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Stężycka O, Kasperkowiak M, Frańska M, Nowak D, Hoffmann M. Oxygen Atom from Carbonyl Group as an Important Binding Agent to the G-Quadruplex - Study Case of Flavonoids. Chempluschem 2024; 89:e202400186. [PMID: 38713672 DOI: 10.1002/cplu.202400186] [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: 03/10/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
In the field of anticancer therapy study it is of great interest to find effective G-quadruplex ligands which may be of potential use in medical treatment or cancer prevention. Since among the compounds of natural origin, flavonoids have attracted notable attention because of their unique properties and promising therapeutic applications, an interesting question was to identify the flavonoid structural features that could provide effective binding properties toward G-quadruplex. By using electrospray ionization mass spectrometry, followed by the survival yield method, it has been shown that the flavonoid molecules which contain an available C4=O carbonyl group form more stable adducts with G-tetrads than the other ones. Molecular docking has shown that C4=O carbonyl group can be a source of hydrogen bonds and/or π-stacking interactions. Therefore, the flavonoid molecules which contain an available C4=O carbonyl group can be regarded as good binders of G-quadruplexes.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Małgorzata Kasperkowiak
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Damian Nowak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
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2
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Stężycka O, Frańska M. Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method. ACS OMEGA 2023; 8:39816-39821. [PMID: 37901583 PMCID: PMC10600882 DOI: 10.1021/acsomega.3c06016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023]
Abstract
Recently, much interest has been devoted to finding effective G-quadruplex ligands, both of synthetic or natural origins, which may be of potential use in the field of cancer therapy. Among compounds of natural origin, a common flavonol quercetin has attracted notable attention. Yet, only a modest number of papers have been concerned with a comparison of quercetin conjugates binding to G-quadruplexes. In this study, we applied the survival yield (SY) method in order to compare the stability of G-tetrad complexes with quercetin and its conjugates, namely, 3-O-glycosides and O-methylated conjugates. According to the determined values of Ecomδ50, flavonol glycosides bind most effectively with G-tetrads, whereas, among flavonols, 3-O-methylquercetin makes the most effective bonds. Because the aglycone structure is of crucial importance for biological processes, 3-O-methylquercetin seems to be a suitable candidate for anticancer therapeutics, and the extracts from the plants, which contain high amounts of 3-O-methylquercetin or its glycosides, should be considered as interesting materials for preparation of pharmaceuticals or dietary supplements.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical
Electrochemistry, Poznań University
of Technology, Berdychowo
4, 60-965 Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical
Electrochemistry, Poznań University
of Technology, Berdychowo
4, 60-965 Poznań, Poland
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3
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Bag S, Ghosal S, Karmakar S, Pramanik G, Bhowmik S. Uncovering the Contrasting Binding Behavior of Plant Flavonoids Fisetin and Morin Having Subsidiary Hydroxyl Groups (-OH) with HRAS1 and HRAS2 i-Motif DNA Structures: Decoding the Structural Alterations and Positional Influences. ACS OMEGA 2023; 8:30315-30329. [PMID: 37636929 PMCID: PMC10448647 DOI: 10.1021/acsomega.3c03105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023]
Abstract
Research on the interactions of naturally existing flavonoids with various noncanonical DNA such as i-motif (IM) DNA structures is helpful in comprehending the molecular basis of binding mode as well as providing future direction for the application and invention of novel effective therapeutic drugs. IM DNA structures have been identified as prospective anticancer therapeutic targets, and flavonoids are smaller molecules with a variety of health-promoting attributes, including anticancer activities. The extensive investigation comprising a series of techniques reveals the contrasting mode of the binding behavior of fisetin and morin with various IM DNA structures. We have discovered that structural alterations of hydroxyl groups located at different places of aromatic rings influence flavonoid's reactivity. This minor structural alteration appears to be critical for fisetin and morin's capacity to interact differentially with HRAS1 and HRAS2 IM DNA. Hence, fisetin appears to be an efficient ligand for HRAS1 and morin is considered to be an efficient ligand for HRAS2 IM DNA. This novel exploration opens up the possibility of employing the strategy for regulation of gene expression in cancerous cells. Our finding also reveals the flavonoid-mediated specific interaction with IM DNA while pointing toward tangible strategies for drug discovery and other essential cellular functions.
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Affiliation(s)
- Sagar Bag
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Souvik Ghosal
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
| | - Sudip Karmakar
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Goutam Pramanik
- UGC−DAE
Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Sudipta Bhowmik
- Department
of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
- Mahatma
Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth
(Deemed to be University), Pondy−Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
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4
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Wang H, Liu X, Tan L. Binding properties of a molecular "light switch" ruthenium(II) polypyridyl complex toward double- and triple-helical forms of RNA. Int J Biol Macromol 2023; 242:124710. [PMID: 37146854 DOI: 10.1016/j.ijbiomac.2023.124710] [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: 01/14/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
To further develop new luminescent probes for RNA, a new ruthenium(II) polypyridyl complex [Ru(dmb)2dppz-idzo]2+ (dmb = 4,4'-dimethyl-2,2'-bipyridine, dppz-idzo = dppz-imidazolone) has been synthesized and characterized in this study. Binding properties of [Ru(dmb)2dppz-idzo]2+ to RNA duplex poly(A) · poly(U) and triplex poly(U) · poly(A) ∗ poly(U) have been explored by spectroscopic techniques and viscometry experiments. The binding modes of [Ru(dmb)2dppz-idzo]2+ to RNA duplex and triplex are intercalation as revealed from spectral titrations and viscosity experiments, while the binding strength of this complex to duplex structure is significantly greater than that of triplex structure. Fluorescence titrations indicate that [Ru(dmb)2dppz-idzo]2+ can act as a molecular "light switch" for both duplex poly(A) · poly(U) and triplex poly(U) · poly(A) ∗ poly(U), while [Ru(dmb)2dppz-idzo]2+ is more sensitive to poly(A) · poly(U) compared to poly(U) · poly(A) ∗ poly(U) and poly(U). Therefore, this complex can distinguish between RNA duplex, triplex and poly(U), and can as luminescent probes for the three RNAs used in this study. In addition, thermal denaturation studies show that [Ru(dmb)2dppz-idzo]2+ is able to significantly increase the Stabilization of RNA duplex and triplex. The results obtained in this study may contribute to further understanding of the binding of Ru(II) complexes with different structural RNAs.
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Affiliation(s)
- Hui Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
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Kashapov R, Razuvayeva Y, Kashapova N, Ziganshina A, Salnikov V, Sapunova A, Voloshina A, Zakharova L. Emergence of Nanoscale Drug Carriers through Supramolecular Self-Assembly of RNA with Calixarene. Int J Mol Sci 2023; 24:ijms24097911. [PMID: 37175618 PMCID: PMC10178118 DOI: 10.3390/ijms24097911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Supramolecular self-assembly is a powerful tool for the development of polymolecular assemblies that can form the basis of useful nanomaterials. Given the increasing popularity of RNA therapy, the extension of this concept of self-assembly to RNA is limited. Herein, a simple method for the creation of nanosized particles through the supramolecular self-assembly of RNA with a three-dimensional macrocycle from the calixarene family was reported for the first time. This self-assembly into nanoparticles was realized using cooperative supramolecular interactions under mild conditions. The obtained nanoparticles are able to bind various hydrophobic (quercetin, oleic acid) and hydrophilic (doxorubicin) drugs, as a result of which their cytotoxic properties are enhanced. This work demonstrates that intermolecular interactions between flexible RNA and rigid calixarene is a promising route to bottom-up assembly of novel supramolecular soft matter, expanding the design possibilities of nanoscale drug carriers.
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Affiliation(s)
- Ruslan Kashapov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Yuliya Razuvayeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Nadezda Kashapova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Albina Ziganshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Vadim Salnikov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Str., 420111 Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18, Kremlyovskaya Str., 420008 Kazan, Russia
| | - Anastasiia Sapunova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Alexandra Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Lucia Zakharova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
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Xie Z, Zhang S, Wu Y, Liang J, Yao W, Qu R, Tong X, Zhang G, Yang H. Interaction of isoquinoline alkaloids with pyrimidine motif triplex DNA by mass spectrometry and spectroscopies reveals diverse mechanisms. Heliyon 2023; 9:e14954. [PMID: 37082631 PMCID: PMC10112036 DOI: 10.1016/j.heliyon.2023.e14954] [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: 07/21/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Isoquinoline alkaloids represent an important class of molecules due to their broad range of pharmacology and clinical utility. Prospective development and use of these alkaloids as effective anticancer agents have elicited great interest. In this study, in order to reveal structure-activity relationship, we present the characterization of bioactive isoquinoline alkaloid-DNA triplex interactions, with particular emphasis on the sequence selectivity and preference of binding to the two types of DNA triplexes, by electrospray ionization mass spectrometry (ESI-MS) and various spectroscopic techniques. The six alkaloids, including coptisine, columbamine, epiberberine, berberrubine, jateorhizine, and fangchinoline, were selected to explore their interactions with the TC and TTT triplex DNA structures. Berberrubine, fangchinoline, coptisine, columbamine, and epiberberine have preference for TC rich DNA sequences compared to TTT rich DNA triplex based on affinity values in MS. The experimental results from different fragmentation modes in tandem MS, subtractive and hyperchromic effects in UV absorption spectra, fluorescence quenching and enhancement in fluorescence spectra, and strong conformational changes in circular dichroism (CD) hinted that the interaction between isoquinoline alkaloid-TC/TTT DNA had diverse mechanisms including at least two different binding modes: the electrostatic binding and the intercalation binding. Interestingly, columbamine, berberrubine, and fangchinoline can stabilize TTT triplex as inferred from optical thermal melting profiles, while it was not the case in TC triplex. These results provide new insights into binding of isoquinoline alkaloids to pyrimidine motif triplex DNA.
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Affiliation(s)
- Zhaoyang Xie
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Sunuo Zhang
- School of Materials Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yi Wu
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Jinling Liang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Wenbin Yao
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Ruoning Qu
- China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Xiaole Tong
- Jilin Jian Yisheng Pharmaceutical Co., Ltd., Jian, 134200, China
| | - Guang Zhang
- China-Japan Union Hospital of Jilin University, Changchun, 130033, China
- Corresponding author.
| | - Hongmei Yang
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
- Corresponding author.
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7
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Yuan F, Liu X, Tan L. Binding and stabilization effect of arene ruthenium(Ⅱ) polypyridyl complexes toward the triple-helical RNA poly(U)•poly(A)⁎poly(U). Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Anti-Mycobacterial Activity of Flavonoid and Pyrimidine Compounds. Molecules 2022; 27:molecules27196714. [PMID: 36235249 PMCID: PMC9572476 DOI: 10.3390/molecules27196714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/17/2022] Open
Abstract
We evaluated the anti-mycobacterial effect of a flavonoid 5,7-dihydroxy-2-(4-hydroxyphenyl) 4H-chromen-4-one (1) and two pyrimidines, 4-hydroxy-2-dimethylamino-5-nitroso-6-aminopyrimidine (2) and 2-chloro-5-n-nonylpyrimidine (3) in vitro against Mycobacterium tuberculosis (M. tuberculosis, H37Ra) and Mycobacterium avium (M. avium), using a Microplate Alamar Blue Assay (MABA). The effects of the compounds 1-3 in combination with first- and second-line anti-TB drugs isoniazid, rifampicin, cycloserine, and clarithromycin on the growth of M. tuberculosis and M. avium were also evaluated in in vitro assays. As a single agent, compounds 1 and 2 exhibited modest activity while compound 3 was the most effective against M. tuberculosis and M. avium. When compounds 1-3 were evaluated at lower than 50% of their inhibitory concentrations in a two-drug combination with isoniazid or rifampicin, they showed additive to synergistic interactions. This inhibitory effect was improved when each of the three compounds was tested together in a three-drug combination with two of the first-line anti-TB drugs. Compounds 1-3 also demonstrated strong synergistic interaction in combination with cycloserine and clarithromycin in inhibiting the growth of M. tuberculosis and M. avium, respectively. This study demonstrated that compounds 1-3 have potential to be developed as effective anti-TB agents with combined use.
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Chen P, Yang Z, Mai Z, Huang Z, Bian Y, Wu S, Dong X, Fu X, Ko F, Zhang S, Zheng W, Zhang S, Zhou W. Electrospun nanofibrous membrane with antibacterial and antiviral properties decorated with Myoporum bontioides extract and silver-doped carbon nitride nanoparticles for medical masks application. Sep Purif Technol 2022; 298:121565. [PMID: 35765307 PMCID: PMC9225951 DOI: 10.1016/j.seppur.2022.121565] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 12/29/2022]
Abstract
Public health safety issues have been plaguing the world since the pandemic outbreak of coronavirus disease (COVID-19). However, most personal protective equipments (PPE) do not have antibacterial and anti- toxicity effects. In this work, we designed and prepared a reusable, antibacterial and anti-toxicity Polyacrylonitrile (PAN) based nanofibrous membrane cooperated with Ag/g-C3N4 (Ag-CN), Myoporum.bontioides (M. bontioides) plant extracts and Ag nanoparticles (NPs) by an electrospinning-process. The SEM and TEM characterization revealed the formation of raised, creased or wrinkled areas on the fiber surface caused by the Ag nanoparticles, the rough surface prevented the aerosol particles on the fiber surface from sliding and stagnating, thus providing excellent filtration performance. The PAN/M. bontioides/Ag-CN/Ag nanofibrous membrane could be employed as a photocatalytic bactericidal material, which not only degraded 96.37% of methylene blue within 150 min, but also exhibited the superior bactericidal effect of 98.65 ± 1.49% and 97.8 ± 1.27% against E. coli and S. aureus, respectively, under 3 hs of light exposure. After 3 cycles of sterilization experiments, the PAN/M. bontioides/Ag-CN/Ag nanofibrous membrane maintained an efficient sterilization effect. Molecular docking revealed that the compounds in M. bontioides extracts interacted with neo-coronavirus targets mainly on Mpro and RdRp proteins, and these compounds had the strongest docking energy with Mpro protein, the shortest docking radius, and more binding sites for key amino acids around the viral protein targets, which influenced the replication and transcription process of neo-coronavirus. The PAN/M.bontioides/Ag-CN/Ag nanofibrous membrane also performed significant inhibition of influenza A virus H3N2. The novel nanofiber membrane is expected to be applied to medical masks, which will improve human isolation and protection against viruses.
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Affiliation(s)
- Pinhong Chen
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Zhi Yang
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
| | - Zhuoxian Mai
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Ziyun Huang
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Yongshuang Bian
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Shangjing Wu
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Xianming Dong
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Xianjun Fu
- Marine Traditional Chinese Medicine Research Center, Qingdao Academy of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Qingdao 266114, China
| | - Frank Ko
- Department of Materials Engineering, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Shiying Zhang
- Hunan Key Laboratory of Applied Environmental Photocatalysis, Changsha University, Changsha 410022, China
| | - Wenxu Zheng
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
| | - Shengsen Zhang
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
| | - Wuyi Zhou
- Key Laboratory of the Ministry of Bio-based Materials and Energy Education, South China Agricultural University, Guangzhou 510642, China
- Research Center of Biomass 3D Printing Materials, College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
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10
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Wang H, Liu X, Tan L. A naked-eye colorimetric molecular "light switch" based on ruthenium(II) polypyridyl complex [Ru(phen) 2ttbd] 2+ as binder and stabilizer for RNA duplex and triplex. Int J Biol Macromol 2022; 215:571-578. [PMID: 35752337 DOI: 10.1016/j.ijbiomac.2022.06.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/05/2022]
Abstract
Binding of [Ru(phen)2ttbd]2+ (phen = 1,10-phenanthroline, ttbd = 4-(6-propenylpyrido-[3,2-a]- phenzain-10-yl-benzene-1,2-diamine) to the RNA triplex poly(U-A*U) (herein "-" and "*" refer to the Watson-Crick and Hoogsteen binding, respectively) and the duplex poly(A-U) have been investigated by spectral technology and viscosity method. Analysis of spectral titrations and viscosity experiments as well as melting measurements suggest that [Ru(phen)2ttbd]2+ binds to the studied RNA triplex and duplex through intercalation, while its binding constant toward the triplex is greater than the duplex. Luminescent titrations indicate that [Ru(phen)2ttbd]2+ can act as a molecular "light switch" for the two RNAs and the switch effect can be detected by the naked-eye. Moreover, the "light switch" can be repeatedly cycled off and on by adjusting the pH of the solution, whereas color change in the case of the triplex is more significant compared with the duplex. To our knowledge, [Ru(phen)2ttbd]2+ is the first small molecule capable of serving as a pH-controlled reversible visual molecular "light switch" for both the RNA triplex poly(U-A*U) and duplex poly(A-U). Thermal denaturation experiments suggest that [Ru(phen)2ttbd]2+ can obviously increase the triplex stabilization, while it stabilizing third-strand is more marked in comparison with the template duplex of the triplex, indicating this complex preferentially binds to third-strand. The obtained results may be useful for understanding the binding of Ru(II) polypyridyl complexes to RNAs.
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Affiliation(s)
- Hui Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China.
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11
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Zhang C, Liu X, Tan L. Interaction of arene ruthenium(II) complexes [(η 6-C 6H 6)Ru(L)Cl]PF 6 (L = o-fpip and p-fpip) with the RNA triplex poly(U)*poly(A)•poly(U). J Inorg Biochem 2022; 232:111813. [PMID: 35405487 DOI: 10.1016/j.jinorgbio.2022.111813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
To comprehend the binding properties of η6-arene Ru(II) complexes with poly(U)*poly(A)•poly(U) triplex, two arene Ru(II) complexes with different fluorine substituent positions, [(η6-C6H6)Ru(o-fpip)Cl]PF6 (Ru1,η6-C6H6 = benzene ring, o-fpip = 2-(2'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline) and [(η6-C6H6)Ru(p-fpip)Cl]PF6 (Ru2,η6-C6H6 = benzene ring, o-fpip = 2-(4'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline), have been synthesized and characterized in this study. The binding of Ru1 and Ru2 with poly(U)*poly(A)•poly(U) triplex has been investigated by viscosity measurement and spectroscopic methods. Analysis of UV-Vis absorption spectral titrations suggests that Ru1 and Ru2 bind to the triplex through an intercalative mode, but the binding affinity of Ru2 is slightly higher than that of Ru1, which is also verified by viscosity and EB (ethidium bromide) competition measurements. Furthermore, the thermal denaturation experiment shows that Ru1 and Ru2 increase the third-strand stabilization to a similar extent. Interestingly, the two complexes have essentially no effect on the stabilization of the template duplex. Considering the structure of Ru1 and Ru2, conceivably besides the intercalation of ligand, the force stabilizing the triplex should also involve covalent binding and electrostatic interaction. The obtained results will contribute to our understanding of the interaction of arene Ru(II) complexes with the poly(U)*poly(A)•poly(U) triplex.
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Affiliation(s)
- Chengqing Zhang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
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12
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Substituent effects on the interactions of ruthenium(II) polypyridyl complexes [Ru(bpy)2(6-R-dppz)]2+ (R = hydroxy and fluorine) with the RNA triplex poly(rU)·poly(rA) × poly(rU). Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Chen Q, He Y, Zhao Y, Chen L. Intervening oxidative stress integrated with an excellent biocompatibility of hemodialysis membrane fabricated by nucleobase-recognized co-immobilization strategy of tannic acid, looped PEtOx brush and heparin. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2021.119174] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Comparative studies on the binding interaction of two chiral Ru(II) polypyridyl complexes with triple- and double-helical forms of RNA. J Inorg Biochem 2020; 214:111301. [PMID: 33166867 DOI: 10.1016/j.jinorgbio.2020.111301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/12/2020] [Accepted: 10/25/2020] [Indexed: 12/27/2022]
Abstract
Two chiral Ru(II) polypyridyl complexes, Δ-[Ru(bpy)2(6-F-dppz)]2+ (Δ-1; bpy = 2,2'-bipyridine, 6-F-dppz = 6-fluorodipyrido[3,2-a:2',3'-c]phenazine) and Λ-[Ru(bpy)2(6-F-dppz)]2+ (Λ-1), have been synthesized and characterized as binders for the RNA poly(U)•poly(A)*poly(U) triplex and poly(A)•poly(U) duplex in this work. Analysis of the UV-Vis absorption spectra and fluorescence emission spectra indicates that the binding of intercalating Δ-1 with the triplex and duplex RNA is greater than that of Λ-1, while the binding affinities of the two enantiomers to triplex structure is stronger than that of duplex structure. Fluorescence titrations show that the two enantiomers can act as molecular "light switches" for triple- and double-helical RNA. Thermal denaturation studies revealed that that the two enantiomers are more stable to Watson-Crick base-paired double strand of the triplex than the Hoogsteen base-paired third strand, but their stability and selectivity are different. For Δ-enantiomer, the increase of the thermal stability of the Watson-Crick base-paired duplex (13 °C) is slightly stronger than of the Hoogsteen base-paired strand (10 °C), displaying no obvious selectivity. However, compared to the Hoogsteen base-paired strand (5 °C), the stability of the Λ-enantiomer to the Watson-Crick base-paired duplex (13 °C) is more significant, which has obvious selectivity. The overall increase in viscosity of the RNA-(Λ-1) system and its curve shape are similar to that of the RNA-(Δ-1) system, suggesting that the binding modes of two enantiomers with RNA are intercalation. The obtained results in this work may be useful for understanding the binding differences in chiral Ru(II) polypyridyl complexes toward RNA triplex and duplex.
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Malina J, Farrell NP, Brabec V. Substitution-Inert Polynuclear Platinum Complexes Inhibit Reverse Transcription Preferentially in RNA Triplex-Forming Templates. Inorg Chem 2020; 59:15135-15143. [PMID: 32988198 DOI: 10.1021/acs.inorgchem.0c02070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA triplexes are significant tertiary structure motifs that are found in many functional RNAs. Hence, small molecules capable of recognition, binding, and stabilization of the triple-helical RNA structures are emerging as attractive potential molecular biology tools and therapeutic agents. Here, we utilize methods of molecular biology and biophysics to study the interactions of a series of antitumor substitution-inert polynuclear platinum complexes (SI-PPCs) with triple-helical RNA structures. We show that SI-PPCs recognize and stabilize RNA triplexes and inhibit reverse transcription preferentially in the RNA template prone to the triplex formation. These so far unexplored properties of SI-PPCs suggest that the targeting of triple-stranded regions in RNA might contribute to the biological effects of SI-PPCs.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, Brno CZ-61265, Czech Republic
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Kralovopolska 135, Brno CZ-61265, Czech Republic
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16
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Dong Z, Liu X, Tan L. Biophysical insights into the interaction of two enantiomers of Ru(II) complex [Ru(bpy) 2(7-CH 3-dppz)] 2+ with the RNA poly(U-A⁎U) triplex. J Biol Inorg Chem 2020; 25:1085-1095. [PMID: 33040210 DOI: 10.1007/s00775-020-01825-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/28/2020] [Indexed: 01/14/2023]
Abstract
To determine the factors affecting the stabilization of RNA triple-stranded structure by chiral Ru(II) polypyridyl complexes, a new pair of enantiomers, ∆-[Ru(bpy)2(7-CH3-dppz)]2+ (∆-1; bpy = 2,2'-bipyridine, 7-CH3-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) and Λ-[Ru(bpy)2(7-CH3-dppz)]2+ (Λ-1), have been synthesized and characterized in this work. Binding properties of the two enantiomers with the RNA poly(U-A⁎U) triplex (where "-" denotes the Watson - Crick base pairing and "⁎" denotes the Hoogsteen base pairing) have been studied by spectroscopy and hydrodynamics methods. Under the conditions used in this study, changes in absorption spectra of the two enantiomers are not very different from each other when bound to the triplex, although the binding affinity of ∆-1 is higher than that of Λ-1. Fluorescence titrations and viscosity experiments give convincing evidence for a true intercalative binding of enantiomers with the triplex. However, melting experiments indicated that the two enantiomers selectively stabilized the triplex. The enantiomer ∆-1 stabilize the template duplex and third-strand of the triplex, while it's more effective for stabilization of the template duplex. In stark contrast to ∆-1, Λ-1 stabilizes the triplex without any effect on the third-strand stabilization, suggesting this one extremely prefers to stabilize the template duplex rather than third-strand. Besides, the triplex stabilization effect of ∆-1 is more marked in comparison with that of Λ-1. The obtained results suggest that substituent effects and chiralities of Ru(II) polypyridyl complexes play important roles in the triplex stabilization. Complexes Λ/Δ-[Ru(bpy)2(7-CH3-dppz)]2+ (Λ/Δ-1; bpy = 2,2'-bipyridine, 7-CH3-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) were prepared as stabilizers for poly(U-A ∗ U) triplex. Results suggest the triplex stabilization depends the chiral structures of Λ/Δ-1, indicating that [Ru(bpy)2(7-CH3-dppz)]2+ is a non-specific intercalator for poly(U-A ∗ U) investigated in this work.
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Affiliation(s)
- Zhan Dong
- College of Chemistry, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-Friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan, 411105, People's Republic of China. .,Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, 411105, People's Republic of China.
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17
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Tan L, Zhang J. A phenolic hydroxyl in the ortho- and meta-positions on the main ligands effect on the interactions of [Ru(phen) 2(o-HPIP)] 2+ and [Ru(phen) 2(m-HPIP)] 2+ with the poly(U)·poly(A)*poly(U) triplex. J Inorg Biochem 2020; 213:111268. [PMID: 33065523 DOI: 10.1016/j.jinorgbio.2020.111268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 01/14/2023]
Abstract
The association of two ruthenium(II) complexes [Ru(phen)2(o-HPIP)]2+ (Ru1; phen = 1,10-phenanthroline, o-HPIP = 2-(2-hydroxyphenyl)-imidazo[4,5-f][1,10] phenanthroline) and [Ru(phen)2(m-HPIP)]2+ (Ru2; m-HPIP = 2-(3-hydroxyphenyl)-imidazo[4,5-f][1,10]phenan- throline) with the RNA poly(U)·poly(A)⁎poly(U) triplex has been investigated by spectrophotometric titrations and melting experiments in this work. All experimental data reveal an intercalative triplex-binding mode of the two complexes, whereas the binding constant for Ru1 is significantly higher than that for Ru2. Circular dichroism spectroscopic investigations show that the two complexes could bind to the chiral environment of the triplex, but the triplex perturbation effects induced by Ru1 are more marked. Thermal denaturation experiments demonstrate that both Ru1 and Ru2 display a large binding preference and stabilizing effect for the third strand over the Watson-Crick base-paired duplex of the triplex. However, the third-strand stabilizing effect of Ru1 is much more effective than that of Ru2. The obtained results suggest that positions of the phenolic group on the main ligands have significant effect on the binding of the two complexes with poly(U)·poly(A)⁎poly(U) triplex.
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Affiliation(s)
- Lifeng Tan
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China; Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
| | - Jingwen Zhang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
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18
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Jiang L, Liu X, Tan L. Synthesis and characterization of chiral Ru(II) polypyridyl complexes and their binding and stabilizing effects toward triple-helical RNA. J Inorg Biochem 2020; 213:111263. [PMID: 33011626 DOI: 10.1016/j.jinorgbio.2020.111263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 01/11/2023]
Abstract
Two novel chiral Ru(II) complexes, Λ- and Δ-[Ru(bpy)2(7-CF3-dppz)]2+ (Λ-1 and Δ-1; bpy = 2,2'-bipyridine, 7-CF3-dppz = 7-trifluoromethyl-dipyrido[3,2-a:2',3'-c]phenazine), were synthesized and characterized in this work. The binding and stabilizing effects of Λ-1 and Δ-1 toward the RNA poly(U)•poly(A)*poly(U) triplex were studied by various biophysical techniques. Absorption spectra and fluorescence quenching indicates that the binding affinity of Δ-1 is slightly higher than that Λ-1. Both enantiomers induce significant positive viscosity changes that are indicative of intercalative binding, whereas changes in the relative viscosities of the triplex are found to be more pronounced with Δ-1. Melting experiments indicate that the triplex stabilization effects of both enantiomers are significantly different from each other. With Λ-1, the stabilization of the Watson-Crick base-paired duplex (the template duplex) of the triplex shows a moderate increase, whereas the stabilization of the Hoogsteen base-paired strand (third-strand) exhibits slight decrease under the same conditions, suggesting Λ-1 prefers to stabilize the template duplex rather than third-strand. In stark contrast to Λ-1, Δ-1 can not only strongly stabilize the template duplex, but also moderately increase the third-strand stabilization, even so, which imply that Δ-1 also prefer to stabilize the template duplex instead of the third-strand. These suggest that the [Ru(bpy)2(7-CF3-dppz)]2+ is similar as a non-specific metallointercalator the triplex studied in this work. Combined with our recent research, the obtained results further indicate that Δ- enantiomers rather than Λ-ones of Ru(II) polypyridyl complexes usually exhibit stronger binding and stabilizing effects toward the triplex.
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Affiliation(s)
- Lijuan Jiang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China; Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan 411105, People's Republic of China.
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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20
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Chen X, He Z, Wu X, Mao D, Feng C, Zhang J, Chen G. Comprehensive study of the interaction between Puerariae Radix flavonoids and DNA: From theoretical simulation to structural analysis to functional analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:118109. [PMID: 32062512 DOI: 10.1016/j.saa.2020.118109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Puerariae Radix (PR) is a natural herb whose active ingredient is mainly flavonoids. To explore the interaction between PR flavonoids and DNA not only has important biological implications for understanding the mechanism of action, but also helps develop PR products for the design of appropriate dietary interventions to aid cancer treatment. In this work, we comprehensively studied the interaction between six kinds of PR flavonoids and DNA from four different and progressive levels, including molecular docking, multi-spectral analysis, and functional analysis in vitro and in cell. Results show that the DNA binding affinity of six flavonoids is in an order of quercetin > formononetin > daidzein > puerarin > 4'-methoxy puerarin > puerarin 6″-O-xyloside (POS), in which quercetin can significantly inhibit DNA amplification owing to its strongest binding affinity. The binding between quercetin and DNA is further revealed to be intercalated binding, which can cause conformational changes in DNA, thereby exhibiting an activity of cell cycle arrest and anti-proliferative. This property of quercetin can be utilized for the further development of flavonoids with anticancer activity. In addition to the potential application, this work also provides a platform for the comprehensive study of the interaction between micromolecules and DNA.
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Affiliation(s)
- Xu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China; Experimental Center for Life Sciences, Shanghai University, Shanghai, PR China
| | - Ziyu He
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Xianyong Wu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China.
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21
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Wang F, Sun Y, Liu X, Li Y, Tan L. Third-strand stabilizing effects of the RNA poly(U)·poly(A)*poly(U) triplex by a ruthenium(II) polypyridine complex and its hexaarginine peptide conjugate. Int J Biol Macromol 2019; 135:1134-1141. [PMID: 31176864 DOI: 10.1016/j.ijbiomac.2019.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/28/2019] [Accepted: 06/04/2019] [Indexed: 01/14/2023]
Abstract
In this work, a Ru(II) complex [Ru(bpy)2(pip-CO2H)]2+ (Ru1) and its hexaarginine peptide conjugate [Ru(bpy)2(pic-Arg6)]8+ (Ru2) have been synthesized and characterized. The binding of Ru1 and Ru2 with poly(U)•poly(A)*poly(U) triplex has been studied. Results suggest that Ru1 binds in the surface of the minor groove while Ru2 binds to the minor groove of the triplex. Consequently, the triplex stabilization is barely affected by Ru1, while with Ru2 the triplex stabilizing effect is so strong that that dissociation of the triplex shows an overlapping of both melting processes with the melting temperature increased to a maximum of 56.1 °C at the CRu2/CUAU ratio of 0.05, where ΔTm1 and ΔTm2 are 19.6 and 10.1 °C, respectively. Furthermore, the effect of Ru2 stabilizing the third strand at such a low binding ratio of 0.05 is more marked than what obsereved for flavone luteolin and [Ru(bpy)2(mdpz)]2+, which are so far the strongest triplex stabilizers in the reported organic small molecules and metal complexes, respectively. Considering the structure natures of Ru2, conceivably except for electrostatic interaction, the forces stabilizing the triplex should also involve hydrophobic interaction and hydrogen bingding. To our knowledge, this work represents a first example of improving the triplex stabilization by a metallopeptide.
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Affiliation(s)
- Fangfang Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Yanmei Sun
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, PR China
| | - Yi Li
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, PR China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, PR China; Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan 411105, PR China.
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Bhuiya S, Chowdhury S, Haque L, Das S. Spectroscopic, photophysical and theoretical insight into the chelation properties of fisetin with copper (II) in aqueous buffered solutions for calf thymus DNA binding. Int J Biol Macromol 2018; 120:1156-1169. [DOI: 10.1016/j.ijbiomac.2018.08.162] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/21/2018] [Accepted: 08/27/2018] [Indexed: 01/29/2023]
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Bhattacharjee S, Chakraborty S, Chorell E, Sengupta PK, Bhowmik S. Importance of the hydroxyl substituents in the B-ring of plant flavonols on their preferential binding interactions with VEGF G-quadruplex DNA: Multi-spectroscopic and molecular modeling studies. Int J Biol Macromol 2018; 118:629-639. [PMID: 29953891 DOI: 10.1016/j.ijbiomac.2018.06.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 10/28/2022]
Abstract
G-quadruplex (G4) structures are known to be promising anticancer drug targets and flavonols (an important class of flavonoids) are small molecules reported to possess several health-promoting properties including those of anticancer activities. In this work, we explored the interactions of the structurally related plant flavonols kaempferol (KAE; 3,5,7,4'OH flavone) and morin (MOR; 3,5,7,2',4'OH flavone) with various G4-DNA sequences along with duplex DNA using a combination of spectroscopic and molecular docking studies. Our results revealed that KAE shows preferential interaction with VEGF G4-DNA in comparison to the other G4 sequences and duplex DNA. Moreover, KAE enhances the thermal stability of VEGF G4-DNA. In contrast, MOR exhibits an appreciably weaker level of interaction with both duplex and various G4-DNAs, with no significant structural specificity. The contrasting DNA binding behaviors suggest a crucial role of the 2'OH substituent in the B-ring of flavonol moiety. While KAE is relatively planar, MOR adopts a significantly non-planar conformation attributable to steric hindrance from the additional 2'OH substituent. This small structural difference is apparently very important for the ability of KAE and MOR to interact with VEGF G4-DNA. Thus, KAE (but not MOR) appears to be an effective ligand for VEGF G4-DNA, opening up possibilities of its application for regulation of gene expression in cancer cells.
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Affiliation(s)
- Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sandipan Chakraborty
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Pradeep K Sengupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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Haque L, Bhuiya S, Das S. Assessment of intercalative interaction of the benzophenanthridine plant alkaloid nitidine with higher-ordered forms of RNA: spectroscopic evaluation. NEW J CHEM 2018. [DOI: 10.1039/c8nj03705a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectrophotometric, spectropolarimetric, viscometric and spectrofluorimetric analysis of the binding of the alkaloid nitidine to double- and triple-helical forms of RNA have served to highlight the ability of this drug to produce changes in the structure of RNA.
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Affiliation(s)
- Lucy Haque
- Department of Chemistry
- Jadavpur University
- Raja S. C. Mullick Road
- Kolkata 700 032
- India
| | - Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Raja S. C. Mullick Road
- Kolkata 700 032
- India
| | - Suman Das
- Department of Chemistry
- Jadavpur University
- Raja S. C. Mullick Road
- Kolkata 700 032
- India
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