1
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Binding characterization of anthraquinone derivatives by stabilizing G-quadruplex DNA leads to an anticancerous activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:648-662. [PMID: 36514353 PMCID: PMC9720492 DOI: 10.1016/j.omtn.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022]
Abstract
G-quadruplex is a non-canonical secondary structure identified in the telomeric region and the promoter of many oncogenes. Anthraquinone derivatives, a well-known inducer of telomere disruption in malignant cells and activate the apoptotic pathway. We used biophysical and biochemical studies to confirm the interaction of synthesized anthraquinone derivatives with the human telomeric G-quadruplex sequence. The binding affinity of N-2DEA and N-1DEA are K b = 4.8 × 106 M-1 and K b = 7.6 × 105 M-1, respectively, leading to hypochroism, fluorescence quenching with minor redshift and ellipticity variations indicating ligand binding in the external groove. We found that sodium ions induced stabilization more rather than potassium ions. Molecular docking of complex demonstrates a molecule's exterior binding to a quadruplex. The investigation of ROS activity indicated that the cell initiates mortality in response to the IC50 concentration. Cellular morphology, nuclear condensation, and fragmentation were altered in the treated cell, impairing cellular function. Finally, the transcriptional regulatory study paves the way for drug design as an anti-cancer agent because of the tremendous possibilities of changing substituent groups on anthraquinones to improve efficacy and selectivity for G-quartet DNA. Our research focused on how ligand binding to telomere sequences induces oxidative stress and inhibits the growth of malignant cells.
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2
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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3
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Dey A, Pandav K, Nath M, Barthwal R, Prasad R. Molecular rec§ognition of telomere DNA sequence by 2, 6 anthraquinone derivatives leads to thermal stabilization and induces apoptosis in cancer cells. Int J Biol Macromol 2022; 221:355-370. [PMID: 36041576 DOI: 10.1016/j.ijbiomac.2022.08.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
According to current research, anti-cancer anthraquinones impact telomere disruption and may interact with G-quadruplex DNA that triggers signaling to apoptosis. The present study represents the biophysical investigation of oxidative stress, late apoptosis, and induced senescence among cancer cells after binding laboratory synthesized piperidine-based anthraquinone derivatives, 2, 6- Bis [(3-piperidino)acetamido)]anthracene-9,10-dione (N1P) and 2, 6-Bis [piperidino)propionamido]anthracene-9,10-dione (N2P), with G-quadruplex DNA. We employed biophysical approaches to explore the interaction of synthetic anthraquinone derivatives with quadruplex DNA sequences to influence biological activities in the presence of K+ and Na+ cations. The binding affinity for N2P and N1P are Kb = 5.8 × 106 M-1 and Kb = 1.0 × 106 M-1, respectively, leading to hypo-/hyper-chromism with 5-7 nm red shift and significant fluorescence quenching and changes in ellipticity resulting in external binding of both the ligands to G-quadruplex DNA. Ligand binding induced enhancement of thermostability of G4 DNA is greater in Na+ environment (ΔTm = 34 °C) as compared to that in K+ environment (ΔTm = 21 °C), thereby restricting telomerase binding access to telomeres. Microscopic images of treated cells indicated cellular shape, nuclear condensation, and fragmentation alterations. The findings pave the path for therapeutic research, given the great potential of modifying anthraquinone substituent groups towards improved efficacy, ROS generation, and G-quadruplex DNA selectivity.
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Affiliation(s)
- Arpita Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
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4
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Guan L, Mao Y, Zhou Y, Feng X, Fu, Yile. Research Progress in Cyanine-Based Recognition Probes for G-Quadruplex DNA. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202203025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Yan C, Chang Y, Gao H, Zhang Q, Peng S, Wang D, Zhou X, Shao Y. G-quadruplex apurinic site-programmed chiral cyanine assemblies for specifically recognizing guanosine and guanine. Analyst 2021; 146:5866-5872. [PMID: 34570847 DOI: 10.1039/d1an01110c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-tuned dye assemblies have received considerable attention toward developing various devices. Owing to easy conformation implementation, G-quadruplexes (G4s) have been extensively used as initiators to grow dye assemblies with controllable chiralities. However, programmed chirality regulation of dye assemblies for a given G4 sequence has not been realized in a straightforward manner. In this work, we replaced a middle guanine in the G-tracts of a human telomeric G4 with an apurinic site (AP site) to meet the programmed dye assemblies. Although all of the AP site replacements altered the G4 conformation from the hybrid to the antiparallel folding, the handedness of pinacyanol (PIN) assemblies grown on the AP site-containing G4 was programmably regulated. The G4 with the AP site at the 5'-most G-tract grew right-handed assemblies, while that with the AP site at the 3'-most G-tract grew left-handed assemblies. The handedness of assemblies almost totally mirrored each other within 450-700 nm. Interestingly, we found that the AP site provided a specific binding site for guanosine and guanine, and this binding event sensitively broke the chiral assemblies. Thus, dye assembly-based sensors can be easily established based on the chiral responses with a high selectivity and sensitivity. Our work first demonstrates the AP site programmed chirality regulation of G4-grown dye assemblies and will find wide application in chiral devices.
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Affiliation(s)
- Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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6
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Schultz CW, McCarthy GA, Nerwal T, Nevler A, DuHadaway JB, McCoy MD, Jiang W, Brown SZ, Goetz A, Jain A, Calvert VS, Vishwakarma V, Wang D, Preet R, Cassel J, Summer R, Shaghaghi H, Pommier Y, Baechler SA, Pishvaian MJ, Golan T, Yeo CJ, Petricoin EF, Prendergast GC, Salvino J, Singh PK, Dixon DA, Brody JR. The FDA-Approved Anthelmintic Pyrvinium Pamoate Inhibits Pancreatic Cancer Cells in Nutrient-Depleted Conditions by Targeting the Mitochondria. Mol Cancer Ther 2021; 20:2166-2176. [PMID: 34413127 DOI: 10.1158/1535-7163.mct-20-0652] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/09/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal aggressive cancer, in part due to elements of the microenvironment (hypoxia, hypoglycemia) that cause metabolic network alterations. The FDA-approved antihelminthic pyrvinium pamoate (PP) has previously been shown to cause PDAC cell death, although the mechanism has not been fully determined. We demonstrated that PP effectively inhibited PDAC cell viability with nanomolar IC50 values (9-93 nmol/L) against a panel of PDAC, patient-derived, and murine organoid cell lines. In vivo, we demonstrated that PP inhibited PDAC xenograft tumor growth with both intraperitoneal (IP; P < 0.0001) and oral administration (PO; P = 0.0023) of human-grade drug. Metabolomic and phosphoproteomic data identified that PP potently inhibited PDAC mitochondrial pathways including oxidative phosphorylation and fatty acid metabolism. As PP treatment reduced oxidative phosphorylation (P < 0.001), leading to an increase in glycolysis (P < 0.001), PP was 16.2-fold more effective in hypoglycemic conditions similar to those seen in PDAC tumors. RNA sequencing demonstrated that PP caused a decrease in mitochondrial RNA expression, an effect that was not observed with established mitochondrial inhibitors rotenone and oligomycin. Mechanistically, we determined that PP selectively bound mitochondrial G-quadruplexes and inhibited mitochondrial RNA transcription in a G-quadruplex-dependent manner. This subsequently led to a 90% reduction in mitochondrial encoded gene expression. We are preparing to evaluate the efficacy of PP in PDAC in an IRB-approved window-of-opportunity trial (IND:144822).
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Affiliation(s)
- Christopher W Schultz
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Grace A McCarthy
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Teena Nerwal
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Avinoam Nevler
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | - Wei Jiang
- Pathology Department, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Samantha Z Brown
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Austin Goetz
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Aditi Jain
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | - Dezhen Wang
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Joel Cassel
- Wistar Institute, Philadelphia, Pennsylvania
| | - Ross Summer
- Jane and Leonard Korman Respiratory Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hoora Shaghaghi
- Jane and Leonard Korman Respiratory Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Yves Pommier
- Developmental Therapeutics Branch, NCI Bethesda, Maryland
| | | | | | - Talia Golan
- Oncology institute, Chaim Sheba Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Charles J Yeo
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | | | - Pankaj K Singh
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Jonathan R Brody
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon.
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7
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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.
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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
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8
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Wickhorst PJ, Ihmels H. Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA. Molecules 2021; 26:2566. [PMID: 33924894 PMCID: PMC8124163 DOI: 10.3390/molecules26092566] [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: 03/25/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2-7 × 105 M-1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.
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Affiliation(s)
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering (Cµ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany;
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9
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Yan C, Zhang Q, Gao H, Zheng X, Yang T, Zheng G, Zhou X, Shao Y. Concurrent formation of H- and J-aggregates of dyes with chiralities individually determined by G-quadruplex handedness. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119270. [PMID: 33310273 DOI: 10.1016/j.saa.2020.119270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/06/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
DNA templated dye assemblies pave an easy way to regulate the optical properties of molecular aggregates. G-quadruplexes (G4s) provide versatile DNA platforms for the dye assemblies since their foldings can be easily tuned by cation ions and sequences. In this work, we found that the G4 handedness can be used to control the aggregate chirality of a dye of 3,3'-diethylthiacarbocyanine (DiSC2(3)). The left-handed and right-handed G4s can template the concurrent formation of the J- and H-aggregates of DiSC2(3) with emergence of the featured absorption spectra. However, the chiral J-aggregate of DiSC2(3) can be formed only on the left-handed G4s, while the chiral H-aggregate is otherwise grown only on the right-handed G4s, as confirmed by the induced circular dichroism (ICD) spectra with the characteristic splitting bands. Additionally, these G4s even at tens of nM level are efficient to produce these chiral aggregates, demonstrating the high sensitivity of G4s in creating these optically active dye assemblies. The possible growth sites of the aggregates are proposed by the sequence length-dependent assemblies. Our work will provide a new way to control the chiral assemblies of dye aggregates via the G4 handedness.
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Affiliation(s)
- Chenxiao Yan
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qingqing Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Heng Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Guoxiang Zheng
- Undergraduate Teaching Department, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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Armstrong-Price DE, Deore PS, Manderville RA. Intrinsic "Turn-On" Aptasensor Detection of Ochratoxin A Using Energy-Transfer Fluorescence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2249-2255. [PMID: 31986034 DOI: 10.1021/acs.jafc.9b07391] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA) is an intrinsically fluorescent phenolic mycotoxin that contaminates a wide range of food products and is a serious health threat to animals and humans. An OTA binding aptamer (OTABA) that folds into an antiparallel G-quadruplex (GQ) in the absence and presence of target OTA has been incorporated into a vast variety of aptasensor platforms for OTA detection. The development of a simple, aptamer-based approach would allow for detection of the toxin without the use of complex analytical instrumentation, which has been the gold standard for OTA detection thus far. However, to date, none of the aptasensor platforms have utilized the natural fluorescence of the phenolic toxin for detection. Herein, we report that OTA binding to OTABA involves π-stacking interactions that lead to GQ-to-toxin energy transfer (ET), which affords a "turn-on" fluorescence self-signaling platform in which the emission of the aptamer-target complex is enhanced in comparison to the free toxin alone. Selective excitation of the GQ-OTA complex at 256 nm leads to a 4-fold enhancement in OTA fluorescence. The GQ-OTA ET detection platform boasts a limit of detection ∼2 ng/mL, which is comparable to a previously demonstrated fluorescence resonance energy transfer immunoassay platform for OTA detection, and displays excellent OTA selectivity and recovery from red wine samples.
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11
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Owens EA, Huynh HT, Stroeva EM, Barman A, Ziabrev K, Paul A, Nguyen SV, Laramie M, Hamelberg D, Germann MW, Wilson WD, Henary M. Second Generation G-Quadruplex Stabilizing Trimethine Cyanines. Bioconjug Chem 2019; 30:2647-2663. [PMID: 31518105 DOI: 10.1021/acs.bioconjchem.9b00571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-Quadruplex DNA has been recognized as a highly appealing target for the development of new selective chemotherapeutics, which could result in markedly reduced toxicity toward normal cells. In particular, the cyanine dyes that bind selectively to G-quadruplex structures without targeting duplex DNA have attracted attention due to their high amenability to structural modifications that allows fine-tuning of their biomolecular interactions. We have previously reported pentamethine and symmetric trimethine cyanines designed to effectively bind G-quadruplexes through end stacking interactions. Herein, we are reporting a second generation of drug candidates, the asymmetric trimethine cyanines. These have been synthesized and evaluated for their quadruplex binding properties. Incorporating a benz[c,d]indolenine heterocyclic unit increased overall quadruplex binding, and elongating the alkyl length increases the quadruplex-to-duplex binding specificity.
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Affiliation(s)
- Eric A Owens
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Hang T Huynh
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | - Ekaterina M Stroeva
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | - Kostiantyn Ziabrev
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States
| | | | | | | | - Donald Hamelberg
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Markus W Germann
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Department of Biology , Georgia State University , Petit Science Center, 100 Piedmont Ave. , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
| | - Maged Henary
- Department of Chemistry , Georgia State University , Petit Science Center, 100 Piedmont Ave SE. Atlanta Georgia 30303 , United States.,Center for Diagnostics and Therapeutics , Georgia State University , Petit Science Center, 100 Piedmont Ave SE , Atlanta , Georgia 30303 , United States
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12
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Van Riesen AJ, Fadock KL, Deore PS, Desoky A, Manderville RA, Sowlati-Hashjin S, Wetmore SD. Manipulation of a DNA aptamer-protein binding site through arylation of internal guanine residues. Org Biomol Chem 2019; 16:3831-3840. [PMID: 29745412 DOI: 10.1039/c8ob00704g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chemically modified aptamers have the opportunity to increase aptamer target binding affinity and provide structure-activity relationships to enhance our understanding of molecular target recognition by the aptamer fold. In the current study, 8-aryl-2'-deoxyguanosine nucleobases have been inserted into the G-tetrad and central TGT loop of the thrombin binding aptamer (TBA) to determine their impact on antiparallel G-quadruplex (GQ) folding and thrombin binding affinity. The aryl groups attached to the dG nucleobase vary greatly in aryl ring size and impact on GQ stability (∼20 °C change in GQ thermal melting (Tm) values) and thrombin binding affinity (17-fold variation in dissociation constant (Kd)). At G8 of the central TGT loop that is distal from the aptamer recognition site, the probes producing the most stable GQ structure exhibited the strongest thrombin binding affinity. However, within the G-tetrad, changes to the electron density of the dG component within the modified nucleobase can diminish thrombin binding affinity. Detailed molecular dynamics (MD) simulations on the modified TBA (mTBA) and mTBA-protein complexes demonstrate how the internal 8-aryl-dG modification can manipulate the interactions between the DNA nucleobases and the amino acid residues of thrombin. These results highlight the potential of internal fluorescent nuclobase analogs (FBAs) to broaden design options for aptasensor development.
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Affiliation(s)
- Abigail J Van Riesen
- Department of Chemistry & Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1.
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13
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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.
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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
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14
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Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
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15
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Buchholz I, Karg B, Dickerhoff J, Sievers-Engler A, Lämmerhofer M, Weisz K. Selective Targeting of G-Quadruplex Structures by a Benzothiazole-Based Binding Motif. Chemistry 2017; 23:5814-5823. [PMID: 28276093 DOI: 10.1002/chem.201700298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 12/28/2022]
Abstract
A benzothiazole derivative was identified as potent ligand for DNA G-quadruplex structures. Fluorescence titrations revealed selective binding to quadruplexes of different topologies including parallel, antiparallel, and (3+1) hybrid structures. The parallel c-MYC sequence was found to constitute the preferred target with dissociation constants in the micromolar range. Binding of the benzothiazole-based ligand to c-MYC was structurally and thermodynamically characterized in detail by employing a comprehensive set of spectroscopic and calorimetric techniques. Job plot analyses and mass spectral data indicate noncooperative ligand binding to form complexes with 1:1 and 2:1 stoichiometries. Whereas stacking interactions are suggested by optical methods, NMR chemical shift perturbations also indicate significant rearrangements of both 5'- and 3'-flanking sequences upon ligand binding. Additional isothermal calorimetry studies yield a thermodynamic profile of the ligand-quadruplex association and reveal enthalpic contributions to be the major driving force for binding. Structural and thermodynamic information obtained in the present work provides the basis for the rational development of benzothiazole derivatives as promising quadruplex binding agents.
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Affiliation(s)
- Ina Buchholz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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16
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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.
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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.
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Pradeep TP, Barthwal R. A 4:1 stoichiometric binding and stabilization of mitoxantrone-parallel stranded G-quadruplex complex established by spectroscopy techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:106-114. [DOI: 10.1016/j.jphotobiol.2016.06.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 06/10/2016] [Accepted: 06/11/2016] [Indexed: 12/30/2022]
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Hahn L, Buurma NJ, Gade LH. A Water-Soluble Tetraazaperopyrene Dye as Strong G-Quadruplex DNA Binder. Chemistry 2016; 22:6314-22. [PMID: 26997208 PMCID: PMC5071672 DOI: 10.1002/chem.201504934] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 01/24/2023]
Abstract
The interactions of the water-soluble tetraazaperopyrene dye 1 with ct-DNA, duplex-[(dAdT)12 ⋅(dAdT)12 ], duplex-[(dGdC)12 ⋅(dGdC)12 ] as well as with two G-quadruplex-forming sequences, namely the human telomeric 22AG and the promotor sequence c-myc, were investigated by means of UV/visible and fluorescence spectroscopy, isothermal titration calorimetry (ITC) and molecular docking studies. Dye 1 exhibits a high affinity for G-quadruplex structures over duplex DNA structures. Furthermore, the ligand shows promising G-quadruplex discrimination, with an affinity towards c-myc of 2×10(7) m(-1) (i.e., Kd =50 nm), which is higher than for 22AG (4×10(6) m(-1) ). The ITC data reveal that compound 1 interacts with c-myc in a stoichiometric ratio of 1:1 but also indicate the presence of two identical lower affinity secondary binding sites per quadruplex. In 22AG, there are two high affinity binding sites per quadruplex, that is, one on each side, with a further four weaker binding sites. For both quadruplex structures, the high affinity interactions between compound 1 and the quadruplex-forming nucleic acid structures are weakly endothermic. Molecular docking studies suggest an end-stacking binding mode for compound 1 interacting with quadruplex structures, and a higher affinity for the parallel conformation of c-myc than for the mixed-hybrid conformation of 22AG. In addition, docking studies also suggest that the reduced affinity for duplex DNA structures is due to the non-viability of an intercalative binding mode.
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Affiliation(s)
- Lena Hahn
- Anorganisch-Chemisches-Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany), Fax
| | - Niklaas J Buurma
- Physical Organic Chemistry Centre, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK), Fax.
| | - Lutz H Gade
- Anorganisch-Chemisches-Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany), Fax.
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