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Perets EA, Olesen KB, Yan ECY. Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5765-5778. [PMID: 35482888 DOI: 10.1021/acs.langmuir.2c00365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.
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Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kristian B Olesen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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Kim Y, Inoue Y, Hasegawa H, Yoshida Y, Sakata T. In Situ Electrical Monitoring of Methylated DNA Based on Its Conformational Change to G-Quadruplex Using a Solution-Gated Field-Effect Transistor. Anal Chem 2021; 93:16709-16717. [PMID: 34859677 DOI: 10.1021/acs.analchem.1c04466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methylated DNA is not only a diagnostic but also a prognostic biomarker for early-stage cancer. However, sodium bisulfite sequencing as a "gold standard" method for detection of methylation markers has some drawbacks such as its time-consuming and labor-intensive procedures. Therefore, simple and reliable methods are required to analyze DNA sequences with or without methylated residues. Herein, we propose a simple and direct method for detecting DNA methylation through its conformation transition to G-quadruplex using a solution-gated field-effect transistor (SG-FET) without using labeled materials. The BCL-2 gene, which is involved in the development of various human tumors, contains G-rich segments and undergoes a conformational change to G-quadruplex depending on the K+ concentration. Stacked G-quadruplex strands move close to the SG-FET sensor surface, resulting in large electrical signals based on intrinsic molecular charges. In addition, a dense hydrophilic polymer brush is grafted using surface-initiated atom transfer radical polymerization onto the SG-FET sensor surface to reduce electrical noise based on nonspecific adsorption of interfering species. In particular, control of the polymer brush thickness induces electrical signals based on DNA molecular charges in the diffusion layer, according to the Debye length limit. A platform based on the SG-FET sensor with a well-defined polymer brush is suitable for in situ monitoring of methylated DNA and realizes a point-of-care device with a high signal-to-noise ratio and without the requirement for additional processes such as bisulfite conversion and polymerase chain reaction.
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Affiliation(s)
- Yeji Kim
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | - Yuuki Inoue
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | - Hijiri Hasegawa
- Advanced Technology Research Dept., LG Japan Lab Inc., Glass Cube Shinagawa, 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
| | | | - Toshiya Sakata
- Department of Materials Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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3
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Metal-dependent electrochemical discrimination of DNA quadruplex sequences. J Biol Inorg Chem 2021; 26:659-666. [PMID: 34347161 PMCID: PMC8437839 DOI: 10.1007/s00775-021-01881-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/09/2021] [Indexed: 11/16/2022]
Abstract
Films of four different DNA quadruplex-forming (G4) sequences (c-KIT, c-MYC, HTelo, and BCL2) on gold surfaces were investigated by electrochemical impedance spectroscopy (EIS) to evaluate whether they evoke unique electrochemical responses that can be used for their identification. This could render EIS an alternative means for the determination of G4 sequences of unknown structure. Towards, this end, cation-dependent topology changes in the presence of either K+, K+ in combination with Li+, or Pb2+ in the presence of Li+ were first evaluated by circular dichroism (CD) spectroscopy, and electrochemical studies were performed subsequently. As a result, G4-sequence specific charge transfer resistance (RCT) patterns were in fact observed for each G4 sequence, allowing their discrimination by EIS.
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Bazoobandi M, Bozorgmehr MR, Mahmoudi A, Morsali A. The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint. Comb Chem High Throughput Screen 2019; 22:546-554. [PMID: 31642773 DOI: 10.2174/1386207322666191022142629] [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: 06/13/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C. MATERIALS AND METHODS RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues. RESULTS The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated. CONCLUSION The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.
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Affiliation(s)
- Mohadeseh Bazoobandi
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
| | | | - Ali Mahmoudi
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
| | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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5
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Omaga CA, Fleming AM, Burrows CJ. The Fifth Domain in the G-Quadruplex-Forming Sequence of the Human NEIL3 Promoter Locks DNA Folding in Response to Oxidative Damage. Biochemistry 2018; 57:2958-2970. [PMID: 29718661 DOI: 10.1021/acs.biochem.8b00226] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA oxidation is an inevitable and usually detrimental process, but the cell is capable of reversing this state because the cell possesses a highly developed set of DNA repair machineries, including the DNA glycosylase NEIL3 that is encoded by the NEIL3 gene. In this work, the G-rich promoter region of the human NEIL3 gene was shown to fold into a dynamic G-quadruplex (G4) structure under nearly physiological conditions using spectroscopic techniques (e.g., nuclear magnetic resonance, circular dichroism, fluorescence, and ultraviolet-visible) and DNA polymerase stop assays. The presence of 8-oxo-7,8-dihydroguanine (OG) modified the properties of the NEIL3 G4 and entailed the recruitment of the fifth domain to function as a "spare tire", in which an undamaged fifth G-track is swapped for the damaged section of the G4. The polymerase stop assay findings also revealed that owing to its dynamic polymorphism, the NEIL3 G4 is more readily bypassed by DNA polymerase I (Klenow fragment) than well-known oncogene G4s are. This study identifies the NEIL3 promoter possessing a G-rich element that can adopt a G4 fold, and when OG is incorporated, the sequence can lock into a more stable G4 fold via recruitment of the fifth track of Gs.
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Affiliation(s)
- Carla A Omaga
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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6
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Huang Y, Xu W, Liu G, Tian L. A pure DNA hydrogel with stable catalytic ability produced by one-step rolling circle amplification. Chem Commun (Camb) 2018; 53:3038-3041. [PMID: 28239729 DOI: 10.1039/c7cc00636e] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A rolling-circle-amplification method was developed to produce DNA hydrogels with horseradish-peroxidase-like catalytic capability. The catalytic hydrogel exhibits highly improved stability at elevated temperatures or during a long-term storage. Integrated with glucose oxidase, the complex hydrogel can be applied to the sensitive and reliable detection of glucose.
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Affiliation(s)
- Yishun Huang
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Wanlin Xu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
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Poudel L, Steinmetz NF, French RH, Parsegian VA, Podgornik R, Ching WY. Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA. Phys Chem Chem Phys 2018; 18:21573-85. [PMID: 27425864 DOI: 10.1039/c6cp04357g] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Roger H French
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - V Adrian Parsegian
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Rudolf Podgornik
- Department of Physics, University of Massachusetts, Amherst, Massachusetts 01003, USA and Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA.
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8
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Karatosun A, Çankaya M, Tekin A. Symmetry-adapted perturbation theory potential for the adenine dimer. Phys Chem Chem Phys 2018; 20:26303-26314. [DOI: 10.1039/c8cp03798a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new ab initio intermolecular interaction potential for the adenine dimer has been developed.
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Affiliation(s)
- Armağan Karatosun
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Mehmet Çankaya
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University
- 34469 Maslak
- Turkey
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9
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Huang H, Zhang J, Harvey SE, Hu X, Cheng C. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes Dev 2017; 31:2296-2309. [PMID: 29269483 PMCID: PMC5769772 DOI: 10.1101/gad.305862.117] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022]
Abstract
Here, Huang et al. investigated the role of RNA secondary structure in splicing regulation and show that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in hnRNPF-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome, thus providing new insights into the regulation of alternative splicing. It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex-forming capacity promote exon inclusion. Destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. Analysis of RNA-binding protein footprints revealed that G quadruplexes are enriched in heterogeneous nuclear ribonucleoprotein F (hnRNPF)-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an epithelial–mesenchymal transition (EMT)-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA (The Cancer Genome Atlas) data sets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.
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Affiliation(s)
- Huilin Huang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jing Zhang
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Samuel E Harvey
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaohui Hu
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chonghui Cheng
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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10
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Manukyan A, Tekin A. The intermolecular dimer potential for guanine. J Chem Phys 2017; 147:154311. [DOI: 10.1063/1.4998792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artür Manukyan
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
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11
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Effects of monovalent cations on folding kinetics of G-quadruplexes. Biosci Rep 2017; 37:BSR20170771. [PMID: 28588052 PMCID: PMC5567087 DOI: 10.1042/bsr20170771] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes are special structures existing at the ends of human telomeres,
the folding kinetics of which are essential for their functions, such as in the
maintenance of genome stability and the protection of chromosome ends. In the
present study, we investigated the folding kinetics of G-quadruplex in different
monovalent cation environments and determined the detailed kinetic parameters
for Na+- and K+-induced G-quadruplex folding, and for its
structural transition from the basket-type Na+ form to the
hybrid-type K+ form. More interestingly, although Li+ was
often used in previous studies of G-quadruplex folding as a control ion supposed
to have no effect, we have found that Li+ can actually influence the
folding kinetics of both Na+- and K+-induced
G-quadruplexes significantly and in different ways, by changing the folding
fraction of Na+-induced G-quadruplexes and greatly increasing the
folding rates of K+-induced G-quadruplexes. The present study may
shed new light on the roles of monovalent cations in G-quadruplex folding and
should be useful for further studies of the underlying folding mechanism.
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12
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Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, Liu Y, Yu L, Shi Y, Chen H, Tang Y. Directly lighting up RNA G-quadruplexes from test tubes to living human cells. Nucleic Acids Res 2015; 43:9575-86. [PMID: 26476445 PMCID: PMC4787783 DOI: 10.1093/nar/gkv1040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022] Open
Abstract
RNA G-quadruplexes (G4s) are one of the key components of the transcriptome that act as efficient post-transcriptional regulatory elements in living cells. To conduct further studies of the unique biological functions of RNA G4s, techniques need to be developed that can efficiently recognize RNA G4 structures under various conditions, in fixed cells and living cells, as well as in vitro. This paper presents the development of such a method, a new technique using a cyanine dye called CyT, which can detect both canonical and non-canonical RNA G4 structures from test tubes to living human cells. The ability of CyT to distinguish between G4 and nonG4 RNA offers a promising tool for future RNA G4-based biomarker discovery and potential diagnostic applications.
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Affiliation(s)
- Shujuan Xu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qian Li
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qianfan Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Aijiao Guan
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lixia Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yan Liu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lijia Yu
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yunhua Shi
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China University of the Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongbo Chen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, P. R. China
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13
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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14
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Goncharova I, Novotná J, Urbanová M. Stacked and continuous helical self-assemblies of guanosine monophosphates detected by vibrational circular dichroism. Anal Bioanal Chem 2012; 403:2635-44. [PMID: 22573058 DOI: 10.1007/s00216-012-6014-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/02/2012] [Accepted: 04/02/2012] [Indexed: 11/25/2022]
Abstract
The aim of this study was to characterize self-assembled structures of guanosine derivatives in aqueous solutions by vibrational circular dichroism (VCD) and electronic circular dichroism (ECD). Three guanosine derivatives were studied [5'-guanosine monophosphate (GMP), diphosphate (GDP), and triphosphate (GTP)] using a broad range of concentrations and various metal/guanosine ratios. VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. It can also help to determine the impact that the cations have, when added to the solution, on the versatile structures of guanine derivatives in terms of their association and disassociation. Based on the markedly different intensities and signs of the VCD signals observed for different concentrations of guanosine derivatives, we propose various structures based on guanine quartets for high guanosine concentrations and high K(+)/guanosine ratios (i.e., columnar helical organization of the quartets, which are rearranged into a continuous helix). We performed a degenerate coupled oscillator (DCO) calculation to interpret the VCD spectra obtained and how they vary during the assembly of guanosine derivatives. The calculations correctly predicted the VCD spectra and enabled us to identify the structures of the metal cation/guanosine monophosphate aggregates. ECD in the ultraviolet region was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the guanine derivative assemblies and the molecular systems studied here. These studies revealed that the VCD technique is a powerful new method for determining the structures of optically active guanosine motifs.
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Affiliation(s)
- Iryna Goncharova
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Czech Republic
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Novotná J, Goncharova I, Urbanová M. Supramolecular arrangement of guanosine/5-guanosine monophosphate binary mixtures studied by methods of circular dichroism. Chirality 2012; 24:432-8. [PMID: 22517502 DOI: 10.1002/chir.22045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 02/23/2012] [Accepted: 02/28/2012] [Indexed: 11/10/2022]
Abstract
Self-assembly of molecules is one of the fundamental processes in biology and in supramolecular chemistry. Guanosine (Guo) and its derivatives are among the widely studied molecules because of self-assembly abilities. Their tetrameric associates are the nature of telomeric DNA, and furthermore they are fundamental building blocks of supramolecular reversible gels, which may arise in certain physical and chemical conditions. Although poorly soluble in water, Guo forms interesting structures with guanosine 5'-monophosphate salt (GMP) in the TRIS buffer. We used electronic circular dichroism and vibrational circular dichroism to describe the thermal response of gels formed by the Guo/GMP binary mixture. Using these complementary techniques suitable to study conformational changes of chiral compounds, we obtained information about the involvement of functional groups and weak interactions in the guanosine quartet (G(4)) and stacked G(4) structures.
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Affiliation(s)
- Jana Novotná
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
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Andrushchenko V, Tsankov D, Krasteva M, Wieser H, Bour P. Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism. J Am Chem Soc 2011; 133:15055-64. [PMID: 21823674 DOI: 10.1021/ja204630k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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Yang S, Xiang J, Yang Q, Zhou Q, Zhang X, Li Q, Tang Y, Xu G. Distinct G-quadruplex structures of human telomeric DNA formed by the induction of sanguinarine and nitidine under salt-deficient condition. Fitoterapia 2010; 81:1026-32. [DOI: 10.1016/j.fitote.2010.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Revised: 06/21/2010] [Accepted: 06/27/2010] [Indexed: 11/15/2022]
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Yang S, Xiang J, Yang Q, Li Q, Zhou Q, Zhang X, Tang Y, Xu G. Formation of Human Telomeric G-quadruplex Structures Induced by the Quaternary Benzophenanthridine Alkaloids: Sanguinarine, Nitidine, and Chelerythrine. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.201090145] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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