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Bian Y, Lv F, Pan H, Ren W, Zhang W, Wang Y, Cao Y, Li W, Wang W. Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation. JACS AU 2024; 4:3690-3704. [PMID: 39328748 PMCID: PMC11423313 DOI: 10.1021/jacsau.4c00690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024]
Abstract
Biomolecular condensation involving proteins and nucleic acids has been recognized to play crucial roles in genome organization and transcriptional regulation. However, the biophysical mechanisms underlying the droplet fusion dynamics and microstructure evolution during the early stage of liquid-liquid phase separation (LLPS) remain elusive. In this work, we study the phase separation of linker histone H1, which is among the most abundant chromatin proteins, in the presence of single-stranded DNA (ssDNA) capable of forming a G-quadruplex by using molecular simulations and experimental characterization. We found that droplet fusion is a rather stochastic and kinetically controlled process. Productive fusion events are triggered by the formation of ssDNA-mediated electrostatic bridges within the droplet contacting zone. The droplet microstructure is size-dependent and evolves driven by maximizing the number of electrostatic contacts. We also showed that the folding of ssDNA to the G-quadruplex promotes LLPS by increasing the multivalency and strength of protein-DNA interactions. These findings provide deep mechanistic insights into the growth dynamics of biomolecular droplets and highlight the key role of kinetic control during the early stage of ssDNA-protein condensation.
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Affiliation(s)
- Yunqiang Bian
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
| | - Fangyi Lv
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Hai Pan
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
| | - Weitong Ren
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
| | - Weiwei Zhang
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
| | - Yanwei Wang
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Yi Cao
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
| | - Wenfei Li
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, Zhejiang, China
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
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Li Z, Hu R, Li T, Zhu J, You H, Li Y, Liu BF, Li C, Li Y, Yang Y. A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending. Proc Natl Acad Sci U S A 2024; 121:e2315401121. [PMID: 38232280 PMCID: PMC10823215 DOI: 10.1073/pnas.2315401121] [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: 09/08/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.
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Affiliation(s)
- Zheyu Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
- Optics Valley Laboratory, Hubei430074, China
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Garaiová Z, Gašperová M, Šubjaková V, Hianik T. Interaction of G-quadruplex Forming DNA Aptamers with PAMAM Dendrimers Studied by Dynamic Light Scattering and UV-VIS Spectrophotometry. Chemphyschem 2023; 24:e202300264. [PMID: 37318900 DOI: 10.1002/cphc.202300264] [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: 04/13/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
The complexes of G-quadruplex forming DNA thrombin binding aptamers (TBA) and polyamidoamine dendrimers (PAMAM) were studied with the aim to form a model targeted drug delivery system. Hydrodynamic diameter, zeta potential and melting temperature (Tm ) were investigated by dynamic light scattering and UV-VIS spectrophotometry. Non-covalent adsorption by means of electrostatic interaction between positively charged amino groups of dendrimers (+) and negatively charged phosphate groups of aptamers (-) has driven the formation of aggregates. The size of complexes was in the range of 0.2-2 μm and depended on the type of dispersant, charge ratio (+/-) and temperature. Raising the temperature increased the polydispersity, new smaller size distributions were observed indicating the G-quadruplex unfolding. The melting transition temperature of TBA aptamer was affected by the presence of amino-terminated PAMAM rather than carboxylated succinic acid PAMAM-SAH dendrimer, thus supporting the electrostatic nature of interaction that disturbed denaturation of target-specific quadruplex aptamer structure.
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Affiliation(s)
- Zuzana Garaiová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Martina Gašperová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Veronika Šubjaková
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovakia
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Sarkar S, Bisoi A, Singh PC. Antimalarial Drugs Induce the Selective Folding of Human Telomeric G-Quadruplex in a Cancer-Mimicking Microenvironment. J Phys Chem B 2023; 127:6648-6655. [PMID: 37467470 DOI: 10.1021/acs.jpcb.3c03042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Regulating the equilibrium between the duplex form of DNA and G-quadruplex (Gq) and stabilizing the folded Gq are the critical factors for any drug to be effective in cancer therapy due to the direct involvement of Gq in controlling the transcription process. Antimalarial drugs are in the trial stage for different types of cancer diseases; however, the plausible mechanism of action of these drug molecules is not well known. Hence, we investigate the plausible role of antimalarial drugs in the folding and stabilization of Gq-forming DNA sequences from the telomere and promoter gene regions by varying the salt (KCl) concentrations, mimicking the in vitro cancerous and normal cell microenvironments. The study reveals that antimalarial drugs fold and stabilize specifically to telomere Gq-forming sequences in the cancerous microenvironment than the DNA sequences located in the promoter region of the gene. Antimalarial drugs are not only able to fold Gq but also efficiently protect them from unfolding by their complementary strands, hence significantly biasing the equilibrium toward the Gq formation from the duplex. In contrast, in a normal cell microenvironment, K+ controls the folding of telomeres, and the role of antimalarial drugs is not prominent. This study suggests that the action of antimalarial drugs is sensitive to the cancer microenvironment as well as selective to the Gq-forming region.
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Affiliation(s)
- Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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5
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Safiarian M, Ugboya A, Khan I, Marichev KO, Grant KB. New Insights into the Phototoxicity of Anthracene-Based Chromophores: The Chloride Salt Effect†. Chem Res Toxicol 2023; 36:1002-1020. [PMID: 37347986 PMCID: PMC10354805 DOI: 10.1021/acs.chemrestox.2c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Indexed: 06/24/2023]
Abstract
Unraveling the causes underlying polycyclic aromatic hydrocarbon phototoxicity is an essential step in understanding the harmful effects of these compounds in nature. Toward this end, we have studied the DNA interactions and photochemistry of N1-(anthracen-9-ylmethyl)ethane-1,2-diaminium dichloride in the presence and absence of NaF, KF, NaCl, KCl, NaBr, KBr, NaI, and KI (350 nm hν, pH 7.0). Exposing pUC19 plasmid to UV light in solutions containing 400 mM KCl formed significantly more direct strand breaks in DNA compared to no-salt control reactions. In contrast, NaCl increased DNA damage moderately, while the sodium(I) and potassium(I) fluoride, bromide, and iodide salts generally inhibited cleavage (I- > Br- > F-). A halide anion-induced heavy-atom effect was indicated by monitoring anthracene photodegradation and by employing the hydroxyl radical (•OH) probe hydroxyphenyl fluorescein (HPF). These studies revealed that among no-salt controls and the eight halide salts, only NaCl and KCl enabled the anthracene to photosensitize the production of high levels of DNA-damaging reactive oxygen species (ROS). Pre-irradiation of N1-(anthracen-9-ylmethyl)ethane-1,2-diaminium dichloride at 350 nm increased the amounts of chloride salt-induced •OH detected by HPF in subsequent anthracene photoactivation experiments. Taking into consideration that •OH and other highly reactive ROS are extremely short-lived, this result suggests that the pre-irradiation step might lead to the formation of oxidized anthracene photoproducts that are exceedingly redox-active. The fluorometric probes HPF and Singlet Oxygen Sensor Green revealed that KCl concentrations ranging from 150 to 400 mM and from 100 to 400 mM, respectively, enhanced N1-(anthracen-9-ylmethyl)ethane-1,2-diaminium dichloride photosensitized •OH and singlet oxygen (1O2) production over no-salt controls. Considering the relatively high levels of Na+, K+, and Cl- ions that exist in the environment and in living organisms, our findings may be relevant to the phototoxic effects exhibited by anthracenes and other polycyclic hydrocarbons in vivo.
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Affiliation(s)
| | | | - Imran Khan
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kostiantyn O. Marichev
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kathryn B. Grant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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6
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Wang W, Cheng S, Zhao Y, Cheng K, Gao M, Lu H, Liu X, Xing X. Colorimetric Detection of S1 Nuclease Activity using a Hairpin DNA with Split G-Quadruplex. ANAL LETT 2023. [DOI: 10.1080/00032719.2023.2193749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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7
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Olejko L, Dutta A, Shahsavar K, Bald I. Influence of Different Salts on the G-Quadruplex Structure Formed from the Reversed Human Telomeric DNA Sequence. Int J Mol Sci 2022; 23:ijms232012206. [PMID: 36293060 PMCID: PMC9602856 DOI: 10.3390/ijms232012206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
G-rich telomeric DNA plays a major role in the stabilization of chromosomes and can fold into a plethora of different G-quadruplex structures in the presence of mono- and divalent cations. The reversed human telomeric DNA sequence (5′-(GGG ATT)4; RevHumTel) was previously shown to have interesting properties that can be exploited for chemical sensing and as a chemical switch in DNA nanotechnology. Here, we analyze the specific G-quadruplex structures formed by RevHumTel in the presence of K+, Na+, Mg2+ and Ca2+ cations using circular dichroism spectroscopy (CDS) and Förster resonance energy transfer (FRET) based on fluorescence lifetimes. CDS is able to reveal strand and loop orientations, whereas FRET gives information about the distances between the 5′-end and the 3′-end, and also, the number of G-quadruplex species formed. Based on this combined information we derived specific G-quadruplex structures formed from RevHumTel, i.e., a chair-type and a hybrid-type G-quadruplex structure formed in presence of K+, whereas Na+ induces the formation of up to three different G-quadruplexes (a basket-type, a propeller-type and a hybrid-type structure). In the presence of Mg2+ and Ca2+ two different parallel G-quadruplexes are formed (one of which is a propeller-type structure). This study will support the fundamental understanding of the G-quadruplex formation in different environments and a rational design of G-quadruplex-based applications in sensing and nanotechnology.
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Liu L, Zhu L, Tong H, Su C, Wells JW, Chalikian TV. Distribution of Conformational States Adopted by DNA from the Promoter Regions of the VEGF and Bcl-2 Oncogenes. J Phys Chem B 2022; 126:6654-6670. [PMID: 36001297 DOI: 10.1021/acs.jpcb.2c04304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We employed a previously described procedure, based on circular dichroism (CD) spectroscopy, to quantify the distribution of conformational states adopted by equimolar mixtures of complementary G-rich and C-rich DNA strands from the promoter regions of the VEGF and Bcl-2 oncogenes. Spectra were recorded at different pHs, concentrations of KCl, and temperatures. The temperature dependences of the fractional populations of the duplex, G-quadruplex, i-motif, and coiled conformations of each promoter were then analyzed within the framework of a thermodynamic model to obtain the enthalpy and melting temperature of each folded-to-unfolded transition involved in the equilibrium. A comparison of the conformational data on the VEGF and Bcl-2 DNA with similar results on the c-MYC DNA, which we reported previously, reveals that the distribution of conformational states depends on the specific DNA sequence and is modulated by environmental factors. Under the physiological conditions of room temperature, neutral pH, and elevated concentrations of potassium ions, the duplex conformation coexists with the G-quadruplex conformation in proportions that depend on the sequence. This observed conformational diversity has biological implications, and it further supports our previously proposed thermodynamic hypothesis of gene regulation. In that hypothesis, a specific distribution of duplex and tetraplex conformations in a promoter region is fine-tuned to maintain the healthy level of gene expression. Any deviation from a healthy distribution of conformational states may result in pathology stemming from up- or downregulation of the gene.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Legeng Zhu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Haoyuan Tong
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Chongyu Su
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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Chitbankluai K, Thavarungkul P, Kanatharana P, Kaewpet M, Buranachai C. Newly found K +-Thioflavin T competitive binding to DNA G-quadruplexes and the development of a label-free fluorescent biosensor with extra low detection limit for K + determination in urine samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121244. [PMID: 35429866 DOI: 10.1016/j.saa.2022.121244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
The determination of potassium ion K+ in body fluids is important in health monitoring and diagnoses. One of the interesting and simple methods for K+ detection is the use of label-free biosensors based on DNA G-quadruplexes (GQs) coupled with a specific fluorescent probe, such as Thioflavin T (ThT), which lights up when bound with K+-stabilized GQs. However, these biosensors are not generally sensitive. In this work, we found a solution: at a low concentration, K+ competes with ThT in binding to a bimolecular GQ or a tetramolecular GQ, resulting in a decrease in ThT fluorescence emission with increasing K+. Therefore, we developed a label-free turn-off fluorescent K+ sensor. The sensor provides a very low detection limit of 21.87 ± 0.59 nM. Other possible interfering components in urine did not exert any effect even at quantities that were 10-fold greater than their upper limit of normal concentrations found in urine samples. With its only requirement of diluting samples, the developed low-cost label-free probe and simple sensor was successfully applied to the direct detection of K+ in normal urine samples with high accuracy (recoveries ranged from 90% to 100%).
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Affiliation(s)
- Khwanrudee Chitbankluai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand
| | - Panote Thavarungkul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Proespichaya Kanatharana
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Morakot Kaewpet
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Chittanon Buranachai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand; Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, 10400, Thailand.
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10
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Ishiguro A, Ishihama A. Essential Roles and Risks of G-Quadruplex Regulation: Recognition Targets of ALS-Linked TDP-43 and FUS. Front Mol Biosci 2022; 9:957502. [PMID: 35898304 PMCID: PMC9309350 DOI: 10.3389/fmolb.2022.957502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to form a square planar arrangement. A set of RNA-binding proteins specifically recognize G4 structures and play certain unique physiological roles. These G4-binding proteins form ribonucleoprotein (RNP) through a physicochemical phenomenon called liquid-liquid phase separation (LLPS). G4-containing RNP granules are identified in both prokaryotes and eukaryotes, but extensive studies have been performed in eukaryotes. We have been involved in analyses of the roles of G4-containing RNAs recognized by two G4-RNA-binding proteins, TDP-43 and FUS, which both are the amyotrophic lateral sclerosis (ALS) causative gene products. These RNA-binding proteins play the essential roles in both G4 recognition and LLPS, but they also carry the risk of agglutination. The biological significance of G4-binding proteins is controlled through unique 3D structure of G4, of which the risk of conformational stability is influenced by environmental conditions such as monovalent metals and guanine oxidation.
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11
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Detecting G4 unwinding. Methods Enzymol 2022; 672:261-281. [DOI: 10.1016/bs.mie.2022.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
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Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
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14
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Chalikian TV, Macgregor RB. Volumetric Properties of Four-Stranded DNA Structures. BIOLOGY 2021; 10:813. [PMID: 34440045 PMCID: PMC8389613 DOI: 10.3390/biology10080813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022]
Abstract
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute-solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.
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Affiliation(s)
- Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada;
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15
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Liu L, Scott L, Tariq N, Kume T, Dubins DN, Macgregor RB, Chalikian TV. Volumetric Interplay between the Conformational States Adopted by Guanine-Rich DNA from the c-MYC Promoter. J Phys Chem B 2021; 125:7406-7416. [PMID: 34185535 DOI: 10.1021/acs.jpcb.1c04075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The kinetic and thermodynamic stabilities of G-quadruplex structures have been extensively studied. In contrast, systematic investigations of the volumetric properties of G-quadruplexes determining their pressure stability are still relatively scarce. The G-rich strand from the promoter region of the c-MYC oncogene (G-strand) is known to adopt a range of conformational states including the duplex, G-quadruplex, and coil states depending on the presence of the complementary C-rich strand (C-strand) and solution conditions. In this work, we report changes in volume, ΔV, and adiabatic compressibility, ΔKS, accompanying interconversions of G-strand between the G-quadruplex, duplex, and coil conformations in the presence and absence of C-strand. We rationalize these volumetric characteristics in terms of the hydration and intrinsic properties of the DNA in each of the sampled conformational states. We further use our volumetric results in conjunction with the reported data on changes in expansibility, ΔE, and heat capacity, ΔCP, associated with G-quadruplex-to-coil transitions to construct the pressure-temperature phase diagram describing the stability of the G-quadruplex. The phase diagram is elliptic in shape, resembling the classical elliptic phase diagram of a globular protein, and is distinct from the phase diagram for duplex DNA. The observed similarity of the pressure-temperature phase diagrams of G-quadruplexes and globular proteins stems from their shared structural and hydration features that, in turn, result in the similarity of their volumetric properties. To the best of our knowledge, this is the first pressure-temperature stability diagram reported for a G-quadruplex.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Lily Scott
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Nabeel Tariq
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Takuma Kume
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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16
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Platella C, Mazzini S, Napolitano E, Mattio LM, Beretta GL, Zaffaroni N, Pinto A, Montesarchio D, Dallavalle S. Plant-Derived Stilbenoids as DNA-Binding Agents: From Monomers to Dimers. Chemistry 2021; 27:8832-8845. [PMID: 33890349 PMCID: PMC8251996 DOI: 10.1002/chem.202101229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 01/18/2023]
Abstract
Stilbenoids are natural compounds endowed with several biological activities, including cardioprotection and cancer prevention. Among them, (±)-trans-δ-viniferin, deriving from trans-resveratrol dimerization, was investigated in its ability to target DNA duplex and G-quadruplex structures by exploiting NMR spectroscopy, circular dichroism, fluorescence spectroscopy and molecular docking. (±)-trans-δ-Viniferin proved to bind both the minor and major grooves of duplexes, whereas it bound the 3'- and 5'-ends of a G-quadruplex by stacking on the outer quartets, accompanied by rearrangement of flanking residues. Specifically, (±)-trans-δ-viniferin demonstrated higher affinity for the investigated DNA targets than its monomeric counterpart. Additionally, the methoxylated derivatives of (±)-trans-δ-viniferin and trans-resveratrol, i. e. (±)-pterostilbene-trans-dihydrodimer and trans-pterostilbene, respectively, were evaluated, revealing similar binding modes, affinities and stoichiometries with the DNA targets as their parent analogues. All tested compounds were cytotoxic at μM concentration on several cancer cell lines, showing DNA damaging activity consistent with their ability to tightly interact with duplex and G-quadruplex structures.
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Affiliation(s)
- Chiara Platella
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DeFENS)Università degli Studi di Milanovia Celoria 220133MilanItaly
| | - Ettore Napolitano
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Luce M. Mattio
- Department of Food, Environmental and Nutritional Sciences (DeFENS)Università degli Studi di Milanovia Celoria 220133MilanItaly
| | - Giovanni Luca Beretta
- Molecular Pharmacology UnitDepartment of Applied Research and Technological Development Fondazione IRCCS Istituto Nazionale Tumorivia Amadeo 4220133MilanItaly
| | - Nadia Zaffaroni
- Molecular Pharmacology UnitDepartment of Applied Research and Technological Development Fondazione IRCCS Istituto Nazionale Tumorivia Amadeo 4220133MilanItaly
| | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS)Università degli Studi di Milanovia Celoria 220133MilanItaly
| | - Daniela Montesarchio
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DeFENS)Università degli Studi di Milanovia Celoria 220133MilanItaly
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17
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Vianney YM, Weisz K. First Tandem Repeat of a Potassium Channel KCNN4 Minisatellite Folds into a V-Loop G-Quadruplex Structure. Biochemistry 2021; 60:1337-1346. [PMID: 33844501 DOI: 10.1021/acs.biochem.1c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The KCNN4 gene encoding a potassium channel protein whose expression has been correlated with tumor progression was found to comprise a guanine-rich minisatellite region with the ability to form a putative G-quadruplex (G4). Given the suggested regulatory role of G4s in gene expression, G-quadruplex formation for the polymorphic first repeat of the minisatellite was studied by nuclear magnetic resonance spectroscopy. A stable G-quadruplex of a truncated mutant sequence was shown to represent one of several coexisting species of the wild-type sequence. The high-resolution structure features a noncanonical G4 with a broken G-column and a V-shaped loop. The presence of a 3'-flanking thymidine interacting with the lateral loop preceding the V loop seems to be critical for the formation of this G4 topology. On the contrary, an additional 5'-flanking residue disfavored but still allowed folding into the V-loop structure. The latter may therefore serve as a putative therapeutic target in strategies for G4-based modulation of KCNN4 expression.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
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18
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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19
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Liu L, Ma C, Wells JW, Chalikian TV. Conformational Preferences of DNA Strands from the Promoter Region of the c-MYC Oncogene. J Phys Chem B 2020; 124:751-762. [PMID: 31923361 DOI: 10.1021/acs.jpcb.9b10518] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized the conformational preferences of DNA in an equimolar mixture of complementary G-rich and C-rich strands from the promoter region of the c-MYC oncogene. Our CD-based approach presupposes that the CD spectrum of such a mixture is the spectral sum of the constituent duplex, G-quadruplex, i-motif, and coiled conformations. Spectra were acquired over a range of temperatures at different pHs and concentrations of KCl. Each spectrum was unmixed in terms of the predetermined spectra of the constituent conformational states to obtain the corresponding weighting factors for their fractional contributions to the total population of DNA. The temperature dependences of those contributions then were analyzed in concert according to a model based on a thermodynamic representation of the underlying equilibria. Fitted estimates of the melting enthalpy and temperature obtained for the duplex, G-quadruplex, and i-motif imply that the driving force behind dissociation of the duplex and the concomitant formation of tetrahelical structures is the folding of the G-strand into the G-quadruplex. The liberated C-strand adopts the i-motif conformation at acidic pH and exists in the coiled state at neutral pH. The i-motif alone cannot induce dissociation of the duplex even at pH 5.0, at which it is most stable. Under the physiological conditions of neutral pH, elevated potassium, and room temperature, the duplex and G-quadruplex conformations coexist with the C-strand in the coiled state. Taken together, our results suggest a novel, thermodynamically controlled mechanism for the regulation of gene expression.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Congshan Ma
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
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20
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Chen B, Fountain G, Sullivan HJ, Paradis N, Wu C. To probe the binding pathway of a selective compound (D089-0563) to c-MYC Pu24 G-quadruplex using free ligand binding simulations and Markov state model analysis. Phys Chem Chem Phys 2020; 22:22567-22583. [DOI: 10.1039/d0cp03863f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
D089-0563 is a highly promising anti-cancer compound that selectively binds the transcription-silencing G-quadruplex element (Pu27) at the promoter region of the human c-MYC oncogene; however, its binding mechanism remains elusive.
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Affiliation(s)
- Brian Chen
- Rowan University
- College of Science and Mathematics
- Glassboro
- USA
| | | | | | | | - Chun Wu
- Rowan University
- College of Science and Mathematics
- Glassboro
- USA
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21
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Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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22
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DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. Proc Natl Acad Sci U S A 2019; 116:20453-20461. [PMID: 31548374 DOI: 10.1073/pnas.1909047116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are noncanonical secondary structures formed in guanine-rich DNA and RNA sequences. MYC, one of the most critical oncogenes, forms a DNA G4 in its proximal promoter region (MycG4) that functions as a transcriptional silencer. However, MycG4 is highly stable in vitro and its regulatory role would require active unfolding. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, is extremely proficient at unfolding MycG4-DNA. Our results show that DDX5 is a highly active G4-resolvase that does not require a single-stranded overhang and that ATP hydrolysis is not directly coupled to G4-unfolding of DDX5. The chromatin binding sites of DDX5 are G-rich sequences. In cancer cells, DDX5 is enriched at the MYC promoter and activates MYC transcription. The DDX5 interaction with the MYC promoter and DDX5-mediated MYC activation is inhibited by G4-interactive small molecules. Our results uncover a function of DDX5 in resolving DNA and RNA G4s and suggest a molecular target to suppress MYC for cancer intervention.
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23
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Paul A, Musetti C, Nanjunda R, Wilson WD. Biosensor-Surface Plasmon Resonance: Label-Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions. Methods Mol Biol 2019; 2035:63-85. [PMID: 31444744 DOI: 10.1007/978-1-4939-9666-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
Abstract
Biosensor-surface plasmon resonance (SPR) technology is now well established as a quantitative approach for the study of nucleic acid interactions in real time, without the need for labeling any components of the interaction. The method provides real-time equilibrium and kinetic characterization for quadruplex DNA interactions and requires small amounts of materials and no external probe. A detailed protocol for quadruplex-DNA interaction analyses with a variety of binding molecules using biosensor-SPR methods is presented. Explanations of the SPR method with basic fundamentals for use and analysis of results are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples. Details of experimental design, quantitative and qualitative data analyses, and presentation are described. Some specific examples of small molecule-DNA quadruplex interactions are presented with results evaluated by both kinetic and steady-state SPR methods.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Caterina Musetti
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Department of Screening, Profiling and Mechanistic Biology, Platform Technology and Science, Glaxo Smith Kline, Collegeville, PA, USA
| | - Rupesh Nanjunda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.,Janssen Research and Development, Spring House, PA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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24
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Arns L, Knop JM, Patra S, Anders C, Winter R. Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes. Biophys Chem 2019; 251:106190. [PMID: 31146215 DOI: 10.1016/j.bpc.2019.106190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
In this review we discuss results from temperature and pressure dependent single-molecule Förster resonance energy transfer (smFRET) studies on nucleic acids in the presence of macromolecular crowders and organic osmolytes. As representative examples, we have chosen fragments of both DNAs and RNAs, i.e., a synthetic DNA hairpin, a human telomeric G-quadruplex and the microROSE RNA hairpin. To mimic the effects of intracellular components, our studies include the macromolecular crowding agent Ficoll, a copolymer of sucrose and epichlorohydrin, and the organic osmolytes trimethylamine N-oxide, urea and glycine as well as natural occurring osmolyte mixtures from deep sea organisms. Furthermore, the impact of mutations in an RNA sequence on the conformational dynamics is examined. Different from proteins, the effects of the osmolytes and crowding agents seem to strongly dependent on the structure and chemical make-up of the nucleic acid.
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Affiliation(s)
- Loana Arns
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Jim-Marcel Knop
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Satyajit Patra
- Aix Marseille Université, CNRS, Centralle Marseille, Institut Fresnel, F-13013 Marseille, France
| | - Christian Anders
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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25
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Li J, Chen C, Wei J, Pan Y, Su C, Zhang X. SpPKE1, a Multiple Stress-Responsive Gene Confers Salt Tolerance in Tomato and Tobacco. Int J Mol Sci 2019; 20:E2478. [PMID: 31137458 PMCID: PMC6566969 DOI: 10.3390/ijms20102478] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Understanding the mechanism of abiotic-tolerance and producing germplasm of abiotic tolerance are important in plant research. Wild species often show more tolerance of environmental stress factors than their cultivated counterparts. Genes from wild species show potential abilities to improve abiotic resistance in cultivated species. Here, a tomato proline-, lysine-, and glutamic-rich type gene SpPKE1 was isolated from abiotic-resistant species (Solanum pennellii LA0716) for over-expression in tomato and tobacco for salt tolerance. The protein encoded by SpPKE1 was predominantly localized in the cytoplasm in tobacco. SpPKE1 and SlPKE1 (from cultivated species S. lycopersicum cv. M82) shared 89.7% similarity in amino acid sequences and their transcripts abundance in flowers and fruits was reduced by the imposition of drought or oxidative stress and the exogenous supply of abscisic acid. The DNA of the PKE1 promoter was highly methylated in fruit and leaf, and the methylation of the coding sequence in leaf was significantly higher than that in fruit at different development stages. The over-expression of SpPKE1 under the control of a CaMV (Cauliflower Mosaic Virus) 35S promoter in transgenic tomato and tobacco plants enhanced their tolerance to salt stress. PKE1 was downregulated by abiotic stresses but enhanced the plant's salt stress tolerance. Therefore, this gene may be involved in post-transcriptional regulation and may be an important candidate for molecular breeding of salt-tolerant plants.
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Affiliation(s)
- Jinhua Li
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chunrui Chen
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Juanjuan Wei
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Yu Pan
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Chenggang Su
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
| | - Xingguo Zhang
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China.
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26
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Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. J Biol Chem 2018; 293:17792-17802. [PMID: 30257865 DOI: 10.1074/jbc.ra118.004499] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/18/2018] [Indexed: 11/06/2022] Open
Abstract
In addition to unwinding double-stranded nucleic acids, helicase activity can also unfold noncanonical structures such as G-quadruplexes. We previously characterized Pif1 helicase catalyzed unfolding of parallel G-quadruplex DNA. Here we characterized unfolding of the telomeric G-quadruplex, which can fold into antiparallel and mixed hybrid structures and found significant differences. Telomeric DNA sequences are unfolded more readily than the parallel quadruplex formed by the c-MYC promoter in K+ Furthermore, we found that under conditions in which the telomeric quadruplex is less stable, such as in Na+, Pif1 traps thermally melted quadruplexes in the absence of ATP, leading to the appearance of increased product formation under conditions in which the enzyme is preincubated with the substrate. Stable telomeric G-quadruplex structures were unfolded in a stepwise manner at a rate slower than that of duplex DNA unwinding; however, the slower dissociation from G-quadruplexes compared with duplexes allowed the helicase to traverse more nucleotides than on duplexes. Consistent with this, the rate of ATP hydrolysis on the telomeric quadruplex DNA was reduced relative to that on single-stranded DNA (ssDNA), but less quadruplex DNA was needed to saturate ATPase activity. Under single-cycle conditions, telomeric quadruplex was unfolded by Pif1, but for the c-MYC quadruplex, unfolding required multiple helicase molecules loaded onto the adjacent ssDNA. Our findings illustrate that Pif1-catalyzed unfolding of G-quadruplex DNA is highly dependent on the specific sequence and the conditions of the reaction, including both the monovalent cation and the order of addition.
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Affiliation(s)
- Alicia K Byrd
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Matthew R Bell
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Kevin D Raney
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
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27
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Yu Z, Zhou W, Ma G, Li Y, Fan L, Li X, Lu Y. Insights into the Competition between K+ and Pb2+ Binding to a G-Quadruplex and Discovery of a Novel K+–Pb2+–Quadruplex Intermediate. J Phys Chem B 2018; 122:9382-9388. [DOI: 10.1021/acs.jpcb.8b08161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ze Yu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Wei Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ge Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yunchao Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Louzhen Fan
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiaohong Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yi Lu
- Department of Chemistry, Department of Materials Science and Engineering, University of Illinois at Urbana and Champaign, Urbana, Illinois 61801, United States
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28
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Liu L, Kim BG, Feroze U, Macgregor RB, Chalikian TV. Probing the Ionic Atmosphere and Hydration of the c-MYC i-Motif. J Am Chem Soc 2018; 140:2229-2238. [DOI: 10.1021/jacs.7b11537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Ujala Feroze
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B. Macgregor
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences,
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College
Street, Toronto, Ontario M5S 3M2, Canada
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29
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Qin QP, Zou BQ, Tan MX, Wang SL, Liu YC, Liang H. Tryptanthrin derivative copper(ii) complexes with high antitumor activity by inhibiting telomerase activity, and inducing mitochondria-mediated apoptosis and S-phase arrest in BEL-7402. NEW J CHEM 2018. [DOI: 10.1039/c8nj03005g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Try-Cu exhibited its antitumor activity mainly via inhibiting telomerase by interaction with the c-myc promoter and disrupting mitochondrial functions.
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Affiliation(s)
- Qi-Pin Qin
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, School of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road
- Yulin 537000
- P. R. China
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road
- Guilin 541004
| | - Bi-Qun Zou
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road
- Guilin 541004
- P. R. China
- Department of Chemistry, Guilin Normal College, 21 Xinyi Road
- Gulin 541001
| | - Ming-Xiong Tan
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, School of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road
- Yulin 537000
- P. R. China
| | - Shu-Long Wang
- Guangxi Key Lab of Agricultural Resources Chemistry and Biotechnology, School of Chemistry and Food Science, Yulin Normal University, 1303 Jiaoyudong Road
- Yulin 537000
- P. R. China
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road
- Guilin 541004
| | - Yan-Cheng Liu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road
- Guilin 541004
- P. R. China
| | - Hong Liang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road
- Guilin 541004
- P. R. China
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30
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Aslanyan L, Ko J, Kim BG, Vardanyan I, Dalyan YB, Chalikian TV. Effect of Urea on G-Quadruplex Stability. J Phys Chem B 2017; 121:6511-6519. [DOI: 10.1021/acs.jpcb.7b03479] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lusine Aslanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Jordan Ko
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ishkhan Vardanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Yeva B. Dalyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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31
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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32
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Guo P, Lam SL. Unusual structures of CCTG repeats and their participation in repeat expansion. Biomol Concepts 2016; 7:331-340. [DOI: 10.1515/bmc-2016-0024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/01/2016] [Indexed: 11/15/2022] Open
Abstract
AbstractCCTG repeat expansion in intron 1 of the cellular nucleic acid-binding protein (CNBP) gene has been identified to be the genetic cause of myotonic dystrophy type 2 (DM2). Yet the underlying reasons for the genetic instability in CCTG repeats remain elusive. In recent years, CCTG repeats have been found to form various types of unusual secondary structures including mini-dumbbell (MDB), hairpin and dumbbell, revealing that there is a high structural diversity in CCTG repeats intrinsically. Upon strand slippage, the formation of unusual structures in the nascent strand during DNA replication has been proposed to be the culprit of CCTG repeat expansions. On the one hand, the thermodynamic stability, size, and conformational dynamics of these unusual structures affect the propensity of strand slippage. On the other hand, these structural properties determine whether the unusual structure can successfully escape from DNA repair. In this short overview, we first summarize the recent advances in elucidating the solution structures of CCTG repeats. We then discuss the potential pathways by which these unusual structures bring about variable sizes of repeat expansion, high strand slippage propensity and efficient repair escape.
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Affiliation(s)
- Pei Guo
- 1Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- 1Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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33
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Kaplan OI, Berber B, Hekim N, Doluca O. G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch. Nucleic Acids Res 2016; 44:9083-9095. [PMID: 27596596 PMCID: PMC5100583 DOI: 10.1093/nar/gkw769] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns.
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Affiliation(s)
- Oktay I Kaplan
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, 13125 Berlin, Germany
- School of Medicine, Istanbul Medeniyet University, 34000 Istanbul, Turkey
| | - Burak Berber
- Department of Biology, Osmangazi University, Eskisehir, 26480, Turkey
| | - Nezih Hekim
- School of Medicine, Istanbul Kemerburgaz University, 34217, Turkey
| | - Osman Doluca
- Department of Biomedical Engineering, Izmir University of Economics, Izmir, 35330, Turkey
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34
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Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL, Gagnon KT. Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP. ACS Chem Biol 2016; 11:2398-406. [PMID: 27467146 DOI: 10.1021/acschembio.6b00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spinach family of RNA aptamers are RNA mimics of green fluorescent protein (GFP) that have previously been designed to address the challenges of imaging RNA inside living cells. However, relatively low levels of free intracellular magnesium limited the practical use of these aptamers. Recent cell-based selections identified the broccoli RNA aptamer, which requires less magnesium for fluorescence, but the basis for magnesium preference remained unclear. Here, we find that the broccoli RNA structure is very similar to that of baby spinach, a truncated version of the spinach aptamer. Differences in stability and metal ion preferences between these two aptamers, and among broccoli mutants, are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Mutation of purine-purine pairs in broccoli at the terminal stem-quadruplex transition caused reversion of broccoli to a higher magnesium dependence. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs likely explain their sensitivity to magnesium for stability and fluorescence. Thus, optimizations designed to improve aptamers should take into consideration the role of metal ions in stabilizing the transitions and interactions between independently folding RNA structural motifs.
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Affiliation(s)
- Eman A. Ageely
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Zachary J. Kartje
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Kushal J. Rohilla
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Christopher L. Barkau
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Keith T. Gagnon
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
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35
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Yu Z, Zhou W, Han J, Li Y, Fan L, Li X. Na+-Induced Conformational Change of Pb2+-Stabilized G-Quadruplex and Its Influence on Pb2+ Detection. Anal Chem 2016; 88:9375-9380. [DOI: 10.1021/acs.analchem.6b02466] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ze Yu
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei Zhou
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Juan Han
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yunchao Li
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Louzhen Fan
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Xiaohong Li
- Key Laboratory of Theoretical
and Computational Photochemistry, Ministry of Education, College of
Chemistry, Beijing Normal University, Beijing, 100875, China
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36
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Kim BG, Chalikian TV. Thermodynamic linkage analysis of pH-induced folding and unfolding transitions of i-motifs. Biophys Chem 2016; 216:19-22. [DOI: 10.1016/j.bpc.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
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37
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Kim BG, Long J, Dubins DN, Chalikian TV. Ionic Effects on VEGF G-Quadruplex Stability. J Phys Chem B 2016; 120:4963-71. [DOI: 10.1021/acs.jpcb.6b03731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Byul G. Kim
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ji Long
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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38
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Wang Z, Zhao J, Bao J, Dai Z. Construction of Metal-Ion-Free G-quadruplex-Hemin DNAzyme and Its Application in S1 Nuclease Detection. ACS APPLIED MATERIALS & INTERFACES 2016; 8:827-833. [PMID: 26666985 DOI: 10.1021/acsami.5b10165] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this work, a new kind of peroxidase-mimicking DNAzyme (G-quadruplex-hemin DNAzyme, G4-hemin) was constructed by using hemin-modified G-rich DNA (hemin-G-DNA). Experimental results demonstrated that the G-rich DNA can form a G-quadruplex structure by the inducement of terminally modified hemin, rendering the assembly of hemin and G-quadruplex structure spontaneously and efficiently. As a result, G-hemin revealed higher peroxidase activity than traditional G-quadruplex/hemin DNAzyme (G4/hemin). Besides, different from G4/hemin, G4-hemin was constructed in one step without the participation of metal ions and adscititious hemin. Accordingly, the construction procedure was significantly simplified and the background signal from dissociative hemin was remarkably reduced. In a proof-of-concept trial, according to the colorimetric signals of G4-hemin, a novel biosensor for the detection of S1 nuclease activity was established, which provides a novel perspective for designing peroxidase-mimicking DNAzyme-based biosensors.
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Affiliation(s)
- Zhaoyin Wang
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing 210023, P. R. China
| | - Jian Zhao
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing 210023, P. R. China
| | - Jianchun Bao
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing 210023, P. R. China
| | - Zhihui Dai
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing 210023, P. R. China
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Guan AJ, Shen MJ, Zhang EX, Li Q, Wang LX, Xu LJ, Xiang JF, Tang YL. Stabilizing G-quadruplex DNA by methylazacalix[ n ]pyridine through shape-complementary interaction. Bioorg Med Chem Lett 2016; 26:609-612. [DOI: 10.1016/j.bmcl.2015.11.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 11/26/2022]
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40
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Functional Hallmarks of a Catalytic DNA that Makes Lariat RNA. Chemistry 2015; 22:3720-8. [DOI: 10.1002/chem.201503238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 12/25/2022]
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