. More importantly, upon binding to G-quadruplexes they display a selective and distinct lengthening of their emission lifetime. We show that this effect can be used to selectively visualise these structures in cells using Phosphorescence Lifetime Imaging Microscopy (PLIM).
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Affiliation(s)
- Jessica Berrones Reyes
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Peter S. Sherin
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Amrita Sarkar
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Ramon Vilar
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
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3
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Berrones Reyes J, Sherin PS, Sarkar A, Kuimova MK, Vilar R. Platinum(II)-Based Optical Probes for Imaging Quadruplex DNA Structures via Phosphorescence Lifetime Imaging Microscopy. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202310402. [PMID: 38516271 PMCID: PMC10952342 DOI: 10.1002/ange.202310402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Indexed: 03/23/2024]
Abstract
G-quadruplex DNA is a non-canonical structure that forms in guanine-rich regions of the genome. There is increasing evidence showing that G-quadruplexes have important biological functions, and therefore molecular tools to visualise these structures are important. Herein we report on a series of new cyclometallated platinum(II) complexes which, upon binding to G-quadruplex DNA, display an increase in their phosphorescence, acting as switch-on probes. More importantly, upon binding to G-quadruplexes they display a selective and distinct lengthening of their emission lifetime. We show that this effect can be used to selectively visualise these structures in cells using Phosphorescence Lifetime Imaging Microscopy (PLIM).
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Affiliation(s)
- Jessica Berrones Reyes
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Peter S. Sherin
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Amrita Sarkar
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
| | - Ramon Vilar
- Department of ChemistryImperial College LondonWhite City Campus82 Wood LaneLondonW12 0BZUK
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4
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Fukuda H, Zou T, Fujii S, Sato S, Wakahara D, Higashi S, Tseng TY, Chang TC, Yada N, Matsuo K, Habu M, Tominaga K, Takeuchi H, Takenaka S. Cyclic anthraquinone derivatives, unique G-quadruplex binders, selectively induce cancer cell apoptosis and inhibit tumor growth. PNAS NEXUS 2023; 2:pgad211. [PMID: 37416876 PMCID: PMC10319625 DOI: 10.1093/pnasnexus/pgad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/14/2023] [Indexed: 07/08/2023]
Abstract
Cyclic anthraquinone derivatives (cAQs), which link two side chains of 1,5-disubstituted anthraquinone as a threading DNA intercalator, have been developed as G-quartet (G4) DNA-specific ligands. Among the cAQs, cAQ-mBen linked through the 1,3-position of benzene had the strongest affinity for G4 recognition and stabilization in vitro and was confirmed to bind to the G4 structure in vivo, selectively inhibiting cancer cell proliferation in correlation with telomerase expression levels and triggering cell apoptosis. RNA-sequencing analysis further indicated that differentially expressed genes regulated by cAQ-mBen were profiled with more potential quadruplex-forming sequences. In the treatment of the tumor-bearing mouse model, cAQ-mBen could effectively reduce tumor tissue and had less adverse effects on healthy tissue. These results suggest that cAQ-mBen can be a potential cancer therapeutic agent as a G4 binder.
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Affiliation(s)
| | | | | | | | - Daiki Wakahara
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Sen Higashi
- Division of Applied Pharmacology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Ting-Yuan Tseng
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Naomi Yada
- Division of Oral Pathology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Kou Matsuo
- Division of Oral Pathology, Department of Health Promotion, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Manabu Habu
- Division of Oral and Maxillofacial Surgery, Department of Science of Physical Functions, Kyushu Dental University, Fukuoka 803-8580, Japan
| | - Kazuhiro Tominaga
- Division of Oral and Maxillofacial Surgery, Department of Science of Physical Functions, Kyushu Dental University, Fukuoka 803-8580, Japan
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5
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Gudanis D, Zielińska K, Baranowski D, Kierzek R, Kozłowski P, Gdaniec Z. Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex-Duplex Hybrid Formation. Biomolecules 2021; 11:biom11081236. [PMID: 34439902 PMCID: PMC8392043 DOI: 10.3390/biom11081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 12/02/2022] Open
Abstract
In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.
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Affiliation(s)
- Dorota Gudanis
- Correspondence: (D.G.); (Z.G.); Tel.: +48-61-852-85-03 (ext. 1286) (D.G.)
| | | | | | | | | | - Zofia Gdaniec
- Correspondence: (D.G.); (Z.G.); Tel.: +48-61-852-85-03 (ext. 1286) (D.G.)
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6
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Lago S, Nadai M, Cernilogar FM, Kazerani M, Domíniguez Moreno H, Schotta G, Richter SN. Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome. Nat Commun 2021; 12:3885. [PMID: 34162892 PMCID: PMC8222265 DOI: 10.1038/s41467-021-24198-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cell identity is maintained by activation of cell-specific gene programs, regulated by epigenetic marks, transcription factors and chromatin organization. DNA G-quadruplex (G4)-folded regions in cells were reported to be associated with either increased or decreased transcriptional activity. By G4-ChIP-seq/RNA-seq analysis on liposarcoma cells we confirmed that G4s in promoters are invariably associated with high transcription levels in open chromatin. Comparing G4 presence, location and transcript levels in liposarcoma cells to available data on keratinocytes, we showed that the same promoter sequences of the same genes in the two cell lines had different G4-folding state: high transcript levels consistently associated with G4-folding. Transcription factors AP-1 and SP1, whose binding sites were the most significantly represented in G4-folded sequences, coimmunoprecipitated with their G4-folded promoters. Thus, G4s and their associated transcription factors cooperate to determine cell-specific transcriptional programs, making G4s to strongly emerge as new epigenetic regulators of the transcription machinery.
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Affiliation(s)
- Sara Lago
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Maryam Kazerani
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Helena Domíniguez Moreno
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Martinsried, Germany.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy.
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7
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Influence of core extension and side chain nature in targeting G-quadruplex structures with perylene monoimide derivatives. Bioorg Chem 2021; 108:104660. [PMID: 33550073 DOI: 10.1016/j.bioorg.2021.104660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/31/2022]
Abstract
A structure-activity relationship (SAR) study in terms of G-quadruplex binding ability and antiproliferative activity of six fluorescent perylenemonoimide (PMIs) derivatives is reported. A positive charge seems to be the key to target G4. This study also reveals the importance of the element substitution in the potential biological activity of PMIs, being the polyethylene glycol (PEG) chains in the peri position responsible for their antiproliferative activity. Among them, the cationic PMI6 with two PEG chains is the most promising compound since its fluorescence is enhanced in the presence of G-quadruplex structures. Moreover, PMI6 binds to the human telomeric G-quadruplex hTelo with high affinity and displays a high antiproliferative potential towards HeLa (cervical adenocarcinoma), A549 (lung adenocarcinoma) and A2780 (ovarian adenocarcinoma) cells. Its fate can be followed inside cells thanks to its fluorescent properties: the compound is found to accumulate in the mitochondria.
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8
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Takenaka S. Detection of Tetraplex DNA and Detection by Tetraplex DNA. ANAL SCI 2021; 37:9-15. [PMID: 33132237 DOI: 10.2116/analsci.20sar09] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
G-quardruplex (G4) DNA forms through the gathering together of G-quartet planes formed with four guanine (G) bases. G4 DNA stabilizes with potassium ions (K+) by coordination with the G-quartet center. Fluorometric G4 DNA carrying the fluorescence resonance energy transfer (FRET) chromophore pair at both termini has been applied for the fluorometric sensing or imaging of K+ under a homogeneous aqueous medium. This system has realized non-conventional K+ selectivity over the sodium ion (Na+). The selectivity of the fluorescence G4 was converted to Na+ from K+ with a modification of its sequence. On the other hand, G4 DNA detection has been achieved in terms of cancer diagnosis because of a strong relationship of G4 DNA and cancer development. Ligands interacting with G4 are expected to have anti-cancer potential. In addition, fluorometric G4 ligands have been developed and tested as tools for the dynamic monitoring of G4 in living cells. Moreover, fluorometric G4 DNA has been utilized to evaluate the G4 ligand performance.
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Affiliation(s)
- Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, 804-8550, Japan
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9
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Visualising G-quadruplex DNA dynamics in live cells by fluorescence lifetime imaging microscopy. Nat Commun 2021; 12:162. [PMID: 33420085 PMCID: PMC7794231 DOI: 10.1038/s41467-020-20414-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4s). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with fluorescence lifetime imaging microscopy (FLIM) can identify G4s within nuclei of live and fixed cells. We present a FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4s and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4s in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo. Direct observation of G-quadruplexes (G4s) in live cells is challenging. Here the authors report a method to identify G4s within the nuclei of live and fixed cells using a fluorescent probe combined with fluorescence lifetime imaging microscopy.
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10
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Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, Hao YH, Zhao Y, Tan Z. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res 2020; 48:11706-11720. [PMID: 33045726 PMCID: PMC7672459 DOI: 10.1093/nar/gkaa841] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Jia-yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Juan-nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yong Zhao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P.R. China
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Gudanis D, Kaniowski D, Kulik K, Baranowski D, Gdaniec Z, Nawrot B. Formation of an RNA Quadruplex-Duplex Hybrid in Living Cells between mRNA of the Epidermal Growth Factor Receptor (EGFR) and a G-Rich Antisense Oligoribonucleotide. Cells 2020; 9:cells9112375. [PMID: 33138194 PMCID: PMC7692301 DOI: 10.3390/cells9112375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023] Open
Abstract
Antisense DNA oligonucleotides, short interfering RNAs (siRNAs), and CRISPR/Cas9 genetic tools are the most useful therapeutic nucleic acids regulating gene expression based on the antisense specificity towards messenger RNA. Here, we present an effective novel strategy for inhibiting translation based on the antisense-controlled formation of an RNA quadruplex-duplex hybrid (QDH) between a G-rich RNA antisense oligoribonucleotide (Q-ASO) and specific mRNA, comprising two distant G-tracts. We selected epidermal growth factor receptor (EGFR) as a well-established target protein in anticancer therapy. The chemically modified, bi-functional anti-EGFR Q-ASO and a 56-nt long EGFR mRNA fragment, in the presence of potassium ions, were shown to form in vitro very stable parallel G-quadruplex containing a 28-nt long external loop folding to two duplex-stem structure. Besides, the Q-ASOs effectively reduced EGFR mRNA levels compared to the non-modified RNA and DNA antisense oligonucleotides (rASO, dASO). In addition, the hybridization specificity of Q-ASO comprising a covalently attached fluorescent tag was confirmed in living cells by visualization of the G4 green fluorescent species in the presence of other antisense inhibitors under competitive conditions. The results presented here offer novel insights into the potential application of Q-ASOs for the detection and/or alteration of (patho)biological processes through RNA:RNA quadruplex-duplex formation in cellular systems.
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Affiliation(s)
- Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
- Correspondence: ; Tel.: +48-61-852-85-03 (ext. 1286)
| | - Damian Kaniowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
| | - Katarzyna Kulik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
| | - Daniel Baranowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (D.B.); (Z.G.)
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Poland; (D.K.); (K.K.); (B.N.)
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12
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Antisense Oligonucleotides Used to Identify Telomeric G-Quadruplexes in Metaphase Chromosomes and Fixed Cells by Fluorescence Lifetime Imaging Microscopy of o-BMVC Foci. Molecules 2020; 25:molecules25184083. [PMID: 32906697 PMCID: PMC7570708 DOI: 10.3390/molecules25184083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 01/01/2023] Open
Abstract
Identification of the existence of G-quadruplex (G4) structure, from a specific G-rich sequence in cells, is critical to the studies of structural biology and drug development. Accumulating evidence supports the existence of G4 structure in vivo. Particularly, time-gated fluorescence lifetime imaging microscopy (FLIM) of a G4 fluorescent probe, 3,6-bis(1-methyl-2-vinylpyridinium) carbazole diiodide (o-BMVC), was used to quantitatively measure the number of G4 foci, not only in different cell lines, but also in tissue biopsy. Here, circular dichroism spectra and polyacrylamide gel electrophoresis assays show that the use of antisense oligonucleotides unfolds their G4 structures in different percentages. Using antisense oligonucleotides, quantitative measurement of the number of o-BMVC foci in time-gated FLIM images provides a method for identifying which G4 motifs form G4 structures in fixed cells. Here, the decrease of the o-BMVC foci number, upon the pretreatment of antisense sequences, (CCCTAA)3CCCTA, in fixed cells and at the end of metaphase chromosomes, allows us to identify the formation of telomeric G4 structures from TTAGGG repeats in fixed cells.
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13
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Effects of Length and Loop Composition on Structural Diversity and Similarity of (G 3TG 3N mG 3TG 3) G-Quadruplexes. Molecules 2020; 25:molecules25081779. [PMID: 32294984 PMCID: PMC7221631 DOI: 10.3390/molecules25081779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 11/17/2022] Open
Abstract
A G-rich sequence containing three loops to connect four G-tracts with each ≥2 guanines can possibly form G-quadruplex structures. Given that all G-quadruplex structures comprise the stacking of G-quartets, the loop sequence plays a major role on their folding topology and thermal stability. Here circular dichroism, NMR, and PAGE are used to study the effect of loop length and base composition in the middle loop, and a single base difference in loop 1 and 3 on G-quadruplex formation of (G3HG3NmG3HG3) sequences with and without flanking nucleotides, where H is T, A, or C and N is T, A, C, or G. In addition, melting curve for G-quadruplex unfolding was used to provide relatively thermal stability of G-quadruplex structure after the addition of K+ overnight. We further studied the effects of K+ concentration on their stability and found structural changes in several sequences. Such (G3HG3NmG3HG3) configuration can be found in a number of native DNA sequences. The study of structural diversity and similarity from these sequences may allow us to establish the correlation between model sequences and native sequences. Moreover, several sequences upon interaction with a G-quadruplex ligand, BMVC, show similar spectral change, implying that structural similarity is crucial for drug development.
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15
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Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids (Changchun, P.R. China, September 6–9, 2019). Biochimie 2020; 168:100-109. [DOI: 10.1016/j.biochi.2019.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022]
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Liu H, Guo C, Guo S, Wang L, Shi D. Design and Synthesis of a Fluorescent Probe with a Large Stokes Shift for Detecting Thiophenols and Its Application in Water Samples and Living Cells. Molecules 2019; 24:molecules24020375. [PMID: 30669672 PMCID: PMC6359167 DOI: 10.3390/molecules24020375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
A turn-on florescent probe (probe-KCP) was developed for highly selective detection of thiophenols based on a donor-excited photo-induced electron transfer mechanism. Herein, the synthesis of the probe, a chalcone derivative, through a simple straightforward combination of a carbazole-chalcone fluorophore with a 2,4-dinitrophenyl functional group. In a kinetic study of the probe-KCP for thiophenols, the probe displayed a short response time (~30 min) and significant fluorescence enhancement. In selection and competition experiments, the probe-KCP exhibited excellent selectivity for thiophenols over glutathione (GSH), cysteine (Cys), sodium hydrosulfide (NaSH), and ethanethiol (C2H5SH) in addition to common anions and metal ions. Using the designed probe, we successfully monitored and quantified thiophenols, which are highly toxic. This turn-on fluorescence probe features a remarkably large Stokes shift (130 nm) and a short response time (30 min), and it is highly selective and sensitive (~160-fold) in the detection of thiophenols, with marked fluorescence in the presence of thiophenols. probe-KCP responds to thiophenols with a good range of linearity (0–15 μM) and a detection limit of 28 nM (R2 = 0.9946) over other tested species mentioned including aliphatic thiols, thiophenol analogues, common anions, and metal ions. The potential applications of this carbazole-chalcone fluorescent probe was successfully used to determine of thiophenols in real water samples and living cells with good performance and low cytotoxicity. Therefore, this probe has great potential application in environment and biological samples.
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Affiliation(s)
- Hua Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chuanlong Guo
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Department of Pharmacy, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shuju Guo
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
| | - Lijun Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
| | - Dayong Shi
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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