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Williams SL, Casas‐Delucchi CS, Raguseo F, Guneri D, Li Y, Minamino M, Fletcher EE, Yeeles JTP, Keyser UF, Waller ZAE, Di Antonio M, Coster G. Replication-induced DNA secondary structures drive fork uncoupling and breakage. EMBO J 2023; 42:e114334. [PMID: 37781931 PMCID: PMC10646557 DOI: 10.15252/embj.2023114334] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023] Open
Abstract
Sequences that form DNA secondary structures, such as G-quadruplexes (G4s) and intercalated-Motifs (iMs), are abundant in the human genome and play various physiological roles. However, they can also interfere with replication and threaten genome stability. Multiple lines of evidence suggest G4s inhibit replication, but the underlying mechanism remains unclear. Moreover, evidence of how iMs affect the replisome is lacking. Here, we reconstitute replication of physiologically derived structure-forming sequences to find that a single G4 or iM arrest DNA replication. Direct single-molecule structure detection within solid-state nanopores reveals structures form as a consequence of replication. Combined genetic and biophysical characterisation establishes that structure stability and probability of structure formation are key determinants of replisome arrest. Mechanistically, replication arrest is caused by impaired synthesis, resulting in helicase-polymerase uncoupling. Significantly, iMs also induce breakage of nascent DNA. Finally, stalled forks are only rescued by a specialised helicase, Pif1, but not Rrm3, Sgs1, Chl1 or Hrq1. Altogether, we provide a mechanism for quadruplex structure formation and resolution during replication and highlight G4s and iMs as endogenous sources of replication stress.
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Affiliation(s)
- Sophie L Williams
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Corella S Casas‐Delucchi
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
| | - Federica Raguseo
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
| | | | - Yunxuan Li
- Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | - Marco Di Antonio
- Chemistry DepartmentImperial College London, MSRHLondonUK
- Institute of Chemical Biology, MSRHLondonUK
- Francis Crick InstituteLondonUK
| | - Gideon Coster
- Genome Replication Lab, Division of Cancer Biology, Institute of Cancer ResearchChester Beatty LaboratoriesLondonUK
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2
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Sharma P, Sweta Jha N. Enhanced antioxidant and cytotoxic activity of ferrocenyl-substituted curcumin via stabilization of promoter c-MYC silencer element. J Biomol Struct Dyn 2023; 41:9539-9550. [PMID: 36345790 DOI: 10.1080/07391102.2022.2143424] [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: 08/01/2022] [Accepted: 10/29/2022] [Indexed: 11/11/2022]
Abstract
We are reporting a successful attachment of ferrocenyl moiety at the active methylene carbon atom of β-diketone of curcumin via Knoevenagel condensation reaction, to utilize the optimum selectivity toward biological targets. The formation of ferrocenyl curcumin (i.e., Fc-cur) has been confirmed by 1H NMR, 13C NMR, and FT-IR spectra analysis. Further, circular dichroism (CD) spectroscopy, thermal denaturation, absorption, and fluorescence spectroscopy have been used to understand the association of ligand (i.e., Fc-cur) with G-quadruplex. Based on these analysis, the binding mechanism of the ligand i.e., Fc-cur to the parallel and hybrid topology present in different G-quadruplex has been proposed. Further, the binding and modes of the interaction of Fc-cur with Pu27 c-MYC silencer element and H-telo G-quadruplex have unravelled selective and stronger binding via intercalation with the parallel topology of c-MYC G-quadruplex rather than the hybrid topology of H-telo quadruplex. The manifestation of better antioxidant activity of Fc-cur has been demonstrated by showing a stronger radical scavenging capability than pristine curcumin. The cytotoxicity analysis of the proposed ligand i.e., Fc-cur against Vero and HeLa cells have clearly reflected the nontoxicity toward Vero cells and quite effective against the HeLa cells which reduces the cancer cells more effectively than the already reported for curcumin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Padma Sharma
- Department of Chemistry, National Institute of Technology, Patna, India
| | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology, Patna, India
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3
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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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4
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Sharma P, Jha NS. Mechanistic aspects of binding of telomeric over parallel G-quadruplex with novel synthesized Knoevenagel condensate 4-nitrobenzylidene curcumin. J Mol Recognit 2023; 36:e3041. [PMID: 37210661 DOI: 10.1002/jmr.3041] [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: 10/06/2022] [Revised: 04/24/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
Abstract
The introduction of small ligands to stabilise G-quadruplex DNA structures is a promising method for developing anti-cancer drugs. It is challenging to stabilise the G-quadruplex structure, which can take on a variety of topologies and is known to inhibit specific biological processes. To achieve this, 4-nitrobenzylidene curcumin (NBC), the Knoevenagel condensate of curcumin, was synthesized and characterized. The interaction of 4-nitrobenzylidene curcumin with parallel (c-MYC) and hybrid (H-telo) G-quadruplex structures was studied by circular dichroism (CD) spectroscopy, UV-thermal melting, differential scanning calorimetry (DSC), absorption spectroscopy, fluorescence spectroscopy and docking studies. The outcome demonstrates that, in a K+ -rich solution, the ligand NBC can stabilise the parallel c-MYC and hybrid H-telo G-quadruplex structures by 5°C. The absorption and fluorescence studies show that the ligand NBC binds to c-MYC and H-telo with affinities of 0.3 × 106 M-1 and 0.6 × 106 M-1 , respectively. The ligand interacts with the terminal G-quartet of the quadruplex structure via intercalation and the groove mode of binding, well supported by docking studies as well. NBC has more potent antioxidant activity as compared to the curcumin and 4-nitro benzaldehyde. It was also found to have higher cytotoxic activity towards cell line such as HeLa and MCF-7, while less cytotoxic for healthy Vero cells. Overall, the results show that the Knoevenagel product of curcumin can work better as a G-quadruplex binder and could be used as a possible treatment.
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Affiliation(s)
- Padma Sharma
- Department of Chemistry, National Institute of Technology, Patna, India
| | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology, Patna, India
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5
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Cadoni E, De Paepe L, Colpaert G, Tack R, Waegeman D, Manicardi A, Madder A. A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA. Nucleic Acids Res 2023; 51:4112-4125. [PMID: 36971129 PMCID: PMC10201448 DOI: 10.1093/nar/gkad189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/03/2023] [Accepted: 03/12/2023] [Indexed: 08/21/2023] Open
Abstract
The importance of non-canonical DNA structures such as G-quadruplexes (G4) and intercalating-motifs (iMs) in the fine regulation of a variety of cellular processes has been recently demonstrated. As the crucial roles of these structures are being unravelled, it is becoming more and more important to develop tools that allow targeting these structures with the highest possible specificity. While targeting methodologies have been reported for G4s, this is not the case for iMs, as evidenced by the limited number of specific ligands able to bind the latter and the total absence of selective alkylating agents for their covalent targeting. Furthermore, strategies for the sequence-specific covalent targeting of G4s and iMs have not been reported thus far. Herein, we describe a simple methodology to achieve sequence-specific covalent targeting of G4 and iM DNA structures based on the combination of (i) a peptide nucleic acid (PNA) recognizing a specific sequence of interest, (ii) a pro-reactive moiety enabling a controlled alkylation reaction, and (iii) a G4 or iM ligand orienting the alkylating warhead to the reactive residues. This multi-component system allows for the targeting of specific G4 or iM sequences of interest in the presence of competing DNA sequences and under biologically relevant conditions.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Ruben Tack
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Dries Waegeman
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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6
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Sarkar S, Colón‐Roura G, Pearse A, Armitage BA. Targeting a KRAS i-motif forming sequence by unmodified and gamma-modified peptide nucleic acid oligomers. Biopolymers 2023; 114:e23529. [PMID: 36573547 PMCID: PMC10078108 DOI: 10.1002/bip.23529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022]
Abstract
Growing interest in i-motif DNA as a transcriptional regulatory element motivates development of synthetic molecules capable of targeting these structures. In this study, we designed unmodified peptide nucleic acid (PNA) and gamma-modified PNA (γPNA) oligomers complementary to an i-motif forming sequence derived from the promoter of the KRAS oncogene. Biophysical techniques such as circular dichroism (CD) spectroscopy, CD melting, and fluorescence spectroscopy demonstrated the successful invasion of the i-motif by PNA and γPNA. Both PNA and γPNA showed very strong binding to the target sequence with high thermal stability of the resulting heteroduplexes. Interestingly fluorescence and CD experiments indicated formation of an intermolecular i-motif structure via the overhangs of target-probe heteroduplexes formed by PNA/γPNA invasion of the intramolecular i-motif. Targeting promoter i-motif forming sequences with high-affinity oligonucleotide mimics like γPNAs may represent a new approach for inhibiting KRAS transcription, thereby representing a potentially useful anti-cancer strategy.
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Affiliation(s)
- Srijani Sarkar
- Department of Chemistry and Center for Nucleic Acids Science and TechnologyCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Gabriela Colón‐Roura
- Department of Chemistry and Center for Nucleic Acids Science and TechnologyCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Alexander Pearse
- Department of Chemistry and Center for Nucleic Acids Science and TechnologyCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and TechnologyCarnegie Mellon UniversityPittsburghPennsylvaniaUSA
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7
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Valiuska S, Psaras AM, Noé V, Brooks TA, Ciudad CJ. Targeting MYC Regulation with Polypurine Reverse Hoogsteen Oligonucleotides. Int J Mol Sci 2022; 24:ijms24010378. [PMID: 36613820 PMCID: PMC9820101 DOI: 10.3390/ijms24010378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
The oncogene MYC has key roles in transcription, proliferation, deregulating cellular energetics, and more. Modulating the expression or function of the MYC protein is a viable therapeutic goal in an array of cancer types, and potential inhibitors of MYC with high specificity and selectivity are of great interest. In cancer cells addicted to their aberrant MYC function, suppression can lead to apoptosis, with minimal effects on non-addicted, non-oncogenic cells, providing a wide therapeutic window for specific and efficacious anti-tumor treatment. Within the promoter of MYC lies a GC-rich, G-quadruplex (G4)-forming region, wherein G4 formation is capable of mediating transcriptional downregulation of MYC. Such GC-rich regions of DNA are prime targets for regulation with Polypurine Reverse Hoogsteen hairpins (PPRHs). The current study designed and examined PPRHs targeting the G4-forming and four other GC-rich regions of DNA within the promoter or intronic regions. Six total PPRHs were designed, examined in cell-free conditions for target engagement and in cells for transcriptional modulation, and correlating cytotoxic activity in pancreatic, prostate, neuroblastoma, colorectal, ovarian, and breast cancer cells. Two lead PPRHs, one targeting the promoter G4 and one targeting Intron 1, were identified with high potential for further development as an innovative approach to both G4 stabilization and MYC modulation.
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Affiliation(s)
- Simonas Valiuska
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Alexandra Maria Psaras
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA
| | - Véronique Noé
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Tracy A. Brooks
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA
- Correspondence: (C.J.C.); (T.A.B.); Tel.: +34-93-403-4455 (C.J.C.)
| | - Carlos J. Ciudad
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (C.J.C.); (T.A.B.); Tel.: +34-93-403-4455 (C.J.C.)
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8
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Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures. J Biol Chem 2022; 298:102670. [PMID: 36334628 PMCID: PMC9709238 DOI: 10.1016/j.jbc.2022.102670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/27/2022] Open
Abstract
I-motifs are four-strand noncanonical secondary structures formed by cytosine (C)-rich sequences in living cells. The structural dynamics of i-motifs play essential roles in many cellular processes, such as telomerase inhibition, DNA replication, and transcriptional regulation. In cells, the structural dynamics of the i-motif can be modulated by the interaction of poly(C)-binding proteins (PCBPs), and the interaction is closely related to human health, through modulating the transcription of oncogenes and telomere stability. Therefore, the mechanisms of how PCBPs interact with i-motif structures are fundamentally important. However, the underlying mechanisms remain elusive. I-motif structures in the promoter of the c-MYC oncogene can be unfolded by heterogeneous nuclear ribonucleoprotein K (hnRNP K), a PCBP, to activate its transcription. Here, we selected this system as an example to comprehensively study the unfolding mechanisms. We found that the promoter sequence containing 5 C-runs preferred folding into type-1245 to type-1234 i-motif structures based on their folding stability, which was further confirmed by single-molecule FRET. In addition, we first revealed that the c-MYC i-motif structure was discretely resolved by hnRNP K through two intermediate states, which were assigned to the opposite hairpin and neighboring hairpin, as further confirmed by site mutations. Furthermore, we found all three KH (hnRNP K homology) domains of hnRNP K could unfold the c-MYC i-motif structure, and KH2 and KH3 were more active than KH1. In conclusion, this study may deepen our understanding of the interactions between i-motifs and PCBPs and may be helpful for drug development.
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9
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures. ChemistryOpen 2022; 11:e202200090. [PMID: 35608081 PMCID: PMC9127747 DOI: 10.1002/open.202200090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 04/22/2022] [Indexed: 12/27/2022] Open
Abstract
DNA G-quadruplexes (G4s) are key structures for the development of targeted anticancer therapies. In this context, ligands selectively interacting with G4s can represent valuable anticancer drugs. Aiming at speeding up the identification of G4-targeting synthetic or natural compounds, we developed an affinity chromatography-based assay, named G-quadruplex on Oligo Affinity Support (G4-OAS), by synthesizing G4-forming sequences on commercially available polystyrene OAS. Then, due to unspecific binding of several hydrophobic ligands on nude OAS, we moved to Controlled Pore Glass (CPG). We thus conceived an ad hoc functionalized, universal support on which both the on-support elongation and deprotection of the G4-forming oligonucleotides can be performed, along with the successive affinity chromatography-based assay, renamed as G-quadruplex on Controlled Pore Glass (G4-CPG) assay. Here we describe these assays and their applications to the screening of several libraries of chemically different putative G4 ligands. Finally, ongoing studies and outlook of our G4-CPG assay are reported.
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Affiliation(s)
- Chiara Platella
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Ettore Napolitano
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Claudia Riccardi
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
| | - Domenica Musumeci
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
- Institute of Biostructures and BioimagesCNRVia Tommaso De Amicis, 9580145NaplesItaly
| | - Daniela Montesarchio
- Department of Chemical SciencesUniversity of Naples Federico IIvia Cintia 2180126NaplesItaly
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10
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Ma X, Feng Y, Yang Y, Li X, Shi Y, Tao S, Cheng X, Huang J, Wang XE, Chen C, Monchaud D, Zhang W. Genome-wide characterization of i-motifs and their potential roles in the stability and evolution of transposable elements in rice. Nucleic Acids Res 2022; 50:3226-3238. [PMID: 35188565 PMCID: PMC8989525 DOI: 10.1093/nar/gkac121] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/13/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
I-motifs (iMs) are non-canonical DNA secondary structures that fold from cytosine (C)-rich genomic DNA regions termed putative i-motif forming sequences (PiMFSs). The structure of iMs is stabilized by hemiprotonated C-C base pairs, and their functions are now suspected in key cellular processes in human cells such as genome stability and regulation of gene transcription. In plants, their biological relevance is still largely unknown. Here, we characterized PiMFSs with high potential for i-motif formation in the rice genome by developing and applying a protocol hinging on an iMab antibody-based immunoprecipitation (IP) coupled with high-throughput sequencing (seq), consequently termed iM-IP-seq. We found that PiMFSs had intrinsic subgenomic distributions, cis-regulatory functions and an intricate relationship with DNA methylation. We indeed found that the coordination of PiMFSs with DNA methylation may affect dynamics of transposable elements (TEs) among different cultivated Oryza subpopulations or during evolution of wild rice species. Collectively, our study provides first and unique insights into the biology of iMs in plants, with potential applications in plant biotechnology for improving important agronomic rice traits.
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Affiliation(s)
- Xing Ma
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Ying Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xin Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - Yining Shi
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Jian Huang
- School of Biology & Basic Medical Science, Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan410125, P.R. China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, P.R. China
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11
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Fluorescent AgNCs Formed on Bifunctional DNA Template for Potassium Ion Detection. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, we examined properties of silver nanoclusters, which are AgNCs stabilized by DNA oligonucleotide scaffold containing G-quadruplex-forming sequences: human telomeric (Tel22) or thrombin-binding aptamer (TBA). Thus, we obtained two fluorescent probes abbreviated as Tel22C12-AgNCs and TBAC12-AgNCs, which were characterized using absorption, circular dichroism and fluorescence spectroscopy. Both probes emit green and red fluorescence. The presence of silver nanoclusters did not destabilize the formed G-quadruplexes. The structural changes of probes upon binding K+ or Na+ ions cause quenching in their red emission. Green emission was slightly quenched only in the case of Tel22C12-AgNCs; on the contrary, for TBAC12-AgNC’s green emission, we observed an increasing fluorescence signal. Moreover, the Tel22C12-AgNCs system shows not only a higher binding preference for K+ over Na+, but it was able to monitor small changes in K+ concentrations in the buffer mimicking extracellular conditions (high content of Na+ ions). These results suggest that Tel22C12-AgNCs exhibit the potential to monitor transmembrane potassium transport.
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12
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Yu G, Niu K, Peng Y, Liu Z, Song Q, Feng Q. Large-scale screening of i-motif binding compounds in the silkworm, Bombyx mori. Biochem Biophys Res Commun 2021; 589:9-15. [PMID: 34883288 DOI: 10.1016/j.bbrc.2021.11.092] [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: 10/17/2021] [Accepted: 11/25/2021] [Indexed: 11/02/2022]
Abstract
DNA secondary structure i-motif involves in gene transcription and considered as a novel target for cancer gene therapy. I-motif-binding compounds can either stabilize or destroy the structure, resulting in change in target gene transcription. In this study, a large-scale screening of binding compounds was conducted using the i-motif structure of BmPOUM2, a transcription factor in silkworm, Bombyx mori. Surface plasmon resonance imaging (SPRi) high-throughput binding screening of 3642 compounds found 60 compounds with an binding affinity Kd of 10-7-10-6 M. SPRi and circular dichroism (CD) double screening demonstrated that the BmPOUM2 i-motif structure bound the compounds IF1, IF3, IF4, IF6 and IF7 with Kd of 10-7 M, and the compounds IF2 and tetrakis (4-N-methylpyridyl) porphine (TMPyP4) with a Kd of 10-8 M. Interestingly, IF2, IF3, IF4, IF6 and IF7 promoted the binding of the i-motif-binding protein BmILF with the i-motif structure, whereas TMPyP4 inhibited the binding. This study provided a list of compounds that have potential applications in functional analysis of i-motif structure and in pesticide and drug development through gene transcription regulation by i-motif structure.
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Affiliation(s)
- Guoxing Yu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhenming Liu
- School of Pharmacy, Peking University, Beijing, 100191, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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13
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Jarošová P, Hannig P, Kolková K, Mazzini S, Táborská E, Gargallo R, Borgonovo G, Artali R, Táborský P. Alkaloid Escholidine and Its Interaction with DNA Structures. BIOLOGY 2021; 10:1225. [PMID: 34943140 PMCID: PMC8698932 DOI: 10.3390/biology10121225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022]
Abstract
Berberine, the most known quaternary protoberberine alkaloid (QPA), has been reported to inhibit the SIK3 protein connected with breast cancer. Berberine also appears to reduce the bcl-2 and XIAP expression-proteins responsible for the inhibition of apoptosis. As some problems in the therapy with berberine arose, we studied the DNA binding properties of escholidine, another QPA alkaloid. CD, fluorescence, and NMR examined models of i-motif and G-quadruplex sequences present in the n-myc gene and the c-kit gene. We provide evidence that escholidine does not induce stabilization of the i-motif sequences, while the interaction with G-quadruplex structures appears to be more significant.
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Affiliation(s)
- Petra Jarošová
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Pavel Hannig
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Kateřina Kolková
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | - Eva Táborská
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic;
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, E-08028 Barcelona, Spain;
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy; (S.M.); (G.B.)
| | | | - Petr Táborský
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (P.J.); (P.H.); (K.K.)
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14
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Sanchez-Martin V, Lopez-Pujante C, Soriano-Rodriguez M, Garcia-Salcedo JA. An Updated Focus on Quadruplex Structures as Potential Therapeutic Targets in Cancer. Int J Mol Sci 2020; 21:ijms21238900. [PMID: 33255335 PMCID: PMC7734589 DOI: 10.3390/ijms21238900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this review, we provide a general overview about recent research on the implications of quadruplex structures in cancer, firstly gathering together DNA G-quadruplexes, RNA G-quadruplexes as well as DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Carmen Lopez-Pujante
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
| | - Miguel Soriano-Rodriguez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
| | - Jose A. Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
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15
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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16
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Characterization of interaction between Bcl-2 oncogene promoter I-Motif DNA and flavonoids using electrospray ionization mass spectrometry and pressure-assisted capillary electrophoresis frontal analysis. Talanta 2020; 215:120885. [DOI: 10.1016/j.talanta.2020.120885] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 11/22/2022]
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17
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Dembska A, Świtalska A, Fedoruk-Wyszomirska A, Juskowiak B. Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences. Sci Rep 2020; 10:11006. [PMID: 32620895 PMCID: PMC7335195 DOI: 10.1038/s41598-020-67745-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022] Open
Abstract
The properties of cytosine- and guanine-rich oligonucleotides contributed to employing them as sensing elements in various biosensors. In this paper, we report our current development of fluorescence oligonucleotide probes based on i-motif or G-quadruplex forming oligonucleotides for cellular measurements or bioimaging applications. Additionally, we also focus on the spectral properties of the new fluorescent silver nanoclusters based system (ChONC12-AgNCs) that is able to anchor at the Langmuir monolayer interface, which is mimicking the surface of living cells membrane.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland.
| | - Angelika Świtalska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland.
| | | | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614, Poznan, Poland
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18
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Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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19
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Tsvetkov VB, Varizhuk AM, Lizunova SA, Nikolenko TA, Ivanov IA, Severov VV, Belyaev ES, Shitikov EA, Pozmogova GE, Aralov AV. Phenoxazine-based scaffold for designing G4-interacting agents. Org Biomol Chem 2020; 18:6147-6154. [DOI: 10.1039/d0ob00983k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A phenoxazine-based scaffold with one or two positively charged arms for selectively G4 stabilizing was synthesized and probed.
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Affiliation(s)
- Vladimir B. Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- I.M. Sechenov First Moscow State Medical University
- Moscow 119991
| | - Anna M. Varizhuk
- 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
| | - Sofia A. Lizunova
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- Moscow Institute of Physics and Technology
- Moscow region 141700
| | - Tatiana A. Nikolenko
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- Moscow Institute of Physics and Technology
- Moscow region 141700
| | - Igor A. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- Moscow 117997
- Russia
| | - Vjacheslav V. Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Evgeny S. Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry
- Moscow 119071
- Russia
| | - Egor A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Galina E. Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- Moscow 117997
- Russia
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20
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Trnkova L, Triskova I, Vorlickova M, Kejnovska I, Dvorakova Z, Pivonkova H, Fiala R. Comparative Electrochemical and Spectroscopic Studies of I‐Motif‐forming DNA Nonamers. ELECTROANAL 2019. [DOI: 10.1002/elan.201900323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Libuse Trnkova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Iveta Triskova
- Department of Chemistry, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
| | - Michaela Vorlickova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Iva Kejnovska
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Zuzana Dvorakova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Hana Pivonkova
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135 CZ-612 65 Brno Czech Republic
| | - Radovan Fiala
- CEITEC MU – Central European Institute of Technology, Faculty of ScienceMasaryk University, Kamenice 5 CZ-625 00 Brno Czech Republic
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21
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Belmonte-Reche E, Morales JC. G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool. NAR Genom Bioinform 2019; 2:lqz005. [PMID: 33575559 PMCID: PMC7671307 DOI: 10.1093/nargab/lqz005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/08/2019] [Accepted: 09/10/2019] [Indexed: 11/15/2022] Open
Abstract
We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain.,Life Sciences Department, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330 Braga, Portugal
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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22
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Dvoráková Z, Renciuk D, Kejnovská I, Školáková P, Bednárová K, Sagi J, Vorlícková M. i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions. Nucleic Acids Res 2019; 46:1624-1634. [PMID: 29378012 PMCID: PMC5829569 DOI: 10.1093/nar/gky035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/01/2022] Open
Abstract
i-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic circular dichroism and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymatic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate additional rules for iM formation.
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Affiliation(s)
- Zuzana Dvoráková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| | - Michaela Vorlícková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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23
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Bielecka P, Dembska A, Juskowiak B. Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC. Molecules 2019; 24:molecules24050952. [PMID: 30857134 PMCID: PMC6429216 DOI: 10.3390/molecules24050952] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023] Open
Abstract
The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of tC fluorophore occurred upon lowering the pH from 8.0 to 5.5. Furthermore, we present and discuss fluorescence spectra of systems containing tC-modified i-motifs and complementary G-rich sequences in the ratios 1:1, 1:2, and 1:3 in response to pH changes. The fluorescence anisotropy was proposed for the study of conformational switching of the i-motif structure for tC-probes in the presence and absence of a complementary sequence. The possibility of using of the sensor for monitoring pH changes was demonstrated.
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Affiliation(s)
- Patrycja Bielecka
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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24
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pH-driven conformational switch between non-canonical DNA structures in a C-rich domain of EGFR promoter. Sci Rep 2019; 9:1210. [PMID: 30718769 PMCID: PMC6362134 DOI: 10.1038/s41598-018-37968-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/17/2018] [Indexed: 01/10/2023] Open
Abstract
EGFR is an oncogene that encodes for a trans-membrane tyrosine kinase receptor. Its mis-regulation is associated to several human cancers that, consistently, can be treated by selective tyrosine kinase inhibitors. The proximal promoter of EGFR contains a G-rich domain located at 272 bases upstream the transcription start site. We previously proved it folds into two main interchanging G-quadruplex structures, one of parallel and one of hybrid topology. Here we present the first evidences supporting the ability of the complementary C-rich strand (EGFR-272_C) to assume an intramolecular i-Motif (iM) structure that, according to the experimental conditions (pH, presence of co-solvent and salts), can coexist with a different arrangement we referred to as a hairpin. The herein identified iM efficiently competes with the canonical pairing of the two complementary strands, indicating it as a potential novel target for anticancer therapies. A preliminary screening for potential binders identified some phenanthroline derivatives as able to target EGFR-272_C at multiple binding sites when it is folded into an iM.
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25
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Amato J, Platella C, Iachettini S, Zizza P, Musumeci D, Cosconati S, Pagano A, Novellino E, Biroccio A, Randazzo A, Pagano B, Montesarchio D. Tailoring a lead-like compound targeting multiple G-quadruplex structures. Eur J Med Chem 2018; 163:295-306. [PMID: 30529547 DOI: 10.1016/j.ejmech.2018.11.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/30/2018] [Accepted: 11/23/2018] [Indexed: 11/27/2022]
Abstract
A focused library of analogs of a lead-like G-quadruplex (G4) targeting compound (4), sharing a furobenzoxazine naphthoquinone core and differing for the pendant groups on the N-atom of the oxazine ring, has been here analyzed with the aim of developing more potent and selective ligands. These molecules have been tested vs. topologically different G4s by the G4-CPG assay, an affinity chromatography-based method for screening putative G4 ligands. The obtained results showed that all these compounds were able to bind several G4 structures, both telomeric and extra-telomeric, thus behaving as multi-target ligands, and two of them fully discriminated G4 vs. duplex DNA. Biological assays proved that almost all the compounds produced effective DNA damage, showing marked antiproliferative effects on tumor cells in the low μM range. Combined analysis of the G4-CPG binding assays and biological data led us to focus on compound S4-5, proved to be less cytotoxic than the parent compound 4 on normal cells. An in-depth biophysical characterization of the binding of S4-5 to different G4s showed that the here identified ligand has higher affinity for the G4s and higher ability to discriminate G4 vs. duplex DNA than 4. Molecular docking studies, in agreement with the NMR data, suggest that S4-5 interacts with the accessible grooves of the target G4 structures, giving clues for its increased G4 vs. duplex selectivity.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, 81100, Caserta, Italy
| | - Alessia Pagano
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
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Shi J, Zhou M. Probing the conformational switch of I-motif DNA using tunable resistive pulse sensing. Biochim Biophys Acta Gen Subj 2018; 1862:2564-2569. [PMID: 30048743 DOI: 10.1016/j.bbagen.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/08/2018] [Accepted: 07/11/2018] [Indexed: 02/04/2023]
Abstract
I-motif DNA, which can fold and unfold reversibly in various environments, plays a significant role in DNA nanotechnology and biological functions. Thus, it is of fundamental importance to identify the different conformations of i-motif DNA. Here, we demonstrate that distinct structures of i-motif DNA conjugated to polystyrene spheres can be distinguished through tunable resistive pulse sensing technique. When dispersed in acidic buffer, i-motif DNA coating on polystyrene spheres would fold into quadruplex structure and subsequently induce an apparent increase in the translocation duration time upon passing through a nanopore due to the shielding effect of the surface charge of the nanospheres. However, if the DNA strands don't have conformational changes in acidic buffer, little shift can be observed in the translocation duration time of the DNA functionalized polystyrene spheres. A before-and-after assay was also performed to illustrate the fast speed of i-motif DNA folding using this technique. The successful implementation of tunable resistive pulse sensing to monitor the conformational transition of i-motif DNA provides a potential tool to detect the structural changes of DNA and an alternative approach to study the function of DNA structures.
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Ming Zhou
- State Key Laboratory of Tribology, Tsinghua University, Beijing 100084, People's Republic of China.
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27
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Morgan RK, Molnar MM, Batra H, Summerford B, Wadkins RM, Brooks TA. Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures. J Nucleic Acids 2018; 2018:9281286. [PMID: 29862069 PMCID: PMC5976936 DOI: 10.1155/2018/9281286] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.
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Affiliation(s)
- Rhianna K. Morgan
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Michael M. Molnar
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Harshul Batra
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Bethany Summerford
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Tracy A. Brooks
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
- School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA
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28
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Kaulage MH, Bhattacharya S, Muniyappa K. Structural Characterization of i-Motif Structure in the Human Acetyl-CoA Carboxylase 1 Gene Promoters and Their Role in the Regulation of Gene Expression. Chembiochem 2018; 19:1078-1087. [DOI: 10.1002/cbic.201800021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Mangesh H. Kaulage
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - K. Muniyappa
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
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29
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Non-canonical DNA structures: Comparative quantum mechanical study. Biophys Chem 2018; 235:19-28. [DOI: 10.1016/j.bpc.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 11/21/2022]
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30
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Zaytseva O, Quinn LM. DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond. Bioessays 2018; 40:e1700235. [PMID: 29504137 DOI: 10.1002/bies.201700235] [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: 12/08/2017] [Revised: 01/29/2018] [Indexed: 01/07/2023]
Abstract
Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control.
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Affiliation(s)
- Olga Zaytseva
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
| | - Leonie M Quinn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
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31
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Qin QP, Meng T, Tan MX, Liu YC, Wang SL, Zou BQ, Liang H. Synthesis, characterization and biological evaluation of six highly cytotoxic ruthenium(ii) complexes with 4'-substituted-2,2':6',2''-terpyridine. MEDCHEMCOMM 2018; 9:525-533. [PMID: 30108943 PMCID: PMC6072480 DOI: 10.1039/c7md00532f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/31/2018] [Indexed: 12/23/2022]
Abstract
Herein, six ruthenium(ii) terpyridine complexes, i.e. [RuCl2(4-EtN-Phtpy)(DMSO)] (Ru1), [RuCl2(4-MeO-Phtpy)(DMSO)] (Ru2), [RuCl2(2-MeO-Phtpy)(DMSO)] (Ru3), [RuCl2(3-MeO-Phtpy)(DMSO)] (Ru4), [RuCl2(1-Bip-Phtpy)(DMSO)] (Ru5), and [RuCl2(1-Pyr-Phtpy)(DMSO)] (Ru6) with 4'-(4-diethylaminophenyl)-2,2':6',2''-terpyridine (4-EtN-Phtpy), 4'-(4-methoxyphenyl)-2,2':6',2''-terpyridine (4-MeO-Phtpy), 4'-(2-methoxyphenyl)-2,2':6',2''-terpyridine (2-MeO-Phtpy), 4'-(3-methoxyphenyl)-2,2':6',2''-terpyridine (3-MeO-Phtpy), 4'-(1-biphenylene)-2,2':6',2''-terpyridine (1-Bip-Phtpy), and 4'-(1-pyrene)-2,2':6',2''-terpyridine (1-Pyr-Phtpy), respectively, were synthesized and fully characterized. The MTT assay demonstrates that the in vitro anticancer activity of Ru1 is higher than that of Ru2-Ru6 and more selective for Hep-G2 cells than for normal HL-7702 cells. In addition, various biological assays show that Ru1 and Ru6, especially the Ru1 complex, are telomerase inhibitors targeting c-myc G4 DNA and also cause apoptosis of Hep-G2 cells. With the same Ru center, the in vitro antitumor activity and cellular uptake ability of the 4-EtN-Phtpy and 1-Bip-Phtpy ligands follow the order 4-EtN-Phtpy > 1-Bip-Phtpy.
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Affiliation(s)
- Qi-Pin Qin
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology , College of Chemistry and Food Science , Yulin Normal University , 1303 Jiaoyudong Road , Yulin 537000 , PR China . ; ; ; Tel: +86 775 2623650
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
| | - Ting Meng
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology , College of Chemistry and Food Science , Yulin Normal University , 1303 Jiaoyudong Road , Yulin 537000 , PR China . ; ; ; Tel: +86 775 2623650
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
| | - Ming-Xiong Tan
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology , College of Chemistry and Food Science , Yulin Normal University , 1303 Jiaoyudong Road , Yulin 537000 , PR China . ; ; ; Tel: +86 775 2623650
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
| | - Yan-Cheng Liu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
| | - Shu-Long Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology , College of Chemistry and Food Science , Yulin Normal University , 1303 Jiaoyudong Road , Yulin 537000 , PR China . ; ; ; Tel: +86 775 2623650
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
| | - Bi-Qun Zou
- Department of Chemistry , Guilin Normal College , 21 Xinyi Road , Gulin 541001 , PR China .
| | - Hong Liang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry and Pharmacy , Guangxi Normal University , 15 Yucai Road , Guilin 541004 , PR China
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32
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NM23/NDPK proteins in transcription regulatory functions and chromatin modulation: emerging trends. J Transl Med 2018; 98:175-181. [PMID: 29083410 PMCID: PMC5854247 DOI: 10.1038/labinvest.2017.98] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
NM23/NDPK proteins have been studied for their metastasis suppressor role but the molecular pathways involved in this process are not very vivid. Nucleotide binding and kinase activities of NM23 proteins implicated in anti-metastatic effects have been widely studied. In addition to these, transcriptional regulation adds another arm to the versatility of NM23 proteins that together with the other functions may contribute to better understanding of underlying mechanisms. In this review we discuss emerging reports describing the role of NM23 proteins in gene regulation and chromatin modulation in association with other factors or on their own.
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33
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Abou Assi H, El-Khoury R, González C, Damha MJ. 2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA. Nucleic Acids Res 2017; 45:11535-11546. [PMID: 29036537 PMCID: PMC5714228 DOI: 10.1093/nar/gkx838] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
Human telomeres and promoter regions of genes fulfill a significant role in cellular aging and cancer. These regions comprise of guanine and cytosine-rich repeats, which under certain conditions can fold into G-quadruplex (G4) and i-motif structures, respectively. Herein, we use UV, circular dichroism and NMR spectroscopy to study several human telomeric sequences and demonstrate that G4/i-motif-duplex interconversion kinetics are slowed down dramatically by 2'-β-fluorination and the presence of G4/i-motif-duplex junctions. NMR-monitored kinetic experiments on 1:1 mixtures of native and modified C- and G-rich human telomeric sequences reveal that strand hybridization kinetics are controlled by G4 or i-motif unfolding. Furthermore, we provide NMR evidence for the formation of a hybrid complex containing G4 and i-motif structures proximal to a duplex DNA segment at neutral pH. While the presence of i-motif and G4 folds may be mutually exclusive in promoter genome sequences, our results suggest that they may co-exist transiently as intermediates in telomeric sequences.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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34
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Bhat J, Mondal S, Sengupta P, Chatterjee S. In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of c-MYC Oncogene. ACS OMEGA 2017; 2:4382-4397. [PMID: 30023722 PMCID: PMC6044917 DOI: 10.1021/acsomega.6b00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/20/2017] [Indexed: 06/08/2023]
Abstract
Overexpression of c-MYC oncogene is associated with cancer pathology. Expression of c-MYC is regulated by the G-quadruplex structure formed in the G-rich segment of nuclease hypersensitive element (NHE III1), that is, "Pu27", which is localized in the promoter region. Ligand-induced stabilization of the Pu27 structure has been identified as a novel target for cancer therapeutics. Here, we have explored the library of synthetic compounds against the predefined binding site of Pu27. Three compounds were selected based on the docking analyses; they were further scrutinized using all atom molecular dynamics simulations in an explicit water model. Simulated trajectories were scrutinized for conformational stability and ligand binding free energy estimation; essential dynamic behavior was determined using principal component analysis. One of the molecules, "TPP (1-(3-(4-(1,2,3-thiadiazol-4-yl)phenoxy)-2-hydroxypropyl)-4-carbamoylpiperidinium)", with the best results was considered for further evaluation. The theoretical observations are supported well by biophysical analysis using circular dichroism, isothermal titration calorimetry, and high-resolution NMR spectroscopy indicating association of TPP with Pu27. The in vitro studies were then translated into c-MYC overexpression in the T47D breast cancer cell line. Biological evaluation through the MTT assay, flow cytometric assay, RT-PCR, and reporter luciferase assay suggests that TPP downregulates the expression of c-MYC oncogene by arresting its promoter region. In silico and in vitro observations cumulatively suggest that the novel skeleton of TPP could be a potential anticancer agent by stabilizing the G-quadruplex formed in the Pu27 and consequently downregulating the expression of c-MYC oncogene. Derivation of new molecules on its skeleton may confer anticancer therapeutics for the next generation.
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35
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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36
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Dembska A, Kierzek E, Juskowiak B. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties. Anal Chim Acta 2017; 990:157-167. [PMID: 29029739 DOI: 10.1016/j.aca.2017.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/21/2017] [Accepted: 07/17/2017] [Indexed: 01/04/2023]
Abstract
Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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37
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Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley LH. Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J Am Chem Soc 2017; 139:8522-8536. [PMID: 28570076 PMCID: PMC5978000 DOI: 10.1021/jacs.7b02046] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
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Affiliation(s)
- Christine E. Kaiser
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalie A. Van Ert
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Prashansa Agrawal
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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38
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Sutherland C, Cui Y, Mao H, Hurley LH. A Mechanosensor Mechanism Controls the G-Quadruplex/i-Motif Molecular Switch in the MYC Promoter NHE III1. J Am Chem Soc 2016; 138:14138-14151. [DOI: 10.1021/jacs.6b09196] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caleb Sutherland
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Yunxi Cui
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Laurence H. Hurley
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
- University of Arizona, College of Pharmacy, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East
Helen Street, Tucson, Arizona 85721, United States
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39
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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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40
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Alba JJ, Sadurní A, Gargallo R. Nucleic Acid i-Motif Structures in Analytical Chemistry. Crit Rev Anal Chem 2016; 46:443-54. [DOI: 10.1080/10408347.2016.1143347] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joan Josep Alba
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Anna Sadurní
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain
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41
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Fujii T, Sugimoto N. Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH. Phys Chem Chem Phys 2016; 17:16719-22. [PMID: 26058487 DOI: 10.1039/c5cp02794b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The stability of i-motif structures at neutral pH is of interest due to the potential of these structures to impact gene expression. A systematic investigation of loop sequence and length revealed that certain loop nucleobases stabilize i-motif quadruplexes.
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Affiliation(s)
- Taiga Fujii
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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42
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Bhat J, Chatterjee S. Skeleton selectivity in complexation of chelerythrine and chelerythrine-like natural plant alkaloids with the G-quadruplex formed at the promoter of c-MYC oncogene: in silico exploration. RSC Adv 2016. [DOI: 10.1039/c6ra04671a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chelerythrine binds at the 5′ end and arrests the G-quadruplex formed in the promoter region ofc-MYConcogene thus restrict thec-MYCexpression. Position of methoxy group over the core skeleton of chelerythrine determines the binding pattern of ligand.
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Affiliation(s)
- Jyotsna Bhat
- Department of Biophysics
- Bose Institute
- Kolkata
- India
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43
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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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44
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Lannes L, Halder S, Krishnan Y, Schwalbe H. Tuning the pH Response of i-Motif DNA Oligonucleotides. Chembiochem 2015; 16:1647-56. [PMID: 26032298 DOI: 10.1002/cbic.201500182] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/19/2022]
Abstract
Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.
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Affiliation(s)
- Laurie Lannes
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany)
| | - Saheli Halder
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India)
| | - Yamuna Krishnan
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).,Department of Chemistry, University of Chicago, E305, GCIS, 929 E, 57th Street, Chicago, IL 60637 (USA)
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany).
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45
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Dembska A, Juskowiak B. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:928-933. [PMID: 26123509 DOI: 10.1016/j.saa.2015.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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46
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Cao Y, Qin Y, Bruist M, Gao S, Wang B, Wang H, Guo X. Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC 4Y m) Monitored with Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:994-1003. [PMID: 25862186 DOI: 10.1007/s13361-015-1093-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(X(n)C(4)Y(m)) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (Tm) obtained in solution show that a non-C base residue located at 5' end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3' end. Detection of penta- and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH = 4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
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47
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Kim BG, Evans HM, Dubins DN, Chalikian TV. Effects of Salt on the Stability of a G-Quadruplex from the Human c-MYC Promoter. Biochemistry 2015; 54:3420-30. [DOI: 10.1021/acs.biochem.5b00097] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Byul G. Kim
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Heather M. Evans
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical
Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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48
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Silver (I) as DNA glue: Ag(+)-mediated guanine pairing revealed by removing Watson-Crick constraints. Sci Rep 2015; 5:10163. [PMID: 25973536 PMCID: PMC4431418 DOI: 10.1038/srep10163] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/01/2015] [Indexed: 12/23/2022] Open
Abstract
Metal ion interactions with DNA have far-reaching implications in biochemistry and DNA nanotechnology. Ag+ is uniquely interesting because it binds exclusively to the bases rather than the backbone of DNA, without the toxicity of Hg2+. In contrast to prior studies of Ag+ incorporation into double-stranded DNA, we remove the constraints of Watson-Crick pairing by focusing on homo-base DNA oligomers of the canonical bases. High resolution electro-spray ionization mass spectrometry reveals an unanticipated Ag+-mediated pairing of guanine homo-base strands, with higher stability than canonical guanine-cytosine pairing. By exploring unrestricted binding geometries, quantum chemical calculations find that Ag+ bridges between non-canonical sites on guanine bases. Circular dichroism spectroscopy shows that the Ag+-mediated structuring of guanine homobase strands persists to at least 90 °C under conditions for which canonical guanine-cytosine duplexes melt below 20 °C. These findings are promising for DNA nanotechnology and metal-ion based biomedical science.
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49
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Školáková P, Foldynová-Trantírková S, Bednářová K, Fiala R, Vorlíčková M, Trantírek L. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA. Nucleic Acids Res 2015; 43:4733-45. [PMID: 25855805 PMCID: PMC4482068 DOI: 10.1093/nar/gkv296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10–15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5′-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5′-C-rich and 3′-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska, 31, 375 05 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
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50
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Chen BJ, Wu YL, Tanaka Y, Zhang W. Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics. Int J Biol Sci 2014; 10:1084-96. [PMID: 25332683 PMCID: PMC4202025 DOI: 10.7150/ijbs.10190] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
The nuclear transcription factor c-Myc is a member of the Myc gene family with multiple functions and located on band q24.1 of chromosome 8. The c-Myc gene is activated by chromosomal translocation, rearrangement, and amplification. Its encoded protein transduces intracellular signals to the nucleus, resulting in the regulation of cell proliferation, differentiation, and apoptosis, and has the ability to transform cells and bind chromosomal DNA. c-Myc also plays a critical role in malignant transformation. The abnormal over-expression of c-Myc is frequently observed in some tumors, including carcinomas of the breast, colon, and cervix, as well as small-cell lung cancer, osteosarcomas, glioblastomas, and myeloid leukemias, therefore making it a possible target for anticancer therapy. In this minireview, we summarize unique characteristics of c-Myc and therapeutic strategies against cancer using small molecules targeting the oncogene, and discuss the prospects in the development of agents targeting c-Myc, in particular G-quadruplexes formed in c-Myc promoter and c-Myc/Max dimerization. Such information will be of importance for the research and development of c-Myc-targeted drugs.
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Affiliation(s)
- Bing-Jia Chen
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yan-Ling Wu
- 2. Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, 630 Xincheng Road, Hangzhou, 310051, China. ; 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
| | - Yoshimasa Tanaka
- 3. Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Wen Zhang
- 1. Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, China
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