1
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Seo SB, Lee J, Kim E, Lim J, Jang S, Son SU, Jeong Y, Kang T, Jung J, Lee KG, Lee SW, Kim K, Lim EK. On-site detection of methicillin-resistant Staphylococcus aureus (MRSA) utilizing G-quadruplex based isothermal exponential amplification reaction (GQ-EXPAR). Talanta 2024; 275:126073. [PMID: 38688085 DOI: 10.1016/j.talanta.2024.126073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has a high incidence in infectious hospitals and communities, highlighting the need for early on-site detection due to its resistance to methicillin antibiotics. The present study introduces a highly sensitive detection system for mecA, a crucial methicillin marker, utilizing an RCA-based isothermal exponential amplification reaction. The G-quadruplex-based isothermal exponential amplification reaction (GQ-EXPAR) method designs probes to establish G-quadruplex secondary structures incorporating thioflavin T for fluorescence. The system, unlike conventional genetic detection methods, works with portable isothermal PCR devices (isoQuark), facilitating on-site detection. A detection limit of 0.1 fmol was demonstrated using synthetic DNA, and effective detection was proven using thermal lysis. The study also validated the detection of targets swabbed from surfaces within bacterial 3D nanostructures using the GQ-EXPAR method. After applying complementary sequences to the padlock probe for the target, the GQ-EXPAR method can be used on various targets. The developed method could facilitate rapid and accurate diagnostics within MRSA strains.
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Affiliation(s)
- Seung Beom Seo
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Cogno-Mechatronics Engineering, Pusan National University, Pusan, 46241, Republic of Korea
| | - Jina Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering and Nano-Bioengineering, Research Center for Bio Materials and Process, Incheon National University, Incheon, 22012, Republic of Korea; Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Medical Device Development Center, Osong Medical Innovation Foundation, 123, Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Soojin Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Seong Uk Son
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Yeonwoo Jeong
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Taejeoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Kyoung G Lee
- Center for Nanobio Develpment, National NanoFab Center (NNFC), Daejeon, 34141, Republic of Korea
| | | | - Kyujung Kim
- Department of Cogno-Mechatronics Engineering, Pusan National University, Pusan, 46241, Republic of Korea.
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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2
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Bednarz A, Rosendal RT, Lund LM, Birkedal V. Probing G-quadruplex-ligand binding using DNA intrinsic fluorescence. Biochimie 2024:S0300-9084(24)00145-7. [PMID: 38936685 DOI: 10.1016/j.biochi.2024.06.009] [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: 12/07/2023] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
G-quadruplexes (G4s) are helical four-stranded nucleic acid structures that can form in guanine-rich sequences, which are mostly found in functional cellular regions, such as telomeres, promoters, and DNA replication origins. Great efforts are being made to target these structures towards the development of specific small molecule G4 binders for novel anti-cancer, neurological, and viral therapies. Here, we introduce an optical assay based on quenching of the intrinsic fluorescence of DNA G-quadruplexes for assessing and comparing the G4 binding affinity of various small molecule ligands in solutions. We show that the approach allows direct quantification of ligand binding to distinctive G4 topologies. We believe that this method will facilitate quick and reliable evaluation of small molecule G4 ligands and support their development.
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Affiliation(s)
- Aleksandra Bednarz
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Rebecca Torp Rosendal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Denmark; Department of Chemistry, Aarhus University, Denmark.
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3
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Wang Q, Jin D, Liu C, Shi L, Li T. A Tumor-Specific Cascade-Activating Smart Prodrug System for Enhanced Targeted Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309482. [PMID: 38150668 DOI: 10.1002/smll.202309482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Developing intelligently targeted drugs with low side effects is urgent for cancer treatment. Toward this goal, a tumor-specific cascade-activating smart prodrug system consisting of a G-quadruplex(G4)-modulated tumor-targeted DNA vehicle and a well-designed cellular stimuli-responsive ligand-drug conjugates (LDCs) is proposed. An original "donor-acceptor" binary fluorescent ligand, with ultrahigh affinity, brightness, and photostability, is engineered to tightly bind G4 structures and significantly improve the nuclease resistance of the DNA vehicle, which serves as a bridge contributing to the construction of the prodrug system, named ApG4/LDCs. Sodium nitroprusside and doxorubicin are loaded into ApG4/LDCs in one pot and generate nitric oxide and superoxide anion in response to cancer cellular environments, which in cascade generates peroxynitrite to cause DNA damage while promoting the self-monitored drug release to achieve enhanced targeted therapy. Such a cascade activation and self-reinforcement process is executed only when the prodrug system targets the tumor tissue followed by cell uptake, showing significant antitumor efficacy and greatly weakening the damage to normal tissues. Given the unique features, the innovative strategy for prodrug design may open a new door to precision disease treatment.
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Affiliation(s)
- Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Duo Jin
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Chengbin Liu
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Lili Shi
- Department of Chemistry, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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4
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Zhao LL, Gu YX, Dong JH, Li XT, Pan HY, Xue CY, Liu Y, Zhou YL, Zhang XX. New G-Triplex DNA Dramatically Activates the Fluorescence of Thioflavin T and Acts as a Turn-On Fluorescent Sensor for Uracil-DNA Glycosylase Activity Detection. Anal Chem 2024; 96:8458-8466. [PMID: 38710075 DOI: 10.1021/acs.analchem.4c00164] [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: 05/08/2024]
Abstract
G-triplexes are G-rich oligonucleotides composed of three G-tracts and have absorbed much attention due to their potential biological functions and attractive performance in biosensing. Through the optimization of loop compositions, DNA lengths, and 5'-flanking bases of G-rich sequences, a new stable G-triplex sequence with 14 bases (G3-F15) was discovered to dramatically activate the fluorescence of Thioflavin T (ThT), a water-soluble fluorogenic dye. The fluorescence enhancement of ThT after binding with G3-F15 reached 3200 times, which was the strongest one by far among all of the G-rich sequences. The conformations of G3-F15 and G3-F15/ThT were studied by circular dichroism. The thermal stability measurements indicated that G3-F15 was a highly stable G-triplex structure. The conformations of G3-F15 and G3-F15/ThT in the presence of different metal cations were studied thoroughly by fluorescent spectroscopy, circular dichroism, and nuclear magnetic resonance. Furthermore, using the G3-F15/ThT complex as a fluorescent probe, a robust and simple turn-on fluorescent sensor for uracil-DNA glycosylase activity was developed. This study proposes a new systematic strategy to explore new functional G-rich sequences and their ligands, which will promote their applications in diagnosis, therapy, and biosensing.
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Affiliation(s)
- Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yi-Xuan Gu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jia-Hui Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Tong Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hui-Yu Pan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100191, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Jeong J, Hu X, Yin R, Fantin M, Das SR, Matyjaszewski K. Nucleic Acid-Binding Dyes as Versatile Photocatalysts for Atom-Transfer Radical Polymerization. J Am Chem Soc 2024; 146:13598-13606. [PMID: 38691811 PMCID: PMC11100002 DOI: 10.1021/jacs.4c03513] [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: 03/11/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
Nucleic acid-binding dyes (NuABDs) are fluorogenic probes that light up after binding to nucleic acids. Taking advantage of their fluorogenicity, NuABDs have been widely utilized in the fields of nanotechnology and biotechnology for diagnostic and analytical applications. We demonstrate the potential of NuABDs together with an appropriate nucleic acid scaffold as an intriguing photocatalyst for precisely controlled atom-transfer radical polymerization (ATRP). Additionally, we systematically investigated the thermodynamic and electrochemical properties of the dyes, providing insights into the mechanism that drives the photopolymerization. The versatility of the NuABD-based platform was also demonstrated through successful polymerizations using several NuABDs in conjunction with diverse nucleic acid scaffolds, such as G-quadruplex DNA or DNA nanoflowers. This study not only extends the horizons of controlled photopolymerization but also broadens opportunities for nucleic acid-based materials and technologies, including nucleic acid-polymer biohybrids and stimuli-responsive ATRP platforms.
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Affiliation(s)
- Jaepil Jeong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaolei Hu
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongguan Yin
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Marco Fantin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35131, Italy
| | - Subha R. Das
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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6
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Edwards A, Iannucci AN, VanDenBerg J, Kesti A, Rice T, Sethi S, Dhakal S, Yangyuoru PM. G-Quadruplex Structure in the ATP-Binding DNA Aptamer Strongly Modulates Ligand Binding Activity. ACS OMEGA 2024; 9:14343-14350. [PMID: 38560010 PMCID: PMC10976393 DOI: 10.1021/acsomega.3c10386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
Secondary structures formed by single-stranded DNA aptamers can allow for the binding of small-molecule ligands. Some of these secondary structures are highly stable in solution and are great candidates for use in the development of molecular tools for biomarker detection, environmental monitoring, and others. In this paper, we explored adenosine triphosphate (ATP)-binding aptamers for the simultaneous detection of two small-molecule ligands: adenosine triphosphate (ATP) and thioflavin T (ThT). The aptamer can form a G-quadruplex (G4) structure with two G-quartets, and our results show that each of these quartets is equally involved in binding. Using fluorescently labeled and label-free methods, we further explored the role of the G4 motif in modulating the ligand binding property of the aptamer by making two extended variants that can form three or four G-quartet G4 structures. Through equilibrium binding and electrospray ionization mass spectrometry (ESI-MS) analysis, we observed a stronger affinity of aptamers to ATP by the variant G4 constructs relative to the native aptamer (Kd range of 0.040-0.042 μM for variants as compared to 0.15 μM for the native ATP aptamer). Additionally, we observed a dual binding of ThT and ATP to the G4 constructs in the label-free and ESI-MS analyses. These findings together suggest that the G4 motif in the ATP aptamer is a critical structural element that is required for optimum ATP binding and can be modulated for the binding of multiple ligands. These findings are instrumental for designing smart molecular tools for a wide range of applications, including biomarker monitoring and ligand binding studies.
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Affiliation(s)
- Aleah
N. Edwards
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
| | - Alexandria N. Iannucci
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
| | - Jacob VanDenBerg
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
| | - Annastiina Kesti
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
| | - Tommie Rice
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
| | - Srishty Sethi
- Virginia
Commonwealth University, 1001 W Main St., Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Virginia
Commonwealth University, 1001 W Main St., Richmond, Virginia 23284, United States
| | - Philip M. Yangyuoru
- Northern
Michigan University, 1401 Presque Isle Ave, Marquette, Michigan 49855, United States
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7
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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8
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Mizunuma M, Suzuki M, Kobayashi T, Hara Y, Kaneko A, Furukawa K, Chuman Y. Development of Mn 2+-Specific Biosensor Using G-Quadruplex-Based DNA. Int J Mol Sci 2023; 24:11556. [PMID: 37511324 PMCID: PMC10380348 DOI: 10.3390/ijms241411556] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Metal ions are used in various situations in living organisms and as a part of functional materials. Since the excessive intake of metal ions can cause health hazards and environmental pollution, the development of new molecules that can monitor metal ion concentrations with high sensitivity and selectivity is strongly desired. DNA can form various structures, and these structures and their properties have been used in a wide range of fields, including materials, sensors, and drugs. Guanine-rich sequences respond to metal ions and form G-quadruplex structures and G-wires, which are the self-assembling macromolecules of G-quadruplex structures. Therefore, guanine-rich DNA can be applied to a metal ion-detection sensor and functional materials. In this study, the IRDAptamer library originally designed based on G-quadruplex structures was used to screen for Mn2+, which is known to induce neurodegenerative diseases. Circular dichroism and fluorescence analysis using Thioflavin T showed that the identified IRDAptamer sequence designated MnG4C1 forms a non-canonical G-quadruplex structure in response to low concentrations of Mn2+. A serum resistance and thermostability analysis revealed that MnG4C1 acquired stability in a Mn2+-dependent manner. A Förster resonance energy transfer (FRET) system using fluorescent molecules attached to the termini of MnG4C1 showed that FRET was effectively induced based on Mn2+-dependent conformational changes, and the limit of detection (LOD) was 0.76 µM for Mn2+. These results suggested that MnG4C1 can be used as a novel DNA-based Mn2+-detecting molecule.
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Affiliation(s)
- Masataka Mizunuma
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Mirai Suzuki
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Tamaki Kobayashi
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yuki Hara
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Atsushi Kaneko
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Kazuhiro Furukawa
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan
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9
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Jain N, Shankar U, Singh A, Sharma TK, Kumar A. G-quadruplex motifs in Neisseria gonorrhoeae as anti-gonococcal targets. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12646-6. [PMID: 37410137 DOI: 10.1007/s00253-023-12646-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Neisseria gonorrhoeae is an obligate human pathogen that causes gonorrhea and has shown a vast emergence of multidrug resistance in recent times. It is necessary to develop novel therapeutic strategies to combat this multidrug-resistant pathogen. The non-canonical stable secondary structures of nucleic acids, G-quadruplexes (GQs), are reported to regulate gene expressions in viruses, prokaryotes, and eukaryotes. Herein, we explored the whole genome of N. gonorrhoeae to mine evolutionary conserved GQ motifs. The Ng-GQs were highly enriched in the genes involved in various important biological and molecular processes of N. gonorrhoeae. Five of these GQ motifs were characterized using biophysical and biomolecular techniques. The GQ-specific ligand, BRACO-19, showed a high affinity towards these GQ motifs and stabilized them in both in vitro and in vivo conditions. The ligand showed potent anti-gonococcal activity and modulated the gene expression of the GQ-harboring genes. Strikingly, BRACO-19 also altered the biofilm formation in N. gonorrhoeae and its adhesion and invasion of the human cervical epithelial cells. In summary, the present study showed a significant role of GQ motifs in N. gonorrhoeae biology and put forward a step closer towards the search for therapeutic measures in combating the emerging antimicrobial resistance in the pathogen. KEY POINTS: •Neisseria gonorrhoeae genome is enriched in non-canonical nucleic acid structures-G-quadruplexes. •These G-quadruplexes might regulate bacterial growth, virulence, and pathogenesis. •G-quadruplex ligands inhibit biofilm formation, adhesion, and invasion of the gonococcus bacterium.
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Affiliation(s)
- Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | - Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India.
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10
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Guo W, Ji D, Kinghorn AB, Chen F, Pan Y, Li X, Li Q, Huck WTS, Kwok CK, Shum HC. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates. J Am Chem Soc 2023; 145:2375-2385. [PMID: 36689740 DOI: 10.1021/jacs.2c11362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Feipeng Chen
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yi Pan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Qingchuan Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
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11
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Jiang B, Umezaki U, Augustine A, Jayasinghe-Arachchige VM, Serafim LF, He ZMS, Wyss KM, Prabhakar R, Martí AA. Deconvoluting binding sites in amyloid nanofibrils using time-resolved spectroscopy. Chem Sci 2023; 14:1072-1081. [PMID: 36756322 PMCID: PMC9891369 DOI: 10.1039/d2sc05418c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023] Open
Abstract
Steady-state fluorescence spectroscopy has a central role not only for sensing applications, but also in biophysics and imaging. Light switching probes, such as ruthenium dipyridophenazine complexes, have been used to study complex systems such as DNA, RNA, and amyloid fibrils. Nonetheless, steady-state spectroscopy is limited in the kind of information it can provide. In this paper, we use time-resolved spectroscopy for studying binding interactions between amyloid-β fibrillar structures and photoluminescent ligands. Using time-resolved spectroscopy, we demonstrate that ruthenium complexes with a pyrazino phenanthroline derivative can bind to two distinct binding sites on the surface of fibrillar amyloid-β, in contrast with previous studies using steady-state photoluminescence spectroscopy, which only identified one binding site for similar compounds. The second elusive binding site is revealed when deconvoluting the signals from the time-resolved decay traces, allowing the determination of dissociation constants of 3 and 2.2 μM. Molecular dynamic simulations agree with two binding sites on the surface of amyloid-β fibrils. Time-resolved spectroscopy was also used to monitor the aggregation of amyloid-β in real-time. In addition, we show that common polypyridine complexes can bind to amyloid-β also at two different binding sites. Information on how molecules bind to amyloid proteins is important to understand their toxicity and to design potential drugs that bind and quench their deleterious effects. The additional information contained in time-resolved spectroscopy provides a powerful tool not only for studying excited state dynamics but also for sensing and revealing important information about the system including hidden binding sites.
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Affiliation(s)
- Bo Jiang
- Department of Chemistry, Rice University Houston TX USA
| | - Utana Umezaki
- Department of Chemistry, Rice University Houston TX USA
| | | | | | | | | | - Kevin M. Wyss
- Department of Chemistry, Rice UniversityHoustonTXUSA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami Coral Gables FL USA
| | - Angel A. Martí
- Department of Chemistry, Rice UniversityHoustonTXUSA,Department of Bioengineering, Rice UniversityHoustonTXUSA,Department of Materials Science & Nanoengineering, Rice UniversityHoustonTXUSA
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12
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Pavlova I, Barinov N, Novikov R, Severov V, Iudin M, Vedekhina T, Larin A, Babenko V, Aralov A, Gnuchikh E, Sardushkin M, Klinov D, Tsvetkov V, Varizhuk A. Modeling G4s in chromatin context confirms partial nucleosome exclusion and reveals nucleosome-disrupting effects of the least selective G4 ligands. Biochimie 2023; 204:8-21. [PMID: 36063975 DOI: 10.1016/j.biochi.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 07/22/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
G-quadruplexes (G4s) are gaining increasing attention as possible regulators of chromatin packaging, and robust approaches to their studies in pseudo-native context are much needed. Here, we designed a simple in vitro model of G4-prone genomic DNA and employed it to elucidate the impact of G4s and G4-stabilizing ligands on nucleosome occupancy. We obtained two 226-bp dsDNA constructs composed of the strong nucleosome positioning sequence and an internucleosomal DNA-imitating tail. The tail was G4-free in the control construct and harbored a "strong" (stable) G4 motif in the construct of interest. An additional "weak" (semi-stable) G4 motif was found within the canonical nucleosome positioning sequence. Both G4s were confirmed by optical methods and 1H NMR spectroscopy. Electrophoretic mobility assays showed that the weak G4 motif did not obstruct nucleosome assembly, while the strong G4 motif in the tail sequence diminished nucleosome yield. Atomic force microscopy data and molecular modeling confirmed that the strong G4 was maintained in the tail of the correctly assembled nucleosome structure. Using both in vitro and in silico models, we probed three known G4 ligands and detected nucleosome-disrupting effects of the least selective ligand. Our results are in line with the negative correlation between stable G4s and nucleosome density, support G4 tolerance between regularly positioned nucleosomes, and highlight the importance of considering chromatin context when targeting genomic G4s.
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Affiliation(s)
- Iuliia Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Nikolay Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Roman Novikov
- Engenlhardt Institute of Molecular Biology, Moscow, 119991, Russia; N.D. Zelinsky Institute of Organic Chemistry, Moscow, 19991, Russia
| | - Vjacheslav Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Mikhail Iudin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Tatiana Vedekhina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vladislav Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Evgeny Gnuchikh
- National Research Center Kurchatov Institute, Kurchatov Genomic Center, Moscow, 123182, Russia
| | - Makar Sardushkin
- Mendeleev University of Chemical Technology of Russia, 125047, Moscow, Russia
| | - Dmitry Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Peoples' Friendship University of Russia (RUDN University), 117198, Moscow, Russia
| | - Vladimir Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Institute of Biodesign and Complex System Modeling, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Leninsky Prospect Str. 29, Moscow, 119991, Russia.
| | - Anna Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
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13
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Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
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14
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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15
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Pramanik S, Mahato P, Pramanik U, Nandy A, Khamari L, Shrivastava S, Rai S, Mukherjee S. DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition. J Phys Chem B 2022; 126:2658-2668. [PMID: 35357836 DOI: 10.1021/acs.jpcb.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This work delineates an integrative approach combining spectroscopic and computational studies to decipher the association-induced fluorescence properties of a fluorescent molecular rotor, viz., auramine O (AuO), after interacting with 20-mer duplex DNA having diverse well-matched base pairs. While exploring the scarcely explored sequence-dependent interaction mechanism of AuO and DNA, we observed that DNA could act as a conducive scaffold to the formation of AuO dimer through noncovalent interactions at lower molecular density. The photophysical properties of AuO depend on the nucleotide compositions as described from sequence-dependent shifting in the emission and absorption maxima. Furthermore, we explored such DNA base pair-dependent fluorescence spectral characteristics of AuO toward discriminating the thermodynamically most stable single nucleotide mismatch in a 20-mer sequence. Our results are interesting and could be useful in developing analogues with further enhanced emission properties toward mismatched DNA sequences.
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Affiliation(s)
- Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Paritosh Mahato
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Ushasi Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Shivam Shrivastava
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
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16
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Yu Z, Huang W, Shi L, Ke S, Xu S. Selective probes targeting c-MYC Pu22 G-quadruplex and their application in live mice imaging. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Kang Y, Wei C. Highly selective turn-on red fluorescence probes for visualization of the G-quadruplexes DNA in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120518. [PMID: 34700155 DOI: 10.1016/j.saa.2021.120518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Studies on small molecule fluorescent probes for detecting G-quadruplexes DNA have bring about an extensive attention in recent years. In this paper, we designed and synthesized three benzothiazole derivatives named 2a-2c under moderate reaction conditions and investigated their interactions with DNA (single-stranded, duplex, i-motif and G-quadruplex) and distribution in living cell. Three compounds present a large Stokes shift (∼90 nm) and a weak red fluorescence emission, and they exhibit a good selectivity and sensitive turn-on fluorescence response for the promoter G-quadruplex DNA (bcl-2, c-myc and c-kit 2) and mitochondria G-quadruplex (KSS). The affinity of 2a and 2b with N-alkyl side chain group to DNA is stronger than that of 2c with an anion group, therefore, they also increase the stability of the G-quadruplex structure. 2b induces the conformational change of both bcl-2 and KSS G-quadruplexes, while all compounds induce the folding of bcl-2 from the coiled structure to the hybrid G-qrudruplex. Three compounds interact with the G-quadruplex DNA mainly by end-stacking mode. Furthermore, MTT assays and confocal fluorescence images show that these compounds can enter the living HepG2 cells with low cytotoxicity. 2a-2c are mainly located in the mitochondrion and interacted with mitochondria G-quadruplex DNA, while only weak fluorescence can be found in cell nucleus. In a word, 2a-2c can be implied in image of G-quadruplex DNA in living cells.
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Affiliation(s)
- Yongqiang Kang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China
| | - Chunying Wei
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China.
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18
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Alavi S, Ghadiri H, Dabirmanesh B, Khajeh K. SPR Analysis of SUMO-Murine Rap1-Interacting Factor 1 C-Terminal Domain Interaction with G4. BIOSENSORS 2022; 12:bios12010037. [PMID: 35049665 PMCID: PMC8774283 DOI: 10.3390/bios12010037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/26/2022]
Abstract
One of the advantages of surface plasmon resonance is its sensitivity and real-time analyses performed by this method. These characteristics allow us to further investigate the interactions of challenging proteins like Rap1-interacting factor 1 (Rif1). Rif1 is a crucial protein responsible for regulating different cellular processes including DNA replication, repair, and transcription. Mammalian Rif1 is yet to be fully characterized, partly because it is predicted to be intrinsically disordered for a large portion of its polypeptide. This protein has recently been the target of research as a potential biomarker in many cancers. Therefore, finding its most potent interacting partner is of utmost importance. Previous studies showed Rif1’s affinity towards structured DNAs and amongst them, T6G24 was superior. Recent studies have shown mouse Rif1 (muRif1) C-terminal domain’s (CTD) role in binding to G-quadruplexes (G4). There were many concerns in investigating the Rif1 and G4 interaction, which can be minimized using SPR. Therefore, for the first time, we have assessed its binding with G4 at nano-molar concentrations with SPR which seems to be crucial for its binding analyses. Our results indicate that muRif1-CTD has a high affinity for this G4 sequence as it shows a very low KD (6 ± 1 nM).
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Affiliation(s)
- Sana Alavi
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
| | - Hamed Ghadiri
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (H.G.); (B.D.)
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (H.G.); (B.D.)
| | - Khosro Khajeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran; (H.G.); (B.D.)
- Correspondence: ; Tel./Fax: +98-(21)-8288-4717
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19
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Sugimoto W, Kinoshita N, Nakata M, Ohyama T, Tateishi-Karimata H, Nishikata T, Sugimoto N, Miyoshi D, Kawauchi K. Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene. Chem Commun (Camb) 2021; 58:48-51. [PMID: 34811561 DOI: 10.1039/d1cc05523b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We identified cytosine-rich regions adjacent to guanine-rich regions in protease genes. A typical GC-rich sequence derived from the TMPRSS2 gene showed structural competition between a G-quadruplex and a hairpin loop, and this competition significantly affected transcription efficiency. These results suggest an impact of neighboring sequences on the gene expression of guanine-rich sequences.
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Affiliation(s)
- Wataru Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Natsuki Kinoshita
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Minori Nakata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Takahito Nishikata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan. .,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-mimamimachi, Chuo-ku, Kobe 650-0047, Japan.
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20
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Zheng J, Li D, Jiao J, Duan C, Wang Z, Xiang Y. Dual aptamer recognition-based G-quadruplex nanowires to selectively analyze cancer-derived exosomes. Talanta 2021; 235:122748. [PMID: 34517616 DOI: 10.1016/j.talanta.2021.122748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/15/2022]
Abstract
Cancer-derived exosomes have emerged as a valuable biomarker for cancer diagnosis and prognosis. However, the heterogeneity of exosomes often leads to low selectivity based on the single recognition method. Given this, we have developed a dual-aptamer recognition strategy based on G-quadruplex nanowires for selective analysis of exosomes. In this work, target exosomes were first captured by CD63 aptamers modified on magnetic beads (MBs) and then combined with AS1411 aptamer, which shows high binding affinity to nucleolin when forming stable G-quadruplex structure. Then the free myc monomer can spontaneously assemble into higher order G-wire superstructures on the allosteric AS1411, and resulting enhanced fluorescence signal, which can realize sensitive and specific analysis of the target exosomes. This dual-aptamer recognition-based method is simple and universal for different types of exosomes, which is of great significance for clinical cancer diagnosis.
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Affiliation(s)
- Ji Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Zhongyun Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
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21
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Jahmidi-Azizi N, Gault S, Cockell CS, Oliva R, Winter R. Ions in the Deep Subsurface of Earth, Mars, and Icy Moons: Their Effects in Combination with Temperature and Pressure on tRNA-Ligand Binding. Int J Mol Sci 2021; 22:ijms221910861. [PMID: 34639202 PMCID: PMC8509373 DOI: 10.3390/ijms221910861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 01/12/2023] Open
Abstract
The interactions of ligands with nucleic acids are central to numerous reactions in the biological cell. How such reactions are affected by harsh environmental conditions such as low temperatures, high pressures, and high concentrations of destructive ions is still largely unknown. To elucidate the ions’ role in shaping habitability in extraterrestrial environments and the deep subsurface of Earth with respect to fundamental biochemical processes, we investigated the effect of selected salts (MgCl2, MgSO4, and Mg(ClO4)2) and high hydrostatic pressure (relevant for the subsurface of that planet) on the complex formation between tRNA and the ligand ThT. The results show that Mg2+ salts reduce the binding tendency of ThT to tRNA. This effect is largely due to the interaction of ThT with the salt anions, which leads to a strong decrease in the activity of the ligand. However, at mM concentrations, binding is still favored. The ions alter the thermodynamics of binding, rendering complex formation that is more entropy driven. Remarkably, the pressure favors ligand binding regardless of the type of salt. Although the binding constant is reduced, the harsh conditions in the subsurface of Earth, Mars, and icy moons do not necessarily preclude nucleic acid–ligand interactions of the type studied here.
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Affiliation(s)
- Nisrine Jahmidi-Azizi
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany;
| | - Stewart Gault
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3FD, UK; (S.G.); (C.S.C.)
| | - Charles S. Cockell
- UK Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Edinburgh EH9 3FD, UK; (S.G.); (C.S.C.)
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany;
- Correspondence: (R.O.); (R.W.)
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany;
- Correspondence: (R.O.); (R.W.)
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22
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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23
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Ghadiri H, Alavi S, Dabirmanesh B, Khajeh K. Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR. BIOCHEMISTRY (MOSCOW) 2021; 86:898-905. [PMID: 34284714 DOI: 10.1134/s0006297921070105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
One of the main players in the cell-specific replication timing pattern is Rap1 interacting factor-1 (Rif1). Rif1 protein consists of N-terminal and C-terminal domains and an intrinsically disordered region in between. It has been suggested that both N- and C-termini of Rif1 are capable of binding to DNA with particularly high affinity to cruciform DNA structures. In the present study, we expressed, solubilized, and purified the maltose-binding protein-tagged murine Rif1 C-terminal domain (MBP-muRif1-CTD). Biological activity of the purified protein was assessed by the electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR). Our results show that the MBP-muRif1-CTD binds G-quadruplex (G4) structure with high affinity (KD 19.0 ± 0.8 nM), as was previously suggested. This study is the first step in investigation of the interaction of MBP-Profinity eXact-muRif1-CTD and G4 by SPR.
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Affiliation(s)
- Hamed Ghadiri
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Sana Alavi
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran. .,Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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24
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Rhodamine 6G-Ligand Influencing G-Quadruplex Stability and Topology. Int J Mol Sci 2021; 22:ijms22147639. [PMID: 34299257 PMCID: PMC8305571 DOI: 10.3390/ijms22147639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
The involvement of G-quadruplex (G4) structures in nucleic acids in various molecular processes in cells such as replication, gene-pausing, the expression of crucial cancer-related genes and DNA damage repair is well known. The compounds targeting G4 usually bind directly to the G4 structure, but some ligands can also facilitate the G4 folding of unfolded G-rich sequences and stabilize them even without the presence of monovalent ions such as sodium or potassium. Interestingly, some G4-ligand complexes can show a clear induced CD signal, a feature which is indirect proof of the ligand interaction. Based on the dichroic spectral profile it is not only possible to confirm the presence of a G4 structure but also to determine its topology. In this study we examine the potential of the commercially available Rhodamine 6G (RhG) as a G4 ligand. RhG tends to convert antiparallel G4 structures to parallel forms in a manner similar to that of Thiazole Orange. Our results confirm the very high selectivity of this ligand to the G4 structure. Moreover, the parallel topology of G4 can be verified unambiguously based on the specific induced CD profile of the G4-RhG complex. This feature has been verified on more than 50 different DNA sequences forming various non-canonical structural motifs.
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25
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Hori D, Yum JH, Sugiyama H, Park S. Tropylium Derivatives as New Entrants that Sense Quadruplex Structures. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daisuke Hori
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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26
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Mimura M, Tomita S, Shinkai Y, Hosokai T, Kumeta H, Saio T, Shiraki K, Kurita R. Quadruplex Folding Promotes the Condensation of Linker Histones and DNAs via Liquid-Liquid Phase Separation. J Am Chem Soc 2021; 143:9849-9857. [PMID: 34152774 DOI: 10.1021/jacs.1c03447] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins and DNA has recently emerged as a possible mechanism underlying the dynamic organization of chromatin. We herein report the role of DNA quadruplex folding in liquid droplet formation via LLPS induced by interactions between DNA and linker histone H1 (H1), a key regulator of chromatin organization. Fluidity measurements inside the droplets, binding assays using G-quadruplex-selective probes, and structural analyses based on circular dichroism demonstrated that quadruplex DNA structures, such as the G-quadruplex and i-motif, promote droplet formation with H1 and decrease molecular motility within droplets. The dissolution of the droplets in the presence of additives and the LLPS of the DNA structural units indicated that, in addition to electrostatic interactions between the DNA and the intrinsically disordered region of H1, π-π stacking between quadruplex DNAs could potentially drive droplet formation, unlike in the electrostatically driven LLPS of duplex DNA and H1. According to phase diagrams of anionic molecules with various conformations, the high LLPS ability associated with quadruplex folding arises from the formation of interfaces consisting of organized planes of guanine bases and the side surfaces with a high charge density. Given that DNA quadruplex structures are well-documented in heterochromatin regions, it is imperative to understand the role of DNA quadruplex folding in the context of intranuclear LLPS.
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Affiliation(s)
- Masahiro Mimura
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.,Health and Medical Research Institute, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoichi Shinkai
- Biomedical Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Takuya Hosokai
- National Metrology Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Hiroyuki Kumeta
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Ryoji Kurita
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.,Health and Medical Research Institute, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.,DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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Exploring the Interaction of Curaxin CBL0137 with G-Quadruplex DNA Oligomers. Int J Mol Sci 2021; 22:ijms22126476. [PMID: 34204214 PMCID: PMC8234370 DOI: 10.3390/ijms22126476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 01/22/2023] Open
Abstract
Curaxins and especially the second-generation derivative curaxin CBL0137 have important antitumor activities in multiple cancers such as glioblastoma, melanoma and others. Although most of the authors suggest that their mechanism of action comes from the activation of p53 and inactivation of NF-kB by targeting FACT, there is evidence supporting the involvement of DNA binding in their antitumor activity. In this work, the DNA binding properties of curaxin CBL0137 with model quadruplex DNA oligomers were studied by 1H NMR, CD, fluorescence and molecular modeling. We provided molecular details of the interaction of curaxin with two G-quadruplex structures, the single repeat of human telomere d(TTAGGGT)4 and the c-myc promoter Pu22 sequence. We also performed 1H and 31P NMR experiments were also performed in order to investigate the interaction with duplex DNA models. Our data support the hypothesis that the interaction of curaxin with G-quadruplex may provide a novel insight into the DNA-binding properties of CBL0137, and it will be helpful for the design of novel selective DNA-targeting curaxin analogues.
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28
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Verma S, Ravichandiran V, Ranjan N. Beyond amyloid proteins: Thioflavin T in nucleic acid recognition. Biochimie 2021; 190:111-123. [PMID: 34118329 DOI: 10.1016/j.biochi.2021.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/01/2023]
Abstract
Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.
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Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India.
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29
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Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation. Sci Rep 2021; 11:9714. [PMID: 33958702 PMCID: PMC8102477 DOI: 10.1038/s41598-021-89215-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.
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30
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Ahmadi Y, Soldo R, Rathammer K, Eibler L, Barišić I. Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes. Anal Chem 2021; 93:5161-5169. [PMID: 33724777 DOI: 10.1021/acs.analchem.0c05052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Regina Soldo
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Krista Rathammer
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Laura Eibler
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
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31
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Gargallo R, Aviñó A, Eritja R, Jarosova P, Mazzini S, Scaglioni L, Taborsky P. Study of alkaloid berberine and its interaction with the human telomeric i-motif DNA structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119185. [PMID: 33234477 DOI: 10.1016/j.saa.2020.119185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 06/11/2023]
Abstract
The alkaloid berberine presents many biological activities related to its potential to bind DNA structures, such as duplex or G-quadruplex. Recently, it has been proposed that berberine may interact with i-motif structures formed from the folding of cytosine-rich sequences. In the present work, the interaction of this alkaloid with the i-motif formed by the human telomere cytosine-rich sequence, as well as with several positive and negative controls, has been studied. Molecular fluorescence and circular dichroism spectroscopies, as well as nuclear magnetic resonance spectrometry and competitive dialysis, have been used with this purpose. The results shown here reveal that the interaction of berberine with this i-motif is weak, mostly electrostatics in nature and takes place with bases not involved in C·C+ base pairs. Moreover, this ligand is not selective for i-motif structures, as binds equally to both, folded structure, and unfolded strand, without producing any stabilization of the i-motif. As a conclusion, the development of analytical methods based on the interaction of fluorescent ligands, such as berberine, with i-motif structures should consider the thermodynamic aspects related with the interaction, as well as the selectivity of the proposed ligands with different DNA structures, including unfolded strands.
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Affiliation(s)
- R Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, E-08028 Barcelona, Spain.
| | - A Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - P Jarosova
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - S Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - L Scaglioni
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - P Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
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32
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G-quadruplex binding properties of a potent PARP-1 inhibitor derived from 7-azaindole-1-carboxamide. Sci Rep 2021; 11:3869. [PMID: 33594142 PMCID: PMC7887208 DOI: 10.1038/s41598-021-83474-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/15/2021] [Indexed: 12/19/2022] Open
Abstract
Poly ADP-ribose polymerases (PARP) are key proteins involved in DNA repair, maintenance as well as regulation of programmed cell death. For this reason they are important therapeutic targets for cancer treatment. Recent studies have revealed a close interplay between PARP1 recruitment and G-quadruplex stabilization, showing that PARP enzymes are activated upon treatment with a G4 ligand. In this work the DNA binding properties of a PARP-1 inhibitor derived from 7-azaindole-1-carboxamide, (2-[6-(4-pyrrolidin-1-ylmethyl-phenyl)-pyrrolo[2,3-b]pyridin-1-yl]-acetamide, compound 1) with model duplex and quadruplex DNA oligomers were studied by NMR, CD, fluorescence and molecular modelling. We provide evidence that compound 1 is a strong G-quadruplex binder. In addition we provide molecular details of the interaction of compound 1 with two model G-quadruplex structures: the single repeat of human telomeres, d(TTAGGGT)4, and the c-MYC promoter Pu22 sequence. The formation of defined and strong complexes with G-quadruplex models suggests a dual G4 stabilization/PARP inhibition mechanism of action for compound 1 and provides the molecular bases of its therapeutic potential.
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33
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Chen X, Cheng Y, Wang Y, Tang J, Wang F, Chen Z. Fluorescence assay based on the thioflavin T-induced conformation switch of G-quadruplexes for TET1 detection. Analyst 2021; 146:2126-2130. [DOI: 10.1039/d1an00109d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A simple and label-free fluorescence method is developed for the highly sensitive detection of TET1 based on ThT/G-quadruplexes in combination with the specific design of oligonucleotides.
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Affiliation(s)
- Xue Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Ying Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Yafen Wang
- College of Chemistry and Molecular Sciences
- Key Laboratory of Biochemical Polymers of Ministry of Education. The Institute for Advanced Studies
- Hubei Province Key Laboratory of Allergy and Immunology
- Wuhan University
- Wuhan
| | - Jing Tang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Fang Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
| | - Zilin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery
- Ministry of Education
- Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals
- and Wuhan University School of Pharmaceutical Sciences
- Wuhan
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34
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Berlyoung AS, Armitage BA. Assembly and Characterization of RNA/DNA Hetero-G-Quadruplexes. Biochemistry 2020; 59:4072-4080. [PMID: 33048532 DOI: 10.1021/acs.biochem.0c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transient association of guanine-rich RNA and DNA in the form of hetero-G-quadruplexes (RDQs) has emerged as an important mechanism for regulating genome transcription and replication but relatively little is known about the structure and biophysical properties of RDQs compared with DNA and RNA homo-G-quadruplexes. Herein, we report the assembly and characterization of three RDQs based on sequence motifs found in human telomeres and mitochondrial nucleic acids. Stable RDQs were assembled using a duplex scaffold, which prevented segregation of the DNA and RNA strands into separate homo-GQs. Each of the RDQs exhibited UV melting temperatures above 50 °C in 100 mM KCl and predominantly parallel morphologies, evidently driven by the RNA component. The fluorogenic dye thioflavin T binds to each RDQ with low micromolar KD values, similar to its binding to RNA and DNA homo-GQs. These results establish a method for assembling RDQs that should be amenable to screening compounds and libraries to identify selective RDQ-binding small molecules, oligonucleotides, and proteins.
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Affiliation(s)
- April S Berlyoung
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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36
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Damase TR, Islam MM, Shipley M, Allen PB. Thioflavin T as a noncovalent reporter for a label-free, non-enzymatic, catalytic DNA amplifier. Methods Appl Fluoresc 2020; 8:045001. [DOI: 10.1088/2050-6120/aba357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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38
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Zhang S, Sun H, Wang L, Liu Y, Chen H, Li Q, Guan A, Liu M, Tang Y. Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe. Nucleic Acids Res 2019; 46:7522-7532. [PMID: 30085206 PMCID: PMC6125622 DOI: 10.1093/nar/gky665] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/13/2018] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.
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Affiliation(s)
- Suge Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Lixia Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yan Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Hongbo Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Meirong Liu
- Center for Physiochemical Analysis & Measurement, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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39
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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40
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Lages A, Proud CG, Holloway JW, Vorechovsky I. Thioflavin T Monitoring of Guanine Quadruplex Formation in the rs689-Dependent INS Intron 1. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:770-777. [PMID: 31150930 PMCID: PMC6539410 DOI: 10.1016/j.omtn.2019.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/27/2019] [Accepted: 04/27/2019] [Indexed: 12/21/2022]
Abstract
The human proinsulin gene (INS) contains a thymine-to-adenine variant (rs689) located in the 3′ splice site (3′ ss) recognition motif of the first intron. The adenine at rs689 is strongly associated with type 1 diabetes. By weakening the polypyrimidine tract, the adenine allele reduces the efficiency of intron 1 splicing, which can be ameliorated by antisense oligonucleotides blocking a splicing silencer located upstream of the 3′ ss. The silencer is surrounded by guanine-rich tracts that may form guanine quadruplexes (G4s) and modulate the accessibility of the silencer. Here, we employed thioflavin T (ThT) to monitor G4 formation in synthetic DNAs and RNAs derived from INS intron 1. We show that the antisense target is surrounded by ThT-positive segments in each direction, with oligoribonucleotides exhibiting consistently higher fluorescence than their DNA counterparts. The signal was reduced for ThT-positive oligonucleotides that were extended into the silencer, indicating that flanking G4s have a potential to mask target accessibility. Real-time monitoring of ThT fluorescence during INS transcription in vitro revealed a negative correlation with ex vivo splicing activities of corresponding INS constructs. Together, these results provide a better characterization of antisense targets in INS primary transcripts for restorative strategies designed to improve the INS splicing defect associated with type 1 diabetes.
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Affiliation(s)
- Ana Lages
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Christopher G Proud
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK; Lifelong Health and Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John W Holloway
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK.
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41
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Sjekloća L, Ferré-D'Amaré AR. Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence. Cell Chem Biol 2019; 26:1159-1168.e4. [PMID: 31178406 DOI: 10.1016/j.chembiol.2019.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
Abstract
Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.
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Affiliation(s)
- Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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42
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Verma S, Ghuge SA, Ravichandiran V, Ranjan N. Spectroscopic studies of Thioflavin-T binding to c-Myc G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:388-395. [PMID: 30703662 DOI: 10.1016/j.saa.2018.12.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/16/2018] [Accepted: 12/22/2018] [Indexed: 05/29/2023]
Abstract
G-quadruplexes are well-known DNA secondary structures which can be formed both within the DNA and the RNA sequences of the human genome. While many functions of G-quadruplex during cell regulatory events are still unknown, a number of reports have established their role in finding new cancer therapies. In this report, we provide a detailed account of Thioflavin T (ThT) interacting with a promoter gene (c-Myc) which has relevance in several types of human cancers. Using a variety of spectroscopic techniques, we have shown that the binding of ThT is selective to c-Myc G-quadruplex only, having poor interactions with the duplex DNA sequences. UV-Visible titration experiments show that binding involves stacking interactions which were further corroborated by CD experiments. Fluorescence studies showed that the binding of ThT to c-Myc G-quadruplex results in a large increase in the fluorescence emission spectrum of c-Myc G-quadruplex while the same to duplex DNAs was much poor. Binding of ThT to c-Myc G-quadruplex results in thermal stabilization of the quadruplex DNA by up to 7.4 °C and Job plot experiments demonstrated the presence of 1:1 and 2:1 ligand to quadruplex complexes. Finally, the docking study suggested that ThT stacks with the guanine bases in one of the grooves which is in agreement with the CD studies. These results are expected to provide leads into the design of new ThT analogs and derivatives for enhancing the stability and selectivity of new G-quadruplex targeting ligands.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India; National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Sandip A Ghuge
- TERI-Deakin Nanobiotechnology Research Center, Sustainable Agriculture Division, The Energy and Resources Institute, New Delhi 110003, India
| | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India.
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43
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Zhou W, Yu Z, Ma G, Jin T, Li Y, Fan L, Li X. Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation. Analyst 2019; 144:2284-2290. [DOI: 10.1039/c8an02430h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).
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Affiliation(s)
- Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Tian Jin
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing
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Kataoka Y, Fujita H, Afanaseva A, Nagao C, Mizuguchi K, Kasahara Y, Obika S, Kuwahara M. High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives. Biochemistry 2018; 58:493-498. [DOI: 10.1021/acs.biochem.8b01181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuka Kataoka
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Arina Afanaseva
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Chioko Nagao
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kenji Mizuguchi
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
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45
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Qin Y, Liao S, Huang Y, Zhao J, Zhao S. Ultrasensitive fluorescent detection of nucleic acids based on label-free enzymatic-assisted cascade signal amplification. Anal Chim Acta 2018; 1039:91-97. [DOI: 10.1016/j.aca.2018.07.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/01/2018] [Accepted: 07/17/2018] [Indexed: 01/21/2023]
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46
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Prado Martins R, Findakly S, Daskalogianni C, Teulade-Fichou MP, Blondel M, Fåhraeus R. In Cellulo Protein-mRNA Interaction Assay to Determine the Action of G-Quadruplex-Binding Molecules. Molecules 2018; 23:E3124. [PMID: 30501034 PMCID: PMC6321085 DOI: 10.3390/molecules23123124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 11/16/2022] Open
Abstract
Protein-RNA interactions (PRIs) control pivotal steps in RNA biogenesis, regulate multiple physiological and pathological cellular networks, and are emerging as important drug targets. However, targeting of specific protein-RNA interactions for therapeutic developments is still poorly advanced. Studies and manipulation of these interactions are technically challenging and in vitro drug screening assays are often hampered due to the complexity of RNA structures. The binding of nucleolin (NCL) to a G-quadruplex (G4) structure in the messenger RNA (mRNA) of the Epstein-Barr virus (EBV)-encoded EBNA1 has emerged as an interesting therapeutic target to interfere with immune evasion of EBV-associated cancers. Using the NCL-EBNA1 mRNA interaction as a model, we describe a quantitative proximity ligation assay (PLA)-based in cellulo approach to determine the structure activity relationship of small chemical G4 ligands. Our results show how different G4 ligands have different effects on NCL binding to G4 of the EBNA1 mRNA and highlight the importance of in-cellulo screening assays for targeting RNA structure-dependent interactions.
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Affiliation(s)
| | - Sarah Findakly
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
| | - Chrysoula Daskalogianni
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Marie-Paule Teulade-Fichou
- Chemistry, Modelling and Imaging for Biology, CNRS UMR9187-Inserm U1196, Institut Curie, Université Paris-Sud, F-91405, Orsay, France.
| | - Marc Blondel
- GGB, Université de Brest, Inserm, CHRU Brest, EFS, UMR 1078, F-29200 Brest, France.
| | - Robin Fåhraeus
- Université Paris 7, Inserm, UMR 1162, 75013 Paris, France.
- ICCVS, University of Gdańsk, Science, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
- Department of Medical Biosciences, Umeå University, 90187 Umeå, Sweden.
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic.
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47
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Riccardi C, Musumeci D, Russo Krauss I, Piccolo M, Irace C, Paduano L, Montesarchio D. Exploring the conformational behaviour and aggregation properties of lipid-conjugated AS1411 aptamers. Int J Biol Macromol 2018; 118:1384-1399. [PMID: 30170359 DOI: 10.1016/j.ijbiomac.2018.06.137] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
Abstract
AS1411 is a nucleolin-binding aptamer which attracted great interest as active targeting ligand for the selective delivery of therapeutic agents to tumour cells. In this work we selected three AS1411 derivatives 5'-conjugated with lipophilic tails and studied their properties in view of their application in liposomial formulations and/or lipid coated-nanoparticles for targeted therapies. The conformational behaviour of these AS1411 analogs has been investigated in comparison with the unmodified aptamer by CD, UV, PAGE, SEC-HPLC, DLS and thioflavin T (ThT) fluorescence assays to get insight in their secondary structure and aggregation properties. This study has been performed in pseudo-physiological buffers mimicking the extra- and intracellular environments, and at different concentrations in the μM range, paying special attention to the effects of the lipophilic tail on the overall aptamer conformation. The 5'-lipidated AS1411 derivatives proved to fold into stable, parallel unimolecular G-quadruplex structures, forming large aggregates, mainly micelles, at conc. >10 μM. Preliminary bioscreenings on selected cancer cells showed that these derivatives are less cytotoxic than AS1411, but maintain a similar biological behaviour. This study demonstrated that lipophilic tails dramatically favour the formation of AS1411 aggregates, however not impairing the formation and thermal stability of its peculiar G4 motifs.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Fi), Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Fi), Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Napoli, Italy; Institute for Endocrinology and Oncology "Gaetano Salvatore", CNR, Via Pansini 5, 80131 Napoli, Italy.
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48
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Zhu J, Yan Z, Zhou W, Liu C, Wang J, Wang E. Lighting Up the Thioflavin T by Parallel-Stranded TG(GA) n DNA Homoduplexes. ACS Sens 2018; 3:1118-1125. [PMID: 29749724 DOI: 10.1021/acssensors.8b00141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thioflavin T (ThT) was once regarded to be a specific fluorescent probe for the human telomeric G-quadruplex, but more other kinds of DNA were found that can also bind to ThT in recent years. Herein, we focus on G-rich parallel-stranded DNA and utilize fluorescence, absorbance, circular dichroism, and surface plasmon resonance spectroscopy to investigate its interaction with ThT. Pyrene label and molecular modeling are applied to unveil the binding mechanism. We find a new class of non-G-quadruplex G-rich parallel-stranded ( ps) DNA with the sequence of TG(GA) n can bind to ThT and increase the fluorescence with an enhancement ability superior to G-quadruplex. The optimal binding specificity for ThT is conferred by two parts. The first part is composed of two bases TG at the 5' end, which is a critical domain and plays an important role in the formation of the binding site for ThT. The second part is the rest alternative d(GA) bases, which forms the ps homoduplex and cooperates with the TG bases at the 5' end to bind the ThT.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Weijun Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chuanbo Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- College of Physics, Jilin University, Changchun 130022, P. R. China
- Department of Chemistry and of Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, United States
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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49
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Kawauchi K, Sugimoto W, Yasui T, Murata K, Itoh K, Takagi K, Tsuruoka T, Akamatsu K, Tateishi-Karimata H, Sugimoto N, Miyoshi D. An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex. Nat Commun 2018; 9:2271. [PMID: 29891945 PMCID: PMC5995912 DOI: 10.1038/s41467-018-04771-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Aberrant activation of RAS signalling pathways contributes to aggressive phenotypes of cancer cells. The RAS-targeted therapies for cancer, therefore, have been recognised to be effective; however, current developments on targeting RAS have not advanced due to structural features of the RAS protein. Here, we show that expression of NRAS, a major isoform of RAS, can be controlled by photo-irradiation with an anionic phthalocyanine, ZnAPC, targeting NRAS mRNA. In vitro experiments reveal that ZnAPC binds to a G-quadruplex-forming oligonucleotide derived from the 5'-untranslated region of NRAS mRNA even in the presence of excess double-stranded RNA, which is abundant in cells, resulting in selective cleavage of the target RNA's G-quadruplex upon photo-irradiation. In line with these results, upon photo-irradiation, ZnAPC decreases NRAS mRNA and NRAS expression and thus viability of cancer cells. These results indicate that ZnAPC may be a prominent photosensitiser for a molecularly targeted photodynamic therapy for cancer.
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Affiliation(s)
- Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.
| | - Wataru Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Takatoshi Yasui
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kohei Murata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Katsuhiko Itoh
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kazuki Takagi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Takaaki Tsuruoka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Kensuke Akamatsu
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.
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50
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Li Q, Fei Y, Gao L, Yu Y, Zhou Y, Ye T, Zhou XS, Shao Y, Yin ZZ. G-Quadruplex DNA with an Apurinic Site as a Soft Molecularly Imprinted Sensing Platform. Anal Chem 2018; 90:5552-5556. [PMID: 29642702 DOI: 10.1021/acs.analchem.8b01097] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecularly imprinted polymers (MIPs) provide versatile sensor platforms to recognize targets by shape complementarity. However, the rigid structure of the classic MIPs compromises the signal transduction with necessary polymer and target modifications. Herein, we tried to use a flexible DNA that has a perfectly structured folding as the soft molecularly imprinted polymer (SMIP) for a straightforward sensor. As a proof of concept, the guanosine SMIP recognition was achieved by removal of a guanosine from a G-quadruplex-forming sequence (G4). The G4 folding structure with such an apurinic site (AP site) provides a well-defined MIP binding accommodation for guanosine according to the shape complementarity. The guanosine binding at the AP site subsequently leads to a conformation change suitable for remote readout using a G4-specific fluorescent ligand. The G4 sequence and AP site position were optimized for this SMIP behavior. Due to the G4 compact structure and the remaining hydrogen bonding pattern, nucleosides other than guanosine and negatively charged nucleotides exhibit no binding with the AP site, suggesting a high selectivity in the SMIP recognition. The proposed rationale was then convinced by the alkaline phosphatase-catalyzed GMP hydrolysis. Our work will inspire more interest in exploring nucleic acids as the SMIP frameworks due to their variant conformations and well-established molecular engineering.
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Affiliation(s)
- Qiusha Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yifan Fei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Longlong Gao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yali Yu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yufeng Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Ting Ye
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Xiao-Shun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences , Zhejiang Normal University , Jinhua 321004 , Zhejiang , China
| | - Zheng-Zhi Yin
- College of Biological, Chemical Sciences and Engineering , Jiaxing University , Jiaxing 314001 , Zhejiang , China
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