1
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Kristoffersen E, Coletta A, Lund L, Schiøtt B, Birkedal V. Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Res 2023; 51:1571-1582. [PMID: 36715345 PMCID: PMC9976873 DOI: 10.1093/nar/gkad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Noncanonical DNA structures, termed G-quadruplexes, are present in human genomic DNA and are important elements in many DNA metabolic processes. Multiple sites in the human genome have G-rich DNA stretches able to support formation of several consecutive G-quadruplexes. One of those sites is the telomeric overhang region that has multiple repeats of TTAGGG and is tightly associated with both cancer and aging. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions using single-molecule FRET spectroscopy, circular dichroism, thermal melting and molecular dynamics simulations. Our observations show coexistence of partially and fully folded DNA, the latter consisting of consecutive G-quadruplexes. Following the folding process over hours in sodium-containing buffers revealed fast G-quadruplex folding but slow establishment of thermodynamic equilibrium. We find that full consecutive G-quadruplex formation is inhibited by the many DNA structures randomly nucleating on the DNA, some of which are off-path conformations that need to unfold to allow full folding. Our study allows describing consecutive G-quadruplex formation in both nonequilibrium and equilibrium conditions by a unified picture, where, due to the many possible DNA conformations, full folding with consecutive G-quadruplexes as beads on a string is not necessarily achieved.
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Affiliation(s)
- Emil Laust Kristoffersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Andrea Coletta
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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2
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Laouer K, Schmid M, Wien F, Changenet P, Hache F. Folding Dynamics of DNA G-Quadruplexes Probed by Millisecond Temperature Jump Circular Dichroism. J Phys Chem B 2021; 125:8088-8098. [PMID: 34279936 DOI: 10.1021/acs.jpcb.1c01993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplexes play important roles in cellular regulatory functions, but despite significant experimental and theoretical efforts, their folding mechanisms remain poorly understood. In this context, we developed a T-jump experiment to access the thermal denaturation and renaturation dynamics of short intramolecular G-quadruplexes in vitro, on the time scale of a few hundred milliseconds. With this new setup, we compared the thermal denaturation and renaturation kinetics of three antiparallel topologies made of the human telomeric sequences d[(5'-GGG(TTAGGG)3-3']/Na+ and d[5'-AGGG(TTAGGG)3-3']/Na+ and the thrombin-binding aptamer sequence d[5'-GGTTGGTGTGGTTGG-3']/K+, with those of the parallel topology made of the human CEB25 minisatellite d[5'-AAGGGTGGGTGTAAGTGTGGGTGGGT-3']/Na+. In all cases, exponential kinetics of the order of several hundred milliseconds were observed. Measurements performed for different initial temperatures revealed distinct denaturation and renaturation dynamics, ruling out a simple two-state mechanism. The parallel topology, in which all guanines adopt an anti conformation, displays much slower dynamics than antiparallel topologies associated with very low activation barriers. This behavior can be explained by the constrained conformational space due to the presence of the single-base propeller loops that likely hinders the movement of the coiled DNA strand and reduces the contribution of the entropy during the renaturation process at high temperatures.
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Affiliation(s)
- K Laouer
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - M Schmid
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Wien
- L'orme des merisiers, Synchrotron SOLEIL, 91192 Gif sur Yvette, France
| | - P Changenet
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
| | - F Hache
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS -INSERM, Institut Polytechnique de Paris, 91128 Cedex Palaiseau, France
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3
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Harkness RW, Hennecker C, Grün JT, Blümler A, Heckel A, Schwalbe H, Mittermaier AK. Parallel reaction pathways accelerate folding of a guanine quadruplex. Nucleic Acids Res 2021; 49:1247-1262. [PMID: 33469659 PMCID: PMC7897495 DOI: 10.1093/nar/gkaa1286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/21/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded, guanine-rich nucleic acid structures that can influence a variety of biological processes such as the transcription and translation of genes and DNA replication. In many cases, a single G4-forming nucleic acid sequence can adopt multiple different folded conformations that interconvert on biologically relevant timescales, entropically stabilizing the folded state. The coexistence of different folded conformations also suggests that there are multiple pathways leading from the unfolded to the folded state ensembles, potentially modulating the folding rate and biological activity. We have developed an experimental method for quantifying the contributions of individual pathways to the folding of conformationally heterogeneous G4s that is based on mutagenesis, thermal hysteresis kinetic experiments and global analysis, and validated our results using photocaged kinetic NMR experiments. We studied the regulatory Pu22 G4 from the c-myc oncogene promoter, which adopts at least four distinct folded isomers. We found that the presence of four parallel pathways leads to a 2.5-fold acceleration in folding; that is, the effective folding rate from the unfolded to folded ensembles is 2.5 times as large as the rate constant for the fastest individual pathway. Since many G4 sequences can adopt many more than four isomers, folding accelerations of more than an order of magnitude are possible via this mechanism.
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Affiliation(s)
- Robert W Harkness
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
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4
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Gao C, Liu Z, Hou H, Ding J, Chen X, Xie C, Song Z, Hu Z, Feng M, Mohamed HI, Xu S, Parkinson GN, Haider S, Wei D. BMPQ-1 binds selectively to (3+1) hybrid topologies in human telomeric G-quadruplex multimers. Nucleic Acids Res 2020; 48:11259-11269. [PMID: 33080032 PMCID: PMC7672424 DOI: 10.1093/nar/gkaa870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
A single G-quadruplex forming sequence from the human telomere can adopt six distinct topologies that are inter-convertible under physiological conditions. This presents challenges to design ligands that show selectivity and specificity towards a particular conformation. Additional complexity is introduced in differentiating multimeric G-quadruplexes over monomeric species, which would be able to form in the single-stranded 3′ ends of telomeres. A few ligands have been reported that bind to dimeric quadruplexes, but their preclinical pharmacological evaluation is limited. Using multidisciplinary approaches, we identified a novel quinoline core ligand, BMPQ-1, which bound to human telomeric G-quadruplex multimers over monomeric G-quadruplexes with high selectivity, and induced the formation of G-quadruplex DNA along with the related DNA damage response at the telomere. BMPQ-1 reduced tumor cell proliferation with an IC50 of ∼1.0 μM and decreased tumor growth rate in mouse by half. Biophysical analysis using smFRET identified a mixture of multiple conformations coexisting for dimeric G-quadruplexes in solution. Here, we showed that the titration of BMPQ-1 shifted the conformational ensemble of multimeric G-quadruplexes towards (3+1) hybrid-2 topology, which became more pronounced as further G-quadruplex units are added.
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Affiliation(s)
- Chao Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Hou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieqin Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqian Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hany I Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Shengzhen Xu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China
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5
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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6
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Du Y, Pan J, Choi JH. A review on optical imaging of DNA nanostructures and dynamic processes. Methods Appl Fluoresc 2019; 7:012002. [PMID: 30523978 DOI: 10.1088/2050-6120/aaed11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
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Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
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7
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Knop JM, Patra S, Harish B, Royer CA, Winter R. The Deep Sea Osmolyte Trimethylamine N-Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G-Quadruplex from Urea and Pressure Stress. Chemistry 2018; 24:14346-14351. [PMID: 29993151 DOI: 10.1002/chem.201802444] [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: 05/16/2018] [Revised: 07/04/2018] [Indexed: 11/10/2022]
Abstract
Organisms are thriving in the deep sea at pressures up to the 1 kbar level, which imposes severe stress on the conformational dynamics and stability of their biomolecules. The impact of osmolytes and macromolecular crowders, mimicking intracellular conditions, on the effect of pressure on the conformational dynamics of a human telomeric G-quadruplex (G4) DNA is explored in this study employing single-molecule Förster resonance energy transfer (FRET) experiments. In neat buffer, pressurization favors the parallel/hybrid state of the G4-DNA over the antiparallel conformation at ≈400 bar, finally leading to unfolding beyond 1000 bar. High-pressure NMR data support these findings. The folded topological conformers have different solvent accessible surface areas and cavity volumes, leading to different volumetric properties and hence pressure stabilities. The deep-sea osmolyte trimethylamine N-oxide (TMAO) and macromolecular crowding agents are able to effectively rescue the G4-DNA from unfolding in the whole pressure range encountered on Earth.
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Affiliation(s)
- Jim-Marcel Knop
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn Str. 4a, 44227, Dortmund, Germany
| | - Satyajit Patra
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn Str. 4a, 44227, Dortmund, Germany
| | - Balasubramanian Harish
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, 12180, NY, USA
| | - Catherine A Royer
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, 12180, NY, USA
| | - Roland Winter
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn Str. 4a, 44227, Dortmund, Germany
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8
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Tucker BA, Hudson JS, Ding L, Lewis E, Sheardy RD, Kharlampieva E, Graves D. Stability of the Na + Form of the Human Telomeric G-Quadruplex: Role of Adenines in Stabilizing G-Quadruplex Structure. ACS OMEGA 2018; 3:844-855. [PMID: 30023791 PMCID: PMC6045420 DOI: 10.1021/acsomega.7b01649] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/09/2018] [Indexed: 06/08/2023]
Abstract
G-quadruplexes are higher order DNA structures that play significant roles in gene transcription and telomeric maintenance. The formation and stability of the G-quadruplex structures are under thermodynamic control and may be of biological significance for regulatory function of cellular processes. Here, we report the structural influence and energetic contributions of the adenine bases in the loop sequences that flank G-repeats in human telomeric DNA sequence. Spectroscopic and calorimetric techniques are used to measure the thermal stability and thermodynamic contributions to the stability of human telomeric G-quadruplexes that have been designed with systematic changes of A to T throughout the telomeric sequence. These studies demonstrate that the thermal stability of the G-quadruplex structure is directly related to the number and position of the adenines that are present in the telomeric sequence. The melting temperature (Tm) was reduced from 59 °C for the wild-type sequence to 47 °C for the sequence where all four adenines were replaced with thymines (0123TTT). Furthermore, the enthalpy required for transitioning from the folded to unfolded G-quadruplex structure was reduced by 15 kcal/mol when the adenines were replaced with thymines (37 kcal/mol for the wild-type telomeric sequence reduced to 22 kcal/mol for the sequence where all four adenines were replaced with thymines (0123TTT)). The circular dichroism melting studies for G-quadruplex sequences having a single A to T change showed significantly sloping pretransition baselines and their differential scanning calorimetry (DSC) thermograms revealed biphasic melting profiles. In contrast, the deoxyoligonucleotides having sequences with two or more A to T changes did not exhibit sloping baselines or biphasic DSC thermograms. We attribute the biphasic unfolding profile and reduction in the enthalpy of unfolding to the energetic contributions of adenine hydrogen bonding within the loops as well as the adenine stacking to the G-tetrads of the G-quadruplex structure.
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Affiliation(s)
- Brenna A. Tucker
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Jason S. Hudson
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Lei Ding
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - Edwin Lewis
- Department
of Chemistry, Mississippi State University, Mississippi, Mississippi
State 39762, United
States
| | - Richard D. Sheardy
- Department
of Chemistry & Biochemistry, Texas Women’s
University, Denton, Texas 782042, United States
| | - Eugenia Kharlampieva
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
| | - David Graves
- Department
of Chemistry, Department of Biochemistry and Molecular Genetics, and Comprehensive
Cancer Center, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United States
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9
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Maleki P, Budhathoki JB, Roy WA, Balci H. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 2017; 292:483-498. [PMID: 28150040 DOI: 10.1007/s00438-017-1288-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/05/2017] [Indexed: 11/26/2022]
Abstract
In this article, we summarize the knowledge and best practices learned from bulk and single-molecule measurements to address some of the frequently experienced difficulties in single-molecule Förster resonance energy transfer (smFRET) measurements on G-quadruplex (GQ) structures. The number of studies that use smFRET to investigate the structure, function, dynamics, and interactions of GQ structures has grown significantly in the last few years, with new applications already in sight. However, a number of challenges need to be overcome before reliable and reproducible smFRET data can be obtained in measurements that include GQ. The annealing and storage conditions, the location of fluorophores on the DNA construct, and the ionic conditions of the experiment are some of the factors that are of critical importance for the outcome of measurements, and many of these manifest themselves in unique ways in smFRET assays. By reviewing these aspects and providing a summary of best practices, we aim to provide a practical guide that will help in successfully designing and performing smFRET studies on GQ structures.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | | | - William A Roy
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA.
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10
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Debnath M, Ghosh S, Panda D, Bessi I, Schwalbe H, Bhattacharyya K, Dash J. Small molecule regulated dynamic structural changes of human G-quadruplexes. Chem Sci 2016; 7:3279-3285. [PMID: 29997820 PMCID: PMC6006475 DOI: 10.1039/c6sc00057f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/02/2016] [Indexed: 01/26/2023] Open
Abstract
A carbazole derivative (BTC) regulates the dynamics of unstructured human c-MYC and h-TELO sequences by folding them into compact quadruplex structures.
The changes in structure and dynamics of oncogenic (c-MYC) and telomeric (h-TELO) G-rich DNA sequences due to the binding of a novel carbazole derivative (BTC) are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K+-folded G-quadruplexes. The results demonstrate that K+ free c-MYC and h-TELO exist as unfolded and partially folded conformations. The binding of BTC shifts the equilibria of both investigated DNA sequences towards the folded G-quadruplex structure, increases the diffusion coefficients and induces faster end-to-end contact formation. BTC recognizes a minor conformation of the c-MYC quadruplex and the two-tetrad basket conformations of the h-TELO quadruplex.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Deepanjan Panda
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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12
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Chung HS, Louis JM, Gopich IV. Analysis of Fluorescence Lifetime and Energy Transfer Efficiency in Single-Molecule Photon Trajectories of Fast-Folding Proteins. J Phys Chem B 2016; 120:680-99. [PMID: 26812046 DOI: 10.1021/acs.jpcb.5b11351] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In single-molecule Förster resonance energy transfer (FRET) spectroscopy, the dynamics of molecular processes are usually determined by analyzing the fluorescence intensity of donor and acceptor dyes. Since FRET efficiency is related to fluorescence lifetimes, additional information can be extracted by analyzing fluorescence intensity and lifetime together. For fast processes where individual states are not well separated in a trajectory, it is not easy to obtain the lifetime information. Here, we present analysis methods to utilize fluorescence lifetime information from single-molecule FRET experiments, and apply these methods to three fast-folding, two-state proteins. By constructing 2D FRET efficiency-lifetime histograms, the correlation can be visualized between the FRET efficiency and fluorescence lifetimes in the presence of the submicrosecond to millisecond dynamics. We extend the previously developed method for analyzing delay times of donor photons to include acceptor delay times. To determine the kinetics and lifetime parameters accurately, we used a maximum likelihood method. We found that acceptor blinking can lead to inaccurate parameters in the donor delay time analysis. This problem can be solved by incorporating acceptor blinking into a model. While the analysis of acceptor delay times is not affected by acceptor blinking, it is more sensitive to the shape of the delay time distribution resulting from a broad conformational distribution in the unfolded state.
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Affiliation(s)
- Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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13
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Noer SL, Preus S, Gudnason D, Aznauryan M, Mergny JL, Birkedal V. Folding dynamics and conformational heterogeneity of human telomeric G-quadruplex structures in Na+ solutions by single molecule FRET microscopy. Nucleic Acids Res 2015; 44:464-71. [PMID: 26615192 PMCID: PMC4705662 DOI: 10.1093/nar/gkv1320] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/11/2015] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex structures can occur throughout the genome, including at telomeres. They are involved in cellular regulation and are potential drug targets. Human telomeric G-quadruplex structures can fold into a number of different conformations and show large conformational diversity. To elucidate the different G-quadruplex conformations and their dynamics, we investigated telomeric G-quadruplex folding using single molecule FRET microscopy in conditions where it was previously believed to yield low structural heterogeneity. We observed four FRET states in Na+ buffers: an unfolded state and three G-quadruplex related states that can interconvert between each other. Several of these states were almost equally populated at low to medium salt concentrations. These observations appear surprising as previous studies reported primarily one G-quadruplex conformation in Na+ buffers. Our results permit, through the analysis of the dynamics of the different observed states, the identification of a more stable G-quadruplex conformation and two transient G-quadruplex states. Importantly these results offer a unique view into G-quadruplex topological heterogeneity and conformational dynamics.
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Affiliation(s)
- Sofie L Noer
- Interdisciplinary Nanoscience center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Søren Preus
- Interdisciplinary Nanoscience center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Daniel Gudnason
- Interdisciplinary Nanoscience center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Mikayel Aznauryan
- Interdisciplinary Nanoscience center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Jean-Louis Mergny
- University of Bordeaux, ARNA Lab, IECB, 33076 Bordeaux, France INSERM, U1212, IECB, 33607 Pessac, France
| | - Victoria Birkedal
- Interdisciplinary Nanoscience center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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14
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Blanchard DJM, Cservenyi TZ, Manderville RA. Dual fluorescent deoxyguanosine mimics for FRET detection of G-quadruplex folding. Chem Commun (Camb) 2015; 51:16829-31. [DOI: 10.1039/c5cc07154b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Replacement of deoxyguanosine (dG) nucleobases within G-tetrads of G-quadruplex folding oligonucleotides with donor (D)/acceptor (A) fluorescent 8aryldG residues provides diagnostic FRET signalling for G-quadruplex detection.
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Affiliation(s)
| | - Thomas Z. Cservenyi
- Departments of Chemistry & Toxicology
- University of Guelph
- Guelph
- Canada N1G 2w1
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15
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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16
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Sun L, Jin H, Zhao X, Liu Z, Guan Y, Yang Z, Zhang L, Zhang L. Unfolding and conformational variations of thrombin-binding DNA aptamers: synthesis, circular dichroism and molecular dynamics simulations. ChemMedChem 2014; 9:993-1001. [PMID: 24715713 DOI: 10.1002/cmdc.201300564] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/14/2014] [Indexed: 01/08/2023]
Abstract
Thrombin-binding DNA aptamer (TBA), with a consensus 15-base sequence: d(GGTTGGTGTGGTTGG), can fold into an antiparallel unimolecular G-quadruplex structure that is necessary for its interaction with thrombin. For the first time, using steered molecular dynamics (SMD) simulations, we have successfully simulated the unfolding process of native TBA G-quadruplex. The unfolding pathway proposed is in agreement with previously reported experimental NMR data. Moreover, the critical intermediate structure in the unfolding pathway, predicted by the NMR results, was identified. The structural characteristics of several TBA oligonucleotides modified with locked nucleoside (LNA) or 2'-O-methyl-nucleoside (MNA) at different positions and number were also investigated by CD spectroscopy. An oligonucleotide substituted with either LNA or MNA at position 2 folds into a native-like G-quadruplex, while doubly substituted derivatives of TBA where LNA or MNA is incorporated at positions 11 and 14 are no longer able to form a G-quadruplex. Starting from the same initial intermediate structure, we successfully overcame sampling limitations, and simulated the large conformational variations in structures of native TBA and modified TBAs by classic MD. Analysis of the models showed that inversion of the glycosyl orientation at position 14 contributes significantly to the disruption of G-quadruplex formation in both of the di-substituted modified TBA systems. Our calculations provide a simple and reliable theoretical model that can be used to investigate and predict the effects of the modifications of an oligonucleotide on the resultant G-quadruplex structure. In addition, the computational protocol described can also be applied for other G-quadruplex systems.
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Affiliation(s)
- Lidan Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191 (P. R. China)
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17
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Lin J, Kaur P, Countryman P, Opresko PL, Wang H. Unraveling secrets of telomeres: one molecule at a time. DNA Repair (Amst) 2014; 20:142-153. [PMID: 24569170 DOI: 10.1016/j.dnarep.2014.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 01/23/2023]
Abstract
Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins.
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Affiliation(s)
- Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA.
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18
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Elahi MY, Bathaie S, Mousavi M, Hoshyar R, Ghasemi S. A new DNA-nanobiosensor based on G-quadruplex immobilized on carbon nanotubes modified glassy carbon electrode. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Zhao XQ, Wu J, Liang JH, Yan JW, Zhu Z, Yang CJ, Mao BW. Single-molecule force spectroscopic studies on intra- and intermolecular interactions of G-quadruplex aptamer with target Shp2 protein. J Phys Chem B 2012; 116:11397-404. [PMID: 22924632 DOI: 10.1021/jp303518b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With widespread applications in biosensors, diagnostics, and therapeutics, much investigation has been made in the structure of the G-quadruplexes and mechanism of their interactions with protein targets. However, in view of AFM based single-molecule force spectroscopic (SMFS) studies of G-quadruplex systems, only bimolecular approaches have been employed. In this article, we present an improved dual-labeling approach for surface immobilization of G-quadruplex DNA apatmers for investigation of intramolecular interaction from an integral unimolecular G-quadruplex system. The melting force of HJ24 G-quadruplex aptamer in the presence of K(+) has been successfully measured. It has been found that dynamic equilibrium exists between unfolding and folding structures of the HJ24 aptamer even in pure water. We also investigated the interactions between the HJ24 aptamer and its target protein (Shp2) under the same solution condition. The HJ24/Shp2 unbinding force in the absence of K(+), 42.0 pN, is about 50% smaller than that in the presence of K(+), 61.7 pN. The great reduction in force in the absence of K(+) suggests that the stability of G-quadruplex secondary structure is important for a stable HJ24/Shp2 binding. The methodology developed and demonstrated in this work is applicable for studying the stability of secondary structures of other unimolecular G-quadruplex aptamers and their interactions with target proteins.
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Affiliation(s)
- Xue-Qin Zhao
- State Key Laboratory of Physical Chemistry of the Solid Surfaces, Department of Chemistry, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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20
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Buscaglia R, Jameson DM, Chaires JB. G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots. Nucleic Acids Res 2012; 40:4203-15. [PMID: 22241767 PMCID: PMC3351194 DOI: 10.1093/nar/gkr1286] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/17/2022] Open
Abstract
The use of time-resolved fluorescence measurements in studies of telomeric G-quadruplex folding and stability has been hampered by the complexity of fluorescence lifetime distributions in solution. The application of phasor diagrams to the analysis of time-resolved fluorescence measurements, collected from either frequency-domain or time-domain instrumentation, allows for rapid characterization of complex lifetime distributions. Phasor diagrams are model-free graphical representations of transformed time-resolved fluorescence results. Simplification of complex fluorescent decays by phasor diagrams is demonstrated here using a 2-aminopurine substituted telomeric G-quadruplex sequence. The application of phasor diagrams to complex systems is discussed with comparisons to traditional non-linear regression model fitting. Phasor diagrams allow for the folding and stability of the telomeric G-quadruplex to be monitored in the presence of either sodium or potassium. Fluorescence lifetime measurements revealed multiple transitions upon folding of the telomeric G-quadruplex through the addition of potassium. Enzymatic digestion of the telomeric G-quadruplex structure, fluorescence quenching and Förster resonance energy transfer were also monitored through phasor diagrams. This work demonstrates the sensitivity of time-resolved methods for monitoring changes to the telomeric G-quadruplex and outlines the phasor diagram approach for analysis of complex time-resolved results that can be extended to other G-quadruplex and nucleic acid systems.
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Affiliation(s)
- Robert Buscaglia
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - David M. Jameson
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock Street, Louisville, KY 40202 and Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
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21
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Yuan G, Zhang Q, Zhou J, Li H. Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation. MASS SPECTROMETRY REVIEWS 2011; 30:1121-1142. [PMID: 21520218 DOI: 10.1002/mas.20315] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 06/09/2010] [Accepted: 06/09/2010] [Indexed: 05/30/2023]
Abstract
G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.
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Affiliation(s)
- Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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22
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Zhou W, Brand NJ, Ying L. G-quadruplexes-novel mediators of gene function. J Cardiovasc Transl Res 2011; 4:256-70. [PMID: 21302011 DOI: 10.1007/s12265-011-9258-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 01/24/2011] [Indexed: 11/30/2022]
Abstract
Since the famous double-helix model was proposed, chromosomal DNA has been regarded as a rigid molecule containing the genetic information of an organism. It is clear now that DNA can adopt many transient, complex structures that can perform different biological functions. The G4 DNA (also called DNA G-quadruplex or G-tetraplex), a four-stranded DNA structure composed of stacked G-tetrads (guanine tetrads), has attracted much attention during the past two decades due to its ability to adopt a variety of structures and its possible biological functions. This review gives a glimpse on the structural diversity and biophysical properties of these fascinating DNA structures. Common methods that are widely used in investigating biophysical properties and biological functions of G4 DNA are described briefly. Next, bioinformatics studies that indicate evidence of evolutionary selection and potential functions of G4 DNA are discussed. Finally, examples of various biological functions of different G4 DNA are given, and potential roles of G4 DNA in respect of cardiovascular science are discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, UK.
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23
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Abstract
Double-helical DNA has been shown to conduct both electrons and electron holes, the latter over distances of >20 nm. DNA is thus a material of significant interest for the bottom-up construction of nanocircuitry. Here, we describe a contractile DNA nanoswitch, which can toggle between a structurally extended "off" state and a contracted "on" state, with a 40-fold conductivity difference between the two. To turn on, two short motifs of guanine-guanine mismatches in an otherwise standard double helix synapse to form a conductive G-quadruplex, bypassing an insulating element within the helix. This switch can be turned repeatedly on by treatment with millimolar concentrations of K(+) and turned off by sequestration of the K(+) by a crown ether. Circular dichroism and thymine-thymine photocross-linking experiments reveal that strand orientations within the on state G-quadruplex are wholly antiparallel and that the two conductive double-helices interface with the same face of the quadruplex. Although this DNA nanoswitch is chemically gated, it should be adaptable to other kinds of gating and thus serve as a prototype for increasingly sophisticated and complex electronic devices made of DNA.
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Affiliation(s)
- Yu Chuan Huang
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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24
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Abstract
Thermodynamic and kinetic studies complement high-resolution structures of G-quadruplexes. Such studies are essential for a thorough understanding of the mechanisms that govern quadruplex folding and conformational changes in quadruplexes. This perspective article reviews representative thermodynamic and kinetic studies of the folding of human telomeric quadruplex structures. Published thermodynamic data vary widely and are inconsistent; possible reasons for these inconsistencies are discussed. The key issue of whether such folding reactions are a simple two-state process is examined. A tentative energy balance for the folding of telomeric quadruplexes in Na(+) and K(+) solution, and for the conformational transition between these forms is presented.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, Kentucky, KY 40202, USA.
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25
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Popova AM, Kálai T, Hideg K, Qin PZ. Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes. Biochemistry 2009; 48:8540-50. [PMID: 19650666 DOI: 10.1021/bi900860w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to "scan" a given DNA molecule in order to interrogate its local structural and dynamic features.
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Affiliation(s)
- Anna M Popova
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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26
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Guédin A, Alberti P, Mergny JL. Stability of intramolecular quadruplexes: sequence effects in the central loop. Nucleic Acids Res 2009; 37:5559-67. [PMID: 19581426 PMCID: PMC2760802 DOI: 10.1093/nar/gkp563] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/16/2009] [Accepted: 06/17/2009] [Indexed: 01/06/2023] Open
Abstract
Hundreds of thousands of putative quadruplex sequences have been found in the human genome. It is important to understand the rules that govern the stability of these intramolecular structures. In this report, we analysed sequence effects in a 3-base-long central loop, keeping the rest of the quadruplex unchanged. A first series of 36 different sequences were compared; they correspond to the general formula GGGTTTGGGHNHGGGTTTGGG. One clear rule emerged from the comparison of all sequence motifs: the presence of an adenine at the first position of the loop was significantly detrimental to stability. In contrast, adenines have no detrimental effect when present at the second or third position of the loop. Cytosines may either have a stabilizing or destabilizing effect depending on their position. In general, the correlation between the T(m) or DeltaG degrees in sodium and potassium was weak. To determine if these sequence effects could be generalized to different quadruplexes, specific loops were tested in different sequence contexts. Analysis of 26 extra sequences confirmed the general destabilizing effect of adenine as the first base of the loop(s). Finally, analysis of some of the sequences by microcalorimetry (DSC) confirmed the differences found between the sequence motifs.
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Affiliation(s)
- Aurore Guédin
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
| | - Patrizia Alberti
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
| | - Jean-Louis Mergny
- INSERM, U565, Acides nucléiques: dynamique, ciblage et fonctions biologiques, 43 rue Cuvier, CP26, Paris Cedex 05, F-75231 and Muséum National d’Histoire Naturelle (MNHN) USM503, CNRS, UMR7196, Département de ‘Régulations, développement et diversité moléculaire’, Laboratoire des Régulations et dynamique des génomes, 43 rue Cuvier, CP26, Paris Cedex 5, F-75231, France
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27
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Herbert BS, Huppert JL, Johnson FB, Lane AN, Phan AT. Meeting report: second international meeting on quadruplex DNA. Biochimie 2009; 91:1059-65. [PMID: 19555734 DOI: 10.1016/j.biochi.2009.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 06/15/2009] [Indexed: 01/27/2023]
Abstract
A two and a half day meeting on G-quadruplexes was held in Louisville, KY, USA (April 18-21, 2009). A specific goal of this conference was to promote discussion on the biology of G-quadruplexes. In practice this was represented in four main ways, namely in biophysics, bio/nanotechnology, therapeutics, and what might be termed "intrinsic biology". Research into the basic biophysical and structural properties of G-quadruplexes continues to be important for understanding biology, and for optimizing aptamers for therapeutic and bio/technological purposes. The meeting comprised two Keynote lectures, twenty-three invited talks, and forty-two posters covering various aspects of these topics using a wide variety of technologies.
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Affiliation(s)
- Brittney-Shea Herbert
- Dept of Medical and Molecular Genetics, Indiana University Melvin and Bren Simon Cancer Center, Indiana University Center for Regenerative Biology and Medicine, Indiana University School of Medicine, IB 242 Indianapolis, IN 46202, USA.
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