151
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Abdelhamid MAS, Gates AJ, Waller ZAE. Destabilization of i-Motif DNA at Neutral pH by G-Quadruplex Ligands. Biochemistry 2018; 58:245-249. [PMID: 30350580 DOI: 10.1021/acs.biochem.8b00968] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Numerous studies have been published stressing the importance of finding ligands that can bind specifically to DNA secondary structures. Several have identified ligands that are presented as having specific binding to the G-quadruplex; however, these were not originally tested on the complementary i-motif structure. The i-motif was overlooked and presumed to be irrelevant due to the belief that the hemiprotonated (cytosine+-cytosine) base pair at the core of the structure required acidic pH. The pathophysiological relevance of i-motifs has since been documented, as well as the discovery of several genomic sequences, which can form i-motif at neutral pH. Using different biophysical methodologies, we provide experimental evidence to show that widely used G-quadruplex ligands interact with i-motif structures at neutral pH, generally leading to their destabilization. Crucially, this has implications both for the search for quadruplex binding compounds as well as for the effects of compounds reported to have G-quadruplex specificity without examining their effects on i-motif.
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Affiliation(s)
- Mahmoud A S Abdelhamid
- School of Pharmacy , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom.,Centre for Molecular and Structural Biochemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom.,School of Biological Sciences , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | - Zoë A E Waller
- School of Pharmacy , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom.,Centre for Molecular and Structural Biochemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
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152
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Rogers RA, Fleming AM, Burrows CJ. Rapid Screen of Potential i-Motif Forming Sequences in DNA Repair Gene Promoters. ACS OMEGA 2018; 3:9630-9635. [PMID: 30198001 PMCID: PMC6120732 DOI: 10.1021/acsomega.8b01551] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
We have studied the in vitro stability of 25 potential i-motif-forming DNA sequences found within the promoter regions of 18 different human DNA repair genes. Three widely available methods of characterization were used to rapidly assess i-motif folding and stability and comprise a simple screen for preliminary identification of physiologically relevant i-motif forming sequences. Four highly pH-stable candidate sequences were identified exhibiting pH transitions (pH at which 50% of the oligodeoxynucleotides in solution are folded) at or above pH 6.6, thermal melting temperatures above 37 °C and isothermal UV difference spectra characteristic of 2'-deoxycytidine imino-nitrogen protonation. These newly identified i-motif forming sequences could represent novel targets for understanding and modulating human DNA repair gene expression.
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153
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Sholokh M, Sharma R, Grytsyk N, Zaghzi L, Postupalenko VY, Dziuba D, Barthes NPF, Michel BY, Boudier C, Zaporozhets OA, Tor Y, Burger A, Mély Y. Environmentally Sensitive Fluorescent Nucleoside Analogues for Surveying Dynamic Interconversions of Nucleic Acid Structures. Chemistry 2018; 24:13850-13861. [PMID: 29989220 DOI: 10.1002/chem.201802297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 11/12/2022]
Abstract
Nucleic acids are characterized by a variety of dynamically interconverting structures that play a major role in transcriptional and translational regulation as well as recombination and repair. To monitor these interconversions, Förster resonance energy transfer (FRET)-based techniques can be used, but require two fluorophores that are typically large and can alter the DNA/RNA structure and protein binding. Additionally, events that do not alter the donor/acceptor distance and/or angular relationship are frequently left undetected. A more benign approach relies on fluorescent nucleobases that can substitute their native counterparts with minimal perturbation, such as the recently developed 2-thienyl-3-hydroxychromone (3HCnt) and thienoguanosine (th G). To demonstrate the potency of 3HCnt and th G in deciphering interconversion mechanisms, we used the conversion of the (-)DNA copy of the HIV-1 primer binding site (-)PBS stem-loop into (+)/(-)PBS duplex, as a model system. When incorporated into the (-)PBS loop, the two probes were found to be highly sensitive to the individual steps both in the absence and the presence of a nucleic acid chaperone, providing the first complete mechanistic description of this critical process in HIV-1 replication. The combination of the two distinct probes appears to be instrumental for characterizing structural transitions of nucleic acids under various stimuli.
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Affiliation(s)
- Marianna Sholokh
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France.,Department of Chemistry, Kyiv National Taras Shevchenko University, 60 Volodymyrska street, 01033, Kyiv, Ukraine
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Natalia Grytsyk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Lyes Zaghzi
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Viktoriia Y Postupalenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Dmytro Dziuba
- Institut de Chimie de Nice, UMR 7272 CNRS, Université Côte d'Azur, Parc Valrose, 06108, Nice, France
| | - Nicolas P F Barthes
- Institut de Chimie de Nice, UMR 7272 CNRS, Université Côte d'Azur, Parc Valrose, 06108, Nice, France
| | - Benoît Y Michel
- Institut de Chimie de Nice, UMR 7272 CNRS, Université Côte d'Azur, Parc Valrose, 06108, Nice, France
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Olga A Zaporozhets
- Department of Chemistry, Kyiv National Taras Shevchenko University, 60 Volodymyrska street, 01033, Kyiv, Ukraine
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272 CNRS, Université Côte d'Azur, Parc Valrose, 06108, Nice, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France
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154
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Pagano A, Iaccarino N, Abdelhamid MAS, Brancaccio D, Garzarella EU, Di Porzio A, Novellino E, Waller ZAE, Pagano B, Amato J, Randazzo A. Common G-Quadruplex Binding Agents Found to Interact With i-Motif-Forming DNA: Unexpected Multi-Target-Directed Compounds. Front Chem 2018; 6:281. [PMID: 30137743 PMCID: PMC6066642 DOI: 10.3389/fchem.2018.00281] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/22/2018] [Indexed: 11/26/2022] Open
Abstract
G-quadruplex (G4) and i-motif (iM) are four-stranded non-canonical nucleic acid structural arrangements. Recent evidences suggest that these DNA structures exist in living cells and could be involved in several cancer-related processes, thus representing an attractive target for anticancer drug discovery. Efforts toward the development of G4 targeting compounds have led to a number of effective bioactive ligands. Herein, employing several biophysical methodologies, we studied the ability of some well-known G4 ligands to interact with iM-forming DNA. The data showed that the investigated compounds are actually able to interact with both DNA in vitro, thus acting de facto as multi-target-directed agents. Interestingly, while all the compounds stabilize the G4, some of them significantly reduce the stability of the iM. The present study highlights the importance, when studying G4-targeting compounds, of evaluating also their behavior toward the i-motif counterpart.
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Affiliation(s)
- Alessia Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Mahmoud A S Abdelhamid
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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155
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Luchinat E, Banci L. In-Cell NMR in Human Cells: Direct Protein Expression Allows Structural Studies of Protein Folding and Maturation. Acc Chem Res 2018; 51:1550-1557. [PMID: 29869502 DOI: 10.1021/acs.accounts.8b00147] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cellular structural biology methods are needed to characterize biological processes at atomic resolution in the physiological environment of the cell. Toward this goal, solution in-cell NMR is a powerful approach because it provides structural and dynamic data on macromolecules inside living cells. Several approaches have been developed for in-cell NMR in cultured human cells, which are needed to study processes related to human diseases that rely on the delivery of exogenous macromolecules to the cells. Such strategies, however, may not be applicable to proteins that are sensitive to the external environment or prone to aggregate and can introduce artifacts during protein purification or delivery. As a complementary approach, direct protein expression for in-cell NMR in human cells was developed. This strategy is especially useful when studying processes like protein folding, maturation, and post-translational modification, starting right after protein synthesis. Compared with the protein expression techniques in mammalian cells commonly used in cellular biology, the low sensitivity of NMR requires higher protein levels. Among the cell lines used for high-yield protein expression, the HEK293T cell line was chosen, as it can be efficiently transfected with a cost-effective reagent. A vector originally designed for secreted proteins allows high-level cytosolic protein expression. For isotopic labeling, commercially available or homemade labeled media are employed. Uniform or amino acid type-selective labeling strategies are possible. Protein expression can be targeted to specific organelles (e.g., mitochondria), allowing for in organello NMR applications. A variant of the approach was developed that allows the sequential expression of two or more proteins, with only one selectively labeled. Protein expression in HEK293T cells was applied to recapitulate the maturation steps of intracellular superoxide dismutase 1 (SOD1) and to study the effect of mutations linked to familial amyotrophic lateral sclerosis (fALS) by in-cell NMR. Intracellular wild-type SOD1 spontaneously binds zinc, while it needs the copper chaperone for superoxide dismutase (CCS) for copper delivery and disulfide bond formation. Some fALS-linked mutations impair zinc binding and cause SOD1 to irreversibly unfold, likely forming the precursor of cytotoxic aggregates. The SOD-like domain of CCS acts as a molecular chaperone toward mutant SOD1, stabilizing its folding and allowing zinc binding and correct maturation. Changes in protein redox state distributions can also be investigated by in-cell NMR. Mitochondrial proteins require the redox-regulating partners glutaredoxin 1 (Grx1) and thioredoxin (Trx) to remain in the reduced, import-competent state in the cytosol, whereas SOD1 requires CCS for disulfide bond formation. In both cases, the proteins do not equilibrate with the cytosolic redox pool. Cysteine oxidation in response to oxidative stress can also be monitored. In the near future, in-cell NMR in human cells will likely benefit from technological advancements in NMR hardware, the development of bioreactor systems for increased sample lifetime, the application of paramagnetic NMR to obtain structural restraints, and advanced tools for genome engineering and should be increasingly integrated with advanced cellular imaging techniques.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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156
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Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S, Trantirek L. Advances in the cellular structural biology of nucleic acids. FEBS Lett 2018; 592:1997-2011. [PMID: 29679394 DOI: 10.1002/1873-3468.13054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023]
Abstract
Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.
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Affiliation(s)
- Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Silvie Foldynova-Trantirkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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157
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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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158
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Dzatko S, Krafcikova M, Hänsel‐Hertsch R, Fessl T, Fiala R, Loja T, Krafcik D, Mergny J, Foldynova‐Trantirkova S, Trantirek L. Evaluation of the Stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells. Angew Chem Int Ed Engl 2018; 57:2165-2169. [PMID: 29266664 PMCID: PMC5820743 DOI: 10.1002/anie.201712284] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 11/21/2022]
Abstract
C-rich DNA has the capacity to form a tetra-stranded structure known as an i-motif. The i-motifs within genomic DNA have been proposed to contribute to the regulation of DNA transcription. However, direct experimental evidence for the existence of these structures in vivo has been missing. Whether i-motif structures form in complex environment of living cells is not currently known. Herein, using state-of-the-art in-cell NMR spectroscopy, we evaluate the stabilities of i-motif structures in the complex cellular environment. We show that i-motifs formed from naturally occurring C-rich sequences in the human genome are stable and persist in the nuclei of living human cells. Our data show that i-motif stabilities in vivo are generally distinct from those in vitro. Our results are the first to interlink the stability of DNA i-motifs in vitro with their stability in vivo and provide essential information for the design and development of i-motif-based DNA biosensors for intracellular applications.
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Affiliation(s)
- Simon Dzatko
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Michaela Krafcikova
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Robert Hänsel‐Hertsch
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeLi Ka Shing CentreCambridgeCB2 0REUK
| | - Tomas Fessl
- Faculty of ScienceUniversity of South Bohemia370 05Ceske BudejoviceCzech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Tomas Loja
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Daniel Krafcik
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
| | - Jean‐Louis Mergny
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320ARNA LaboratoryIECBPessacFrance
- Institute of BiophysicsAcademy of Sciences of the Czech Republic612 65BrnoCzech Republic
| | - Silvie Foldynova‐Trantirkova
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
- Institute of BiophysicsAcademy of Sciences of the Czech Republic612 65BrnoCzech Republic
| | - Lukas Trantirek
- CEITEC-Central European Institute of TechnologyMasaryk UniversityBrno625 00Czech Republic
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