1
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Wang Z, Cui R, Liu L, Li L, Li Z, Liu X, Guo Y. Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure. J Phys Chem B 2024; 128:6830-6837. [PMID: 38959208 DOI: 10.1021/acs.jpcb.4c02021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The i-motif, a secondary structure of a four-helix formed by cytosine-rich DNA (i-DNA) through C-C+ base pairing, is prevalent in human telomeres and promoters. This structure creates steric hindrance, thereby inhibiting both gene expression and protein coding. The conformation of i-DNA is intricately linked to the intracellular ionic environment. Hence, investigating its conformation under various ion conditions holds significant importance. In this study, we explored the impact of cations on the i-motif structure at the single-molecule level using the α-hemolysin (α-HL) nanochannel. Our findings reveal that the ability of i-DNA to fold into the i-motif structure follows the order Cs+ > Na+ > K+ > Li+ for monovalent cations. Furthermore, we observed the interconversion of single-stranded DNA (ss-DNA) and the i-motif structure at high and low concentrations of Mg2+ and Ba2+ electrolyte solutions. This study not only has the potential to extend the application of i-motif-based sensors in complex solution environments but also provides a new idea for the detection of metal ions.
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Affiliation(s)
- Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710127, P. R. China
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2
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Yu H, Li F, Yang B, Qi Y, Guneri D, Chen W, Waller ZE, Li K, Ding Y. iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning. Nucleic Acids Res 2024; 52:W19-W28. [PMID: 38676949 PMCID: PMC11223794 DOI: 10.1093/nar/gkae315] [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: 02/13/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
DNA, beyond its canonical B-form double helix, adopts various alternative conformations, among which the i-motif, emerging in cytosine-rich sequences under acidic conditions, holds significant biological implications in transcription modulation and telomere biology. Despite recognizing the crucial role of i-motifs, predictive software for i-motif forming sequences has been limited. Addressing this gap, we introduce 'iM-Seeker', an innovative computational platform designed for the prediction and evaluation of i-motifs. iM-Seeker exhibits the capability to identify potential i-motifs within DNA segments or entire genomes, calculating stability scores for each predicted i-motif based on parameters such as the cytosine tracts number, loop lengths, and sequence composition. Furthermore, the webserver leverages automated machine learning (AutoML) to effortlessly fine-tune the optimal i-motif scoring model, incorporating user-supplied experimental data and customised features. As an advanced, versatile approach, 'iM-Seeker' promises to advance genomic research, highlighting the potential of i-motifs in cell biology and therapeutic applications. The webserver is freely available at https://im-seeker.org.
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Affiliation(s)
- Haopeng Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fan Li
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Bibo Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yiman Qi
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Wenqian Chen
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Ke Li
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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3
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Jakab K, Melios N, Tsekenis G, Shaban A, Horváth V, Keresztes Z. Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form. Biomolecules 2023; 13:1363. [PMID: 37759762 PMCID: PMC10526194 DOI: 10.3390/biom13091363] [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: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer's 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer's behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered.
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Affiliation(s)
- Kristóf Jakab
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
| | - Nikitas Melios
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - George Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - Abdul Shaban
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
| | - Viola Horváth
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
- ELKH-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zsófia Keresztes
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
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4
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Pandey A, Roy S, Srivatsan SG. Probing the Competition between Duplex, G-Quadruplex and i-Motif Structures of the Oncogenic c-Myc DNA Promoter Region. Chem Asian J 2023; 18:e202300510. [PMID: 37541298 DOI: 10.1002/asia.202300510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/09/2023] [Indexed: 08/06/2023]
Abstract
Development of probe systems that provide unique spectral signatures for duplex, G-quadruplex (GQ) and i-motif (iM) structures is very important to understand the relative propensity of a G-rich-C-rich promoter region to form these structures. Here, we devise a platform using a combination of two environment-sensitive nucleoside analogs namely, 5-fluorobenzofuran-modified 2'-deoxyuridine (FBF-dU) and 5-fluoro-2'-deoxyuridine (F-dU) to study the structures adopted by a promoter region of the c-Myc oncogene. FBF-dU serves as a dual-purpose probe containing a fluorescent and 19 F NMR label. When incorporated into the C-rich sequence, it reports the formation of different iMs via changes in its fluorescence properties and 19 F signal. F-dU incorporated into the G-rich ON reports the formation of a GQ structure whose 19 F signal is clearly different from the signals obtained for iMs. Rewardingly, the labeled ONs when mixed with respective complementary strands allows us to determine the relative population of different structures formed by the c-Myc promoter by the virtue of the probe's ability to produce distinct and resolved 19 F signatures for different structures. Our results indicate that at physiological pH and temperature the c-Myc promoter forms duplex, random coil and GQ structures, and does not form an iM. Whereas at acidic pH, the mixture largely forms iM and GQ structures. Taken together, our system will complement existing tools and provide unprecedented insights on the population equilibrium and dynamics of nucleic acid structures under different conditions.
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Affiliation(s)
- Akanksha Pandey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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5
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Somkuti J, Molnár OR, Smeller L. Revealing unfolding steps and volume changes of human telomeric i-motif DNA. Phys Chem Chem Phys 2020; 22:23816-23823. [DOI: 10.1039/d0cp03894f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The i-motif structure of the human telomeric DNA was destabilized by pressure and unfolded with a negative volume change.
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Affiliation(s)
- Judit Somkuti
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
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6
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Megalathan A, Cox BD, Wilkerson PD, Kaur A, Sapkota K, Reiner JE, Dhakal S. Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles. Nucleic Acids Res 2019; 47:7199-7212. [PMID: 31287873 PMCID: PMC6698746 DOI: 10.1093/nar/gkz565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Peter D Wilkerson
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
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7
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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8
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Manna S, Srivatsan SG. Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments. RSC Adv 2018; 8:25673-25694. [PMID: 30210793 PMCID: PMC6130854 DOI: 10.1039/c8ra03708f] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022] Open
Abstract
Biophysical and biochemical investigations provide compelling evidence connecting the four-stranded G-quadruplex (GQ) structure with its role in regulating multiple cellular processes. Hence, modulating the function of GQs by using small molecule binders is being actively pursued as a strategy to develop new chemotherapeutic agents. However, sequence diversity and structural polymorphism of GQs have posed immense challenges in terms of understanding what conformation a G-rich sequence adopts inside the cell and how to specifically target a GQ motif amidst several other GQ-forming sequences. In this context, here we review recent developments in the applications of biophysical tools that use fluorescence readout to probe the GQ structure and recognition in cell-free and cellular environments. First, we provide a detailed discussion on the utility of covalently labeled environment-sensitive fluorescent nucleoside analogs in assessing the subtle difference in GQ structures and their ligand binding abilities. Furthermore, a detailed discussion on structure-specific antibodies and small molecule probes used to visualize and confirm the existence of DNA and RNA GQs in cells is provided. We also highlight the open challenges in the study of tetraplexes (GQ and i-motif structures) and how addressing these challenges by developing new tools and techniques will have a profound impact on tetraplex-directed therapeutic strategies.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
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9
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Zamiri B, Mirceta M, Abu-Ghazalah R, Wold MS, Pearson CE, Macgregor RB. Stress-induced acidification may contribute to formation of unusual structures in C9orf72-repeats. Biochim Biophys Acta Gen Subj 2018; 1862:1482-1491. [PMID: 29550431 DOI: 10.1016/j.bbagen.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/22/2018] [Accepted: 03/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Expansion of the C9orf72 hexanucleotide repeat (GGGGCC)n·(GGCCCC)n is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both strands of the C9orf72 repeat have been shown to form unusual DNA and RNA structures that are thought to be involved in mutagenesis and/or pathogenesis. We previously showed that the C-rich DNA strands from the C9orf72 repeat can form four-stranded quadruplexes at neutral pH. The cytosine residues become protonated under slightly acidic pH (pH 4.5-6.2), facilitating the formation of intercalated i-motif structures. METHODS Using CD spectroscopy, UV melting, and gel electrophoresis, we demonstrate a pH-induced structural transition of the C-rich DNA strand of the C9orf72 repeat at pHs reported to exist in living cells under stress, including during neurodegeneration and cancer. RESULTS We show that the repeats with lengths of 4, 6, and 8 units, form intercalated quadruplex i-motifs at low pH (pH < 5) and monomolecular hairpins and monomolecular quadruplexes under neutral-basic conditions (pH ≥ 8). Furthermore, we show that the human replication protein A (RPA) binds to the G-rich and C-rich DNA strands under acidic conditions, suggesting that it can bind to i-motif structures. CONCLUSIONS In the proper sequence context, i-motif structures can form at pH values found in some cells in vivo. GENERAL SIGNIFICANCE DNA conformational plasticity exists over broad range of solution conditions.
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Affiliation(s)
- Bita Zamiri
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mila Mirceta
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Rashid Abu-Ghazalah
- W. Booth School of Engineering Technology Practice and Technology, McMaster University, Hamilton, Ontario L8S 0A3, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
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10
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Debnath M, Ghosh S, Chauhan A, Paul R, Bhattacharyya K, Dash J. Preferential targeting of i-motifs and G-quadruplexes by small molecules. Chem Sci 2017; 8:7448-7456. [PMID: 29163897 PMCID: PMC5674183 DOI: 10.1039/c7sc02693e] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
i-Motifs and G-quadruplexes are dynamic nucleic acid secondary structures, which are believed to play key roles in gene expression. We herein report two peptidomimetic ligands (PBP1 and PBP2) that selectively target i-motifs and G-quadruplexes over double-stranded DNA. These peptidomimetics, regioisomeric with respect to the position of triazole/prolinamide motifs, have been synthesized using a modular method involving Cu(i)-catalyzed azide and alkyne cycloaddition. The para-isomer, PBP1 exhibits high selectivity for i-motifs while the meta-isomer PBP2 binds selectively to G-quadruplex structures. Interestingly, these ligands have the ability to induce G-quadruplex or i-motif structures from the unstructured single-stranded DNA conformations, as observed using single molecule Förster resonance energy transfer (smFRET) studies. The quantitative real-time polymerase chain reaction (qRT-PCR), western blot, and dual-luciferase assays indicate that PBP1 upregulates and PBP2 downregulates BCL-2 gene expression in cancer cells.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Ajay Chauhan
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Rakesh Paul
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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11
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Kumar V, kashav T, Islam A, Ahmad F, Hassan MI. Structural insight into C9orf72 hexanucleotide repeat expansions: Towards new therapeutic targets in FTD-ALS. Neurochem Int 2016; 100:11-20. [DOI: 10.1016/j.neuint.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
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12
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Li H, Hai J, Zhou J, Yuan G. The formation and characteristics of the i-motif structure within the promoter of the c-myb proto-oncogene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:625-632. [PMID: 27487467 DOI: 10.1016/j.jphotobiol.2016.07.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/21/2016] [Accepted: 07/24/2016] [Indexed: 12/11/2022]
Abstract
C-myb proto-oncogene is a potential therapeutic target for some human solid tumors and leukemias. A long cytosine-rich sequence, which locates the downstream of the transcription initiation site, is demonstrated to fold into an intramolecular i-motif DNA using electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. Effects of factors, including the pH value, the number of C:C(+) dimers, the concentration of buffer, the molecular crowding condition, and the coexistence of the complementary DNA, on the formation and the structural stability of the i-motif DNA are systematically studied. We have demonstrated that the i-motif folding in the c-myb promoter could be accelerated upon synergistic physiological stimuli including intracellular molecular crowding and low pH values, as well as the large number of the i-motif C:C(+) dimers. Meanwhile, various inputs, such as acids/bases and metal ions, have exhibited their abilities in controlling the conformational switch of the c-myb GC-rich DNA. Acidic pH values and the presence of K(+) ions can induce the dissociation of the double helix. Our present strategy can greatly extend the potential usages of i-motif DNA molecules with specific sequences as conformational switch-controlled devices. Moreover, this work demonstrates the superiority of CD spectroscopy associated with ESI-MS as a rapid, more cost-effective and sensitive structural change responsive method in the research of DNA conformational switching.
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Affiliation(s)
- Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China; Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada.
| | - Jinhui Hai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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13
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Zhang W, Wang F, Wang Y, Wang J, Yu Y, Guo S, Chen R, Zhou D. pH and near-infrared light dual-stimuli responsive drug delivery using DNA-conjugated gold nanorods for effective treatment of multidrug resistant cancer cells. J Control Release 2016; 232:9-19. [PMID: 27072026 DOI: 10.1016/j.jconrel.2016.04.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/25/2016] [Accepted: 04/01/2016] [Indexed: 01/01/2023]
Abstract
A thiolated pH-responsive DNA conjugated gold nanorod (GNR) was developed as a multifunctional nanocarrier for targeted, pH-and near infrared (NIR) radiation dual-stimuli triggered drug delivery. It was further passivated by a thiolated poly(ethylene glycol)-biotin to improve its cancer targeting ability by specific binding to cancer cell over-expressed biotin receptors. Doxorubicin (DOX), a widely used clinical anticancer drug, was conveniently loaded into nanocarrier by intercalating inside the double-stranded pH-responsive DNAs on the GNR surface to complete the construction of the multifunctional nanomedicine. The nanomedicine can rapidly and effectively release its DOX payload triggered by an acidic pH environment (pH~5) and/or applying an 808nm NIR laser radiation. Compared to free DOX, the biotin-modified nanomedicine displayed greatly increased cell uptake and significantly reduced drug efflux by model multidrug resistant (MDR) breast cancer cell lines (MCF-7/ADR). The application of NIR radiation further increased the DOX release and facilitated its nuclear accumulation. As a result, this new DNA-GNR based multifunctional nanomedicine exerted greatly increased potency (~67 fold) against the MDR cancer cells over free DOX.
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Affiliation(s)
- Wenjun Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Feihu Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Yun Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Jining Wang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Yanna Yu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Shengrong Guo
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
| | - Rongjun Chen
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Dejian Zhou
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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14
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Xu L, Hong S, Sun N, Wang K, Zhou L, Ji L, Pei R. Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems. Chem Commun (Camb) 2016; 52:179-82. [DOI: 10.1039/c5cc08242k] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.
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Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Na Sun
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Kewei Wang
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Liya Ji
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou, 215123
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15
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Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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16
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Bielecka P, Juskowiak B. Fluorescent Sensor for PH Monitoring Based on an i-Motif---Switching Aptamer Containing a Tricyclic Cytosine Analogue (tC). Molecules 2015; 20:18511-25. [PMID: 26473815 PMCID: PMC6332284 DOI: 10.3390/molecules201018511] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/24/2015] [Accepted: 10/06/2015] [Indexed: 12/16/2022] Open
Abstract
There are cytosine-rich regions in the genome that bind protons with high specificity. Thus protonated C-rich sequence may undergo folding to tetraplex structures called i-motifs. Therefore, one can regard such specific C-rich oligonucleotides as aptamers that recognize protons and undergo conformational transitions. Proper labeling of the aptamer with a fluorescent tag constitutes a platform to construct a pH-sensitive aptasensor. Since the hemiprotonated C-C⁺ base pairs are responsible for the folded tetraplex structure of i-motif, we decided to substitute one of cytosines in an aptamer sequence with its fluorescent analogue, 1,3-diaza-2-oxophenothiazine (tC). In this paper we report on three tC-modified fluorescent probes that contain RET related sequences as a proton recognizing aptamer. Results of the circular dichroism (CD), UV absorption melting experiments, and steady-state fluorescence measurements of these tC-modified i-motif probes are presented and discussed. The pH-induced i-motif formation by the probes resulted in fluorescence quenching of tC fluorophore. Efficiency of quenching was related to the pH variations. Suitability of the sensor for monitoring pH changes was also demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b 61-614 Poznan, Poland.
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17
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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18
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Huang H, Hong X, Liu F, Li N. A simple approach to study the conformational switching of i-motif DNA by fluorescence anisotropy. Analyst 2015; 140:5987-91. [DOI: 10.1039/c5an01011j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fluorescence anisotropy is a simple, reliable and sensitive approach to study the conformational switching of the i-motif structure.
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Affiliation(s)
- Hongduan Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Xinying Hong
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
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19
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Unconventional features of C9ORF72 expanded repeat in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Neurobiol Aging 2014; 35:2421.e1-2421.e12. [PMID: 24836899 DOI: 10.1016/j.neurobiolaging.2014.04.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/31/2014] [Accepted: 04/13/2014] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are devastating neurodegenerative diseases that form two ends of a complex disease spectrum. Aggregation of RNA binding proteins is one of the hallmark pathologic features of ALS and FTDL and suggests perturbance of the RNA metabolism in their etiology. Recent identification of the disease-associated expansions of the intronic hexanucleotide repeat GGGGCC in the C9ORF72 gene further substantiates the case for RNA involvement. The expanded repeat, which has turned out to be the single most common genetic cause of ALS and FTLD, may enable the formation of complex DNA and RNA structures, changes in RNA transcription, and processing and formation of toxic RNA foci, which may sequester and inactivate RNA binding proteins. Additionally, the transcribed expanded repeat can undergo repeat-associated non-ATG-initiated translation resulting in accumulation of a series of dipeptide repeat proteins. Understanding the basis of the proposed mechanisms and shared pathways, as well as interactions with known key proteins such as TAR DNA-binding protein (TDP-43) are needed to clarify the pathology of ALS and/or FTLD, and make possible steps toward therapy development.
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20
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Kang HJ, Kendrick S, Hecht SM, Hurley LH. The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc 2014; 136:4172-85. [PMID: 24559432 PMCID: PMC3985447 DOI: 10.1021/ja4109352] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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In a companion paper (DOI: 10.021/ja410934b) we demonstrate that the C-rich
strand of the cis-regulatory element in the BCL2 promoter element
is highly dynamic in nature and can form either an i-motif or a flexible
hairpin. Under physiological conditions these two secondary DNA structures
are found in an equilibrium mixture, which can be shifted by the addition
of small molecules that trap out either the i-motif (IMC-48) or the
flexible hairpin (IMC-76). In cellular experiments we demonstrate
that the addition of these molecules has opposite effects on BCL2 gene expression and furthermore that these effects
are antagonistic. In this contribution we have identified a transcriptional
factor that recognizes and binds to the BCL2 i-motif
to activate transcription. The molecular basis for the recognition
of the i-motif by hnRNP LL is determined, and we demonstrate that
the protein unfolds the i-motif structure to form a stable single-stranded
complex. In subsequent experiments we show that IMC-48 and IMC-76
have opposite, antagonistic effects on the formation of the hnRNP
LL–i-motif complex as well as on the transcription factor occupancy
at the BCL2 promoter. For the first time we propose
that the i-motif acts as a molecular switch that controls gene expression
and that small molecules that target the dynamic equilibrium of the
i-motif and the flexible hairpin can differentially modulate gene
expression.
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Affiliation(s)
- Hyun-Jin Kang
- College of Pharmacy and §BIO5 Institute, University of Arizona , Tucson, Arizona 85721, United States
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21
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Benabou S, Aviñó A, Eritja R, González C, Gargallo R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv 2014. [DOI: 10.1039/c4ra02129k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.
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Affiliation(s)
- S. Benabou
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
| | - A. Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - R. Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN Networking Centre on Bioengineering
- Biomaterials and Nanomedicine
- E-08034 Barcelona, Spain
| | - C. González
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- E-28006 Madrid, Spain
| | - R. Gargallo
- Department of Analytical Chemistry
- University of Barcelona
- E-08028 Barcelona, Spain
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22
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Choi J, Tanaka A, Cho DW, Fujitsuka M, Majima T. Efficient Electron Transfer in i-Motif DNA with a Tetraplex Structure. Angew Chem Int Ed Engl 2013; 52:12937-41. [DOI: 10.1002/anie.201306017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/11/2013] [Indexed: 11/08/2022]
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