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Kouz S, Raouafi A, Ouhibi A, Lorrain N, Essafi M, Mejri M, Raouafi N, Moadhen A, Guendouz M. Detection of SARS-CoV-2 N protein using AgNPs-modified aligned silicon nanowires BioSERS chip. RSC Adv 2024; 14:12071-12080. [PMID: 38628480 PMCID: PMC11019291 DOI: 10.1039/d4ra00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The SARS-CoV-2 (COVID-19) pandemic had a strong impact on societies and economies worldwide and tests for high-performance detection of SARS-CoV-2 biomarkers are still needed for potential future outbreaks of the disease. In this paper, we present the different steps for the design of an aptamer-based surface-enhanced Raman scattering (BioSERS) sensing chip capable of detecting the coronavirus nucleocapsid protein (N protein) in spiked phosphate-buffered solutions and real samples of human blood serum. Optimization of the preparation steps in terms of the aptamer concentration used for the functionalization of the silver nanoparticles, time for affixing the aptamer, incubation time with target protein, and insulation of the silver active surface with cysteamine, led to a sensitive BioSERS chip, which was able to detect the N protein in the range from 1 to 75 ng mL-1 in spiked phosphate-buffered solutions with a detection limit of 1 ng mL-1 within 30 min. Furthermore, the BioSERS chip was used to detect the target protein in scarcely spiked human serum. This study demonstrates the possibility of a clinical application that can improve the detection limit and accuracy of the currently commercialized SARS-CoV-2 immunodiagnostic kit. Additionally, the system is modular and can be applied to detect other proteins by only changing the aptamer.
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Affiliation(s)
- Sadok Kouz
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Amal Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Awatef Ouhibi
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Nathalie Lorrain
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Makram Essafi
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Manel Mejri
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Noureddine Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Adel Moadhen
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Mohammed Guendouz
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
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Moscato D, Gabas F, Conte R, Ceotto M. Vibrational spectroscopy simulation of solvation effects on a G-quadruplex. J Biomol Struct Dyn 2023; 41:14248-14258. [PMID: 36856120 DOI: 10.1080/07391102.2023.2180435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
It is commonly believed that solvation effects on the vibrational properties of a solute are easily accounted for by simple rules of thumbs, that is, solvating a polar molecule in a polar medium has the only effect of red shifting all its spectroscopical features and, similarly, solvating a polar molecule in a nonpolar medium has the opposite effect. In this work, we use theoretical vibrational spectroscopy at quasi-classical and quantum approximate semiclassical level to gain atomistic insights about solvent-solute interactions for 2'-deoxyguanosine and the G-quadruplex. We employ the quasi-classical trajectory method to include full anharmonicity into our calculated spectra, and then introduce quantum nuclear effects by means of divide-and-conquer semiclassical spectroscopy calculations. Solvation is treated explicitly leading to a good reproducibility of the available experimental data and reliable predictions when an experimental reference is missing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
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3
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Zhang Y, Zhan DS, Xu XY, Zhang Z, Hafez ME, He Y, Li Y, Li DW. Label-free detection of DNA methylation by surface-enhanced Raman spectroscopy using zirconium-modified silver nanoparticles. Talanta 2023; 253:123941. [DOI: 10.1016/j.talanta.2022.123941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/28/2022] [Accepted: 09/14/2022] [Indexed: 10/14/2022]
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Balanikas E, Gustavsson T, Markovitsi D. Fluorescence of Bimolecular Guanine Quadruplexes: From Femtoseconds to Nanoseconds. J Phys Chem B 2023; 127:172-179. [PMID: 36577031 DOI: 10.1021/acs.jpcb.2c07647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The paper deals with the fluorescence of guanine quadruplexes (G4) formed by association of two DNA strands d(GGGGTTTTGGGG) in the presence of K+ cations, noted as OXY/K+ in reference to the protozoon Oxytricha nova, whose telomere contains TTTTGGGG repeats. They were studied by steady-state and time-resolved techniques, time-correlated single photon counting, and fluorescence upconversion. The maximum of the OXY/K+ fluorescence spectrum is located at 334 nm, and the quantum yield is 5.8 × 10-4. About 75% of the photons are emitted before 100 ps and stem from ππ* states, possibly with a small contribution of charge transfer. Time-resolved fluorescence anisotropy measurements indicate that ultrafast (<330 fs) excitation transfer, due to internal conversion among exciton states, is more efficient in OXY/K+ compared to previously studied G4 structures. This is attributed to the arrangement of the peripheral thymines in two diagonal loops with restricted mobility, facilitating the interaction among them and with guanines. Thymines should also be responsible for a weak intensity excimer/exciplex emission band, peaking at 445 nm. Finally, the longest living fluorescence component (∼2.1 ns) is observed at the blue side of the spectrum. So far, high-energy long-lived emitting states had been reported only for double-stranded structures but not for G4.
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Affiliation(s)
| | - Thomas Gustavsson
- CEA, CNRS, LIDYL, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- CEA, CNRS, LIDYL, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.,CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, 91405 Orsay, France
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5
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Revealing the specific interactions between G-quadruplexes and ligands by surface-enhanced Raman spectroscopy. Int J Biol Macromol 2022; 222:2948-2956. [DOI: 10.1016/j.ijbiomac.2022.10.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/05/2022]
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Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy. Toxins (Basel) 2022; 14:toxins14090622. [PMID: 36136560 PMCID: PMC9505997 DOI: 10.3390/toxins14090622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.
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Xiang X, Bao Y, Zhang Y, Xu G, Zhao B, Guo X. Accurate assembly and direct characterization of DNA nanogels crosslinked by G-quadruplex, i-motif and duplex with surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121161. [PMID: 35306309 DOI: 10.1016/j.saa.2022.121161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/22/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The direct characterization of DNA nanogels at the atomic level is desirable and of great significance, however, has been challenging because of structural complexity and the larger size of nanogels. Herein, we demonstrated a simple, sensitive and reliable SERS (Surface-enhanced Raman spectroscopy)-based approach towards direct monitoring microstructures, such as three types of nanogels crosslinked by DNA G-quadruplex, i-motif and GC duplex. The achievement is attributed to the detection of featured Raman bands corresponding to the formation of Watson-Crick and Hoogsteen hydrogen bonds as well as C·C+ base pairs. Importantly, this work reveals that the silver nanoparticles attaching on the surface of nanogels can form local 'hotspots' and produce high-quality of Raman spectra under the assistance of iodide, aluminum ions and dichloromethane, therefore, shows great potential for wide applications in accurate characterization of various DNA nanostructures.
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Affiliation(s)
- Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Guantong Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, China.
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Libera V, Bianchi F, Rossi B, D’Amico F, Masciovecchio C, Petrillo C, Sacchetti F, Paciaroni A, Comez L. Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding. Int J Mol Sci 2022; 23:ijms23095123. [PMID: 35563512 PMCID: PMC9100830 DOI: 10.3390/ijms23095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Federico Bianchi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Francesco D’Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Claudio Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- Correspondence: (A.P.); (L.C.)
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (A.P.); (L.C.)
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Zhang Y, Sun L, Xiang X, Bao Y, Guo X. Adenine shares the plane with G-quartet detected by surface-enhanced Raman spectroscopy. Talanta 2021; 235:122777. [PMID: 34517634 DOI: 10.1016/j.talanta.2021.122777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/28/2021] [Accepted: 07/31/2021] [Indexed: 11/19/2022]
Abstract
DNA G-quadruplexes (G4s) formed by guanine(G)-rich sequences show diversity of structural topologies. The detection of structural details is of great significance for understanding of their functions and for the target drug design, but is very challenging. Herein, we demonstrate that the surface-enhanced Raman spectroscopy (SERS) via Ag IANPs as substrates is able to identify the numbers of Adenine (A) located on the G-quartet of the G4s. Eight G4s are selected for SERS studies. Besides the detection of series of characteristic bands indicating the formation of G4s, the intensity of the band represented A base ring breath (νA, ~733 cm-1) is observed particularly enhanced when there are A bases coplanar with G-quartet, and which is higher than the intensity of the band corresponding to G base ring breath (νG, ~655 cm-1). Furthermore, the band intensity ratio of νA to νG versus the ratio of the numbers of A on the plane to the sum of numbers of A and G shows very good linear relationship. Thus, based on the band intensities of νA to νG and their ratio in the SERS spectrum, the G-quadruplexes with or without a coplanar A base and numbers of A bases on the plane of G-quartet can be facilely identified. The method is simple, fast, low cost and sensitive to provide particular details of the structure in aqueous solution, therefore, implies widespread applications.
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Affiliation(s)
- Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Likang Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Ying Bao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, PR China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, PR China.
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Di Fonzo S, Amato J, D'Aria F, Caterino M, D'Amico F, Gessini A, Brady JW, Cesàro A, Pagano B, Giancola C. Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy. Phys Chem Chem Phys 2020; 22:8128-8140. [PMID: 32246758 DOI: 10.1039/d0cp01022g] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-Quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of several biological processes of many organisms. The rational design of G4-targeting molecules developed as potential anticancer and antiviral therapeutics is a complex problem intrinsically due to the structural polymorphism of these peculiar DNA structures. The aim of the present work is to show how Ultraviolet Resonance Raman (UVRR) spectroscopy can complement other techniques in providing valuable information about ligand/G4 interactions in solution. Here, the binding of BRACO-19 and Pyridostatin - two of the most potent ligands - to selected biologically relevant G4s was investigated by polarized UVRR scattering at 266 nm. The results give new insights into the binding mode of these ligands to G4s having different sequences and topologies by performing an accurate analysis of peaks assigned to specific groups and their changes upon binding. Indeed, the UVRR data not only show that BRACO-19 and Pyridostatin interact with different G4 sites, but also shed light on the ligand and G4 chemical groups really involved in the interaction. In addition, UVRR results complemented by circular dichroism data clearly indicate that the binding mode of a ligand can also depend on the conformation(s) of the target G4. Overall, these findings demonstrate the utility of using UVRR spectroscopy in the investigation of G4s and G4-ligand interactions in solution.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York, NY 14853, USA
| | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy. and Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, I-34127, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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Papi F, Kenđel A, Ratkaj M, Piantanida I, Gratteri P, Bazzicalupi C, Miljanić S. Effect of structure levels on surface-enhanced Raman scattering of human telomeric G-quadruplexes in diluted and crowded media. Anal Bioanal Chem 2019; 411:5197-5207. [PMID: 31119345 DOI: 10.1007/s00216-019-01894-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/26/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Human telomeric G-quadruplexes are emerging targets in anticancer drug discovery since they are able to efficiently inhibit telomerase, an enzyme which is greatly involved in telomere instability and immortalization process in malignant cells. G-quadruplex (G4) DNA is highly polymorphic and can adopt different topologies upon addition of electrolytes, additives, and ligands. The study of G-quadruplex forms under various conditions, however, might be quite challenging. In this work, surface-enhanced Raman scattering (SERS) spectroscopy has been applied to study G-quadruplexes formed by human telomeric sequences, d[A3G3(TTAGGG)3A2] (Tel26) and d[(TTAGGG)4T2] (wtTel26), under dilute and crowding conditions. The SERS spectra distinctive of hybrid-1 and hybrid-2 G-quadruplexes of Tel26 and wtTel26, respectively, were observed for the sequences folded in the presence of K+ ions (110 mM) in a buffered solution, representing the diluted medium. Polyethylene glycol (5, 10, 15, 20, and 40% v/v PEG) was used to create a molecular-crowded environment, resulting in the formation of the parallel G-quadruplexes of both studied human telomeric sequences. Despite extensive overlap by the crowding agent bands, the SERS spectral features indicative of parallel G4 form of Tel26 were recognized. The obtained results implied that SERS of G-quadruplexes reflected not only the primary structure of the studied human telomeric sequence, including its nucleobase composition and sequence, but also its secondary structure in the sense of Hoogsteen hydrogen bonds responsible for the guanine tetrad formation, and finally its tertiary structure, defining a three-dimensional DNA shape, positioned close to the enhancing metallic surface. Graphical abstract.
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Affiliation(s)
- Francesco Papi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy. .,Department NEUROFARBA - Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
| | - Adriana Kenđel
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Marina Ratkaj
- Teva Pharmaceutical Industries Ltd., Research and Development, PLIVA Croatia, Prilaz baruna Filipovića 29, 10000, Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002, Zagreb, Croatia
| | - Paola Gratteri
- Department NEUROFARBA - Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Snežana Miljanić
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia.
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Di Fonzo S, Bottari C, Brady JW, Tavagnacco L, Caterino M, Petraccone L, Amato J, Giancola C, Cesàro A. Crowding and conformation interplay on human DNA G-quadruplex by ultraviolet resonant Raman scattering. Phys Chem Chem Phys 2019; 21:2093-2101. [DOI: 10.1039/c8cp04728f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The G-quadruplex-forming telomeric sequence (TTAGGG)4TT was investigated by polarized Ultraviolet Resonance Raman Scattering (UVRR) at 266 nm.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
| | - Cettina Bottari
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
- Department of Physics
| | - John W. Brady
- Department of Food Science
- Cornell University
- Ithaca
- USA
| | - Letizia Tavagnacco
- Department of Chemical and Pharmaceutical Sciences
- University of Trieste
- Trieste
- Italy
| | - Marco Caterino
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Luigi Petraccone
- Department of Chemical Sciences
- University of Naples Federico II
- Naples
- Italy
| | - Jussara Amato
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | | | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A
- Science Park
- Trieste
- Italy
- Department of Chemical and Pharmaceutical Sciences
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13
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Bianchi F, Comez L, Biehl R, D’Amico F, Gessini A, Longo M, Masciovecchio C, Petrillo C, Radulescu A, Rossi B, Sacchetti F, Sebastiani F, Violini N, Paciaroni A. Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway. Nucleic Acids Res 2018; 46:11927-11938. [PMID: 30407585 PMCID: PMC6294516 DOI: 10.1093/nar/gky1092] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.
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Affiliation(s)
- Federico Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Ralf Biehl
- JCNS & ICS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
| | - Francesco D’Amico
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Marialucia Longo
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Aurel Radulescu
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Federico Sebastiani
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Nicolò Violini
- JCNS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
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14
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Li Y, Han X, Zhou S, Yan Y, Xiang X, Zhao B, Guo X. Structural Features of DNA G-Quadruplexes Revealed by Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2018; 9:3245-3252. [PMID: 29847941 DOI: 10.1021/acs.jpclett.8b01353] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) has been successfully used for the label-free detection of single-stranded oligonucleotides. However, the detection of complex DNA secondary structures remains a challenge. Structural features of diverse DNA G-quadruplexes were investigated via a novel SERS method. As a result, a series of highly reproducible and sensitive SERS signatures featuring the structures of G-quadruplexes were obtained. For the first time, we reported remarkably enhanced SERS bands corresponding to purine ring breathing vibrations. Moreover, we observed that by measuring the intensity of the bands corresponding to intramolecular hydrogen bonds, we could quantitatively assess the stability of the G-quadruplexes. Because no labels on DNA strands were present as the experiments were carried out in the solution, the fingerprint peaks reflect the native, internal structure of the G-quadruplexes accurately. The method here detailed provides new insights into the promising applications of diverse DNA structural studies.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
| | - Xiaoxia Han
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
| | - Shan Zhou
- School of Future Technology , University of Chinese Academy of Sciences , Beijing 100000 , P. R. China
| | - Yuting Yan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
| | - Bing Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , 2699 Qianjin Street , Changchun 130012 , P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science , Jilin University , Changchun 130012 , P. R. China
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15
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Stelling AL, Xu Y, Zhou H, Choi SH, Clay MC, Merriman DK, Al-Hashimi HM. Robust IR-based detection of stable and fractionally populated G-C + and A-T Hoogsteen base pairs in duplex DNA. FEBS Lett 2017; 591:1770-1784. [PMID: 28524232 PMCID: PMC5584567 DOI: 10.1002/1873-3468.12681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/28/2017] [Accepted: 05/06/2017] [Indexed: 11/11/2022]
Abstract
Noncanonical G-C+ and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C+ and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C+ Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
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Affiliation(s)
- Allison L Stelling
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Yu Xu
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Seung H Choi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Mary C Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
- Department of Chemistry, Duke University, Durham, NC, USA
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16
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Miljanić S, Ratkaj M, Matković M, Piantanida I, Gratteri P, Bazzicalupi C. Assessment of human telomeric G-quadruplex structures using surface-enhanced Raman spectroscopy. Anal Bioanal Chem 2017; 409:2285-2295. [DOI: 10.1007/s00216-016-0172-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 10/20/2022]
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17
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Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
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18
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Takahara M, Budinova GALG, Nakazawa H, Mori Y, Umetsu M, Kamiya N. Salt-Switchable Artificial Cellulase Regulated by a DNA Aptamer. Biomacromolecules 2016; 17:3356-3362. [PMID: 27602779 DOI: 10.1021/acs.biomac.6b01141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel artificial cellulase was developed by conjugating a DNA aptamer to an endoglucanase catalytic domain, thereby substituting the natural carbohydrate-binding module. Circular dichroism spectroscopy and adsorption isotherm showed the binding motif of cellulose-binding DNA aptamer (CelApt) was G-quadruplex and stem-loop structures stabilized in the presence of salts, and CelApt binding preferred the amorphous region of the solid cellulose. By introducing the revealed salt-switchable cellulose-binding nature of CelApt into a catalytic domain of a cellulase, we created CelApt-catalytic domain conjugate possessing both controllable adsorption on the solid substrates and equal enzymatic activity to the wild-type cellulase. Thus potential use of a responsive DNA aptamer for biocatalysis at a solid surface was demonstrated.
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Affiliation(s)
- Mari Takahara
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan
| | | | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Yutaro Mori
- Biomass Engineering Program, RIKEN , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan
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19
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Chinnathambi S, Karthikeyan S, Velmurugan D, Hanagata N, Aruna P, Ganesan S. Investigations on the Interactions of 5-Fluorouracil with Herring Sperm DNA: Steady State/Time Resolved and Molecular Modeling Studies. ACTA ACUST UNITED AC 2015. [DOI: 10.1142/s1793048015500034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the present study, the interaction of 5-Fluorouracil with herring sperm DNA is reported using spectroscopic and molecular modeling techniques. This binding study of 5-FU with hs-DNA is of paramount importance in understanding chemico–biological interactions for drug design, pharmacy and biochemistry without altering the original structure. The challenge of the study was to find the exact binding mode of the drug 5-Fluorouracil with hs-DNA. From the absorption studies, a hyperchromic effect was observed for the herring sperm DNA in the presence of 5-Fluorouracil and a binding constant of 6.153 × 103 M-1 for 5-Fluorouracil reveals the existence of weak interaction between the 5-Fluorouracil and herring sperm DNA. Ethidium bromide loaded herring sperm DNA showed a quenching in the fluorescence intensity after the addition of 5-Fluorouracil. The binding constants for 5-Fluorouracil stranded DNA and competitive bindings of 5-FU interacting with DNA–EB systems were examined by fluorescence spectra. The Stern–Volmer plots and fluorescence lifetime results confirm the static quenching nature of the drug-DNA complex. The binding constant Kb was 2.5 × 104 L mol-1 and the number of binding sites are 1.17. The 5-FU on DNA system was calculated using double logarithmic plot. From the Forster nonradiative energy transfer study it has been found that the distance of 5-FU from DNA was 4.24 nm. In addition to the spectroscopic results, the molecular modeling studies also revealed the major groove binding as well as the partial intercalation mode of binding between the 5-Fluorouracil and herring sperm DNA. The binding energy and major groove binding as -6.04 kcal mol-1 and -6.31 kcal mol-1 were calculated from the modeling studies. All the testimonies manifested that binding modes between 5-Fluorouracil and DNA were evidenced to be groove binding and in partial intercalative mode.
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Affiliation(s)
| | - Subramani Karthikeyan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai 600025, India
- Bioinformatics Infrastructure Facility, University of Madras, Chennai 600025, India
| | - Nobutaka Hanagata
- Nanotechnology Innovation Station, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
- Graduate School of Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0812, Japan
| | - Prakasarao Aruna
- Department of Medical Physics, Anna University, Chennai 600025, India
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20
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Jangir DK, Mehrotra R. Raman spectroscopic evaluation of DNA adducts of a platinum containing anticancer drug. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:386-389. [PMID: 24810023 DOI: 10.1016/j.saa.2014.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 03/30/2014] [Accepted: 04/04/2014] [Indexed: 06/03/2023]
Abstract
Mechanistic understanding of the interaction of drugs with their target molecules is important for better understanding of their mode of action and to improve their efficacy. Carboplatin is a platinum containing anticancer drug, used to treat different type of tumors. In the present work, we applied Raman spectroscopy to study the interaction of carboplatin with DNA at molecular level using different carboplatin-DNA molar ratios. These Raman spectroscopic results provide comprehensive understanding on the carboplatin-DNA interactions and indicate that DNA cross-linked adducts formed by carboplatin are similar to cisplatin adducts. The results indicate that guanine N7 and adenine N7 are the putative sites for carboplatin interaction. It is observed that carboplatin has some affinity toward cytosine in DNA. Phosphate sugar backbone of DNA showed conformation perturbation in DNA which were easily sensible at higher concentrations of carboplatin. Most importantly, carboplatin interaction induces intermediate A- and B-DNA conformations at the cross-linking sites.
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Affiliation(s)
- Deepak K Jangir
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India
| | - Ranjana Mehrotra
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India.
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21
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Nowicka AM, Krasnodebska-Ostrega B, Wrzosek B, Jastrzebska M, Sadowska M, Mackiewicz M, Stojek Z. Detection of Oxidative Damage of Synthetic Oligonucleotides Caused by Thallium(III) Complexes. ELECTROANAL 2013. [DOI: 10.1002/elan.201300489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Cao C, Zhang J, Wen X, Dodson SL, Dao NT, Wong LM, Wang S, Li S, Phan AT, Xiong Q. Metamaterials-based label-free nanosensor for conformation and affinity biosensing. ACS NANO 2013; 7:7583-91. [PMID: 23952283 DOI: 10.1021/nn401645t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that highly tunable plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g., G-quadruplexes, in different environments. We further demonstrate the use of the metamaterials for fingerprinting and detection of the arginine-glycine-glycine domain of nucleolin, a cancer biomarker that specifically binds to a G-quadruplex, with the picomolar sensitivity.
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Affiliation(s)
- Cuong Cao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371
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23
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Giraud-Panis MJ, Pisano S, Benarroch-Popivker D, Pei B, Le Du MH, Gilson E. One identity or more for telomeres? Front Oncol 2013; 3:48. [PMID: 23509004 PMCID: PMC3598436 DOI: 10.3389/fonc.2013.00048] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 02/23/2013] [Indexed: 12/19/2022] Open
Abstract
A major issue in telomere research is to understand how the integrity of chromosome ends is controlled. The fact that different types of nucleoprotein complexes have been described at the telomeres of different organisms raises the question of whether they have in common a structural identity that explains their role in chromosome protection. We will review here how telomeric nucleoprotein complexes are structured, comparing different organisms and trying to link these structures to telomere biology. It emerges that telomeres are formed by a complex and specific network of interactions between DNA, RNA, and proteins. The fact that these interactions and associated activities are reinforcing each other might help to guarantee the robustness of telomeric functions across the cell cycle and in the event of cellular perturbations. We will also discuss the recent notion that telomeres have evolved specific systems to overcome the DNA topological stress generated during their replication and transcription. This will lead to revisit the way we envisage the functioning of telomeric complexes since the regulation of topology is central to DNA stability, replication, recombination, and transcription as well as to chromosome higher-order organization.
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Affiliation(s)
- Marie-Josèphe Giraud-Panis
- Faculté de Médecine de Nice, Université de Nice-Sophia Antipolis, Institute for Research on Cancer and Aging Nice, UMR 7284 CNRS, U1081 INSERM Nice, France
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24
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Nemecek D, Stepanek J, Thomas GJ. Raman Spectroscopy of Proteins and Nucleoproteins. ACTA ACUST UNITED AC 2013; Chapter 17:Unit17.8. [DOI: 10.1002/0471140864.ps1708s71] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Daniel Nemecek
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda Maryland
- Central European Institute of Technology, Masaryk University Brno Czech Republic
| | - Josef Stepanek
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics Prague Czech Republic
| | - George J. Thomas
- School of Biological Sciences, University of Missouri‐Kansas City Kansas City Missouri
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25
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Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. Nucleic Acids Res 2013; 41:1005-16. [PMID: 23193257 PMCID: PMC3553954 DOI: 10.1093/nar/gks1135] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/22/2012] [Indexed: 01/16/2023] Open
Abstract
DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K(+)-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. As Raman spectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G(3)(TTAG(3))(3) in the presence of K(+) and Na(+) ions throughout wide range of DNA concentrations. We demonstrate that the K(+)-structure of G(3)(TTAG(3))(3) at low DNA concentration is close to the antiparallel fold of Na(+)-stabilized quadruplex. On the increase of G(3)(TTAG(3))(3) concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K(+)-stabilized samples. The transition is synergically supported by increased K(+) concentration. However, even for extremely high G(3)(TTAG(3))(3) and K(+) concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K(+) ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na(+)-stabilized G(3)(TTAG(3))(3) retains its antiparallel folding regardless of the extremely high DNA and/or Na(+) concentrations, thermal destabilization or annealing.
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Affiliation(s)
- Jan Palacký
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Iva Kejnovská
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Peter Mojzeš
- Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics, Ke Karlovu 5, CZ-121 16 Prague 2, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno and CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
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26
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Abu-Ghazalah RM, Rutledge S, Lau LWY, Dubins DN, Macgregor RB, Helmy AS. Concentration-dependent structural transitions of human telomeric DNA sequences. Biochemistry 2012; 51:7357-66. [PMID: 22931349 DOI: 10.1021/bi300689t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Oligodeoxyribonucleotides (ODNs) that have four repeats of the human telomeric sequence d(TTAGGG)(n) can assume multiple monomolecular G-quadruplex topologies. These are determined by the cation species present, the bases at the 5' or 3' end, and the sample preparation technique. In this work, we report our studies of the concentration dependence of the circular dichroism (CD) and the vibrational modes probed by Raman scattering of three previously characterized monomolecular G-quadruplexes: H-Tel, d[5'-A(GGGTTA)(3)GGG-3']; hybrid-1, d[5'-AAA(GGGTTA)(3)GGGAA-3']; and hybrid-2, d[5'-TTA(GGGTTA)(3)GGGTT-3']. At high (millimolar) ODN concentrations, we observed a transformation of the CD spectrum of H-Tel, with a relaxation time on the order of 10 h. Analysis of the kinetics of this process is consistent with the formation of an aggregated complex of folded H-Tel monomers. Upon dilution, the aggregates dissociate rapidly, yielding spectra identical to those of monomeric H-Tel. Both hybrid sequences undergo a similar transition under high-salt (1 M) conditions. The measurements suggest that for these ODN concentrations, which are typically used in high-resolution spectroscopies, the monomolecular G-quadruplex structures undergo a transition to multimolecular structures at room temperature. Guided by our findings, we propose that the terminal bases of the hybrid-1 and hybrid-2 ODNs impede the formation of these aggregates; however, in solutions containing 1 M salt, the hybrid oligonucleotides aggregate.
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Affiliation(s)
- Rashid M Abu-Ghazalah
- Edward S. Rogers Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
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Kumamoto Y, Taguchi A, Smith NI, Kawata S. Deep ultraviolet resonant Raman imaging of a cell. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:076001. [PMID: 22894484 DOI: 10.1117/1.jbo.17.7.076001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We report the first demonstration of deep ultraviolet (DUV) Raman imaging of a cell. Nucleotide distributions in a HeLa cell were observed without any labeling at 257 nm excitation with resonant bands attributable to guanine and adenine. Obtained images represent DNA localization at nucleoli in the nucleus and RNA distribution in the cytoplasm. The presented technique extends the potential of Raman microscopy as a tool to selectively probe nucleic acids in a cell with high sensitivity due to resonance.
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Affiliation(s)
- Yasuaki Kumamoto
- RIKEN, Nanophotonics Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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28
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Jangir DK, Dey SK, Kundu S, Mehrotra R. Assessment of amsacrine binding with DNA using UV-visible, circular dichroism and Raman spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 114:38-43. [PMID: 22677564 DOI: 10.1016/j.jphotobiol.2012.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 04/16/2012] [Accepted: 05/08/2012] [Indexed: 11/15/2022]
Abstract
Proper understanding of the mechanism of binding of drugs to their targets in cell is a fundamental requirement to develop new drug therapy regimen. Amsacrine is a rationally designed anticancer drug, used to treat leukemia and lymphoma. Binding with cellular DNA is a crucial step in its mechanism of cytotoxicity. Despite numerous studies, DNA binding properties of amsacrine are poorly understood. Its reversible binding with DNA does not permit X-ray crystallography or NMR spectroscopic evaluation of amsacrine-DNA complexes. In the present work, interaction of amsacrine with calf thymus DNA is investigated at physiological conditions. UV-visible, FT-Raman and circular dichroism spectroscopic techniques were employed to determine the binding mode, binding constant, sequence specificity and conformational effects of amsacrine binding to native calf thymus DNA. Our results illustrate that amsacrine interacts with DNA by and large through intercalation between base pairs. Binding constant of the amsacrine-DNA complex was found to be K=1.2±0.1×10(4) M(-1) which is indicative of moderate type of binding of amsacrine to DNA. Raman spectroscopic results suggest that amsacrine has a binding preference of intercalation between AT base pairs of DNA. Minor groove binding is also observed in amsacrine-DNA complexes. These results are in good agreement with in silico investigation of amsacrine binding to DNA and thus provide detailed insight into DNA binding properties of amsacrine, which could ultimately, renders its cytotoxic efficacy.
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Affiliation(s)
- Deepak Kumar Jangir
- Quantum Optics and Photon Physics, National Physical Laboratory, Council of Scientific and Industrial Research, Dr. K.S. Krishnan Road, New Delhi 110 012, India
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29
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Rusciano G, De Luca AC, Pesce G, Sasso A, Oliviero G, Amato J, Borbone N, D'Errico S, Piccialli V, Piccialli G, Mayol L. Label-free probing of G-quadruplex formation by surface-enhanced Raman scattering. Anal Chem 2011; 83:6849-55. [PMID: 21780762 DOI: 10.1021/ac201783h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, we establish the use of surface-enhanced Raman scattering (SERS) as a label-free analytical technique for the direct detection of G-quadruplex formation. In particular, we demonstrate that SERS analysis allows the evaluation of the relative stability of G quadruplexes that differ for the number of G tetrads and investigate several structural features of quadruplexes, such as the orientation of glycosidic bonds, the identification of distortions in the sugar-phosphate backbone, and the degree of hydrogen-bond solvation. Herein, the fluctuation of the SERS spectra, due to the specific interaction of vibrational modes with the SERS-active substrate, is quantitatively analyzed before and after quadruplex formation. The results of this study suggest a perpendicular orientation of the quadruplexes (with or without the 3'-tetra end linker) with respect to the silver colloidal surface, which opens new perspectives for the use of SERS as a label-free analytical tool for the study of the binding mode between quadruplexes and their ligands.
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Affiliation(s)
- Giulia Rusciano
- Dipartimento di Scienze Fisiche, Complesso Universitario, Universitá di Napoli Federico II, Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy.
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30
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Pagba CV, Lane SM, Wachsmann-Hogiu S. Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2010; 2:207-17. [PMID: 21339867 PMCID: PMC3038437 DOI: 10.1364/boe.2.000207] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/07/2010] [Accepted: 12/18/2010] [Indexed: 05/02/2023]
Abstract
Quadruplex structures are higher order structures formed by guanine-rich oligonucleotides. In the present study, temperature-induced conformational changes in the quadruplex structures of aptamers and other guanine-rich oligonucleotides are probed by Raman spectroscopy. In particular, dramatic changes in the fingerprint region are observed in the spectra of thrombin binding aptamer at higher temperatures. These changes are accompanied by a decrease in the intensity of the 1480 cm(-1) peak (attributed to C8 = N7-H2), which is diagnostic of the quadruplex structure. We also show that these changes can be reversed (to a certain extent) by addition of K(+) ions.
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Affiliation(s)
- Cynthia V. Pagba
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
| | - Stephen M. Lane
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Neurological Surgery, University of California Davis, 4860 Y Street, Sacramento, CA 95817
| | - Sebastian Wachsmann-Hogiu
- Center for Biophotonics Science and Technology, University of California Davis, 2700 Stockton Blvd., Suite 1400, Sacramento, CA 95817
- Department of Pathology and Internal Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817
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31
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Pagba CV, Lane SM, Cho H, Wachsmann-Hogiu S. Direct detection of aptamer-thrombin binding via surface-enhanced Raman spectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:047006. [PMID: 20799837 DOI: 10.1117/1.3465594] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this study, we exploit the sensitivity offered by surface-enhanced Raman scattering (SERS) for the direct detection of thrombin using the thrombin-binding aptamer (TBA) as molecular receptor. The technique utilizes immobilized silver nanoparticles that are functionalized with thiolated thrombin-specific binding aptamer, a 15-mer (5'-GGTTGGTGTGGTTGG-3') quadruplex forming oligonucleotide. In addition to the Raman vibrational bands corresponding to the aptamer and blocking agent, new peaks (mainly at 1140, 1540, and 1635 cm(-1)) that are characteristic of the protein are observed upon binding of thrombin. These spectral changes are not observed when the aptamer-nanoparticle assembly is exposed to a nonbinding protein such as bovine serum albumin (BSA). This methodology could be further used for the development of label-free biosensors for direct detection of proteins and other molecules of interest for which aptamers are available.
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Affiliation(s)
- Cynthia V Pagba
- University of California, Davis, Sacramento, California 95817, USA.
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32
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Abu-Ghazalah RM, Irizar J, Helmy AS, Macgregor RB. A study of the interactions that stabilize DNA frayed wires. Biophys Chem 2010; 147:123-9. [PMID: 20122787 DOI: 10.1016/j.bpc.2010.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
Abstract
Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine-guanine interactions. To probe the hydrogen bonding involved in the stabilization of d(A(15)G(15)) frayed wires, we used Raman spectroscopy in which the DNA sample is held in photonic crystal fibers. This technique significantly enhances the signals thus allowing the use of very low laser power. Based on our results for d(A(15)G(15)) and those of incorporating the isoelectronic guanine analog pyrazolo[3,4,-d]pyrimidine or PPG, into a frayed wire-forming sequence, we provide evidence that these structures are based on the G-quadruplex model. Furthermore, from the Raman spectrum, we observed markers that are consistent with the presence of deoxyguanosine residues in the syn conformation, this suggests the presence of anti-parallel G-quadruplexes. To identify the species that contain syn guanine residues, we used circular dichroism and gel electrophoresis to study an ODN in which all of the guanine residues were brominated, d(A(15)(8-Br)G(15)). In the presence of potassium, d(A(15)(8-Br)G(15)) forms what appears to be an anti-parallel dimeric G-quadruplex. To our knowledge, this is the first report of a DNA sequence having all its guanine residues replaced by 8-bromo-guanine and maintaining its ability to form a G-quadruplex structure.
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Affiliation(s)
- Rashid M Abu-Ghazalah
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario, Canada
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33
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Stepánek J, Kopecký V, Mezzetti A, Turpin PY, Paulin D, Alpert B, Zentz C. Structural and dynamic changes of the serum response element and the core domain of serum response factor induced by their association. Biochem Biophys Res Commun 2009; 391:203-8. [PMID: 19903461 DOI: 10.1016/j.bbrc.2009.11.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Accepted: 11/05/2009] [Indexed: 11/26/2022]
Abstract
Transcriptional activity of serum response factor (SRF) is dependent on its binding to the CC(A/T)(6)GG box (CArG box) of serum response element (SRE). By Raman spectroscopy, we carried out a comparative analysis, in solution, of the complexes obtained from the association of core-SRF with 20-mer SREs bearing wild-type and mutated c-fos CArG boxes. In case of association with the wild type c-fos CArG box, the complex does not bring out the expected Raman signature of a stable bending of the targeted SRE but keeps a bend-linear conformer oligonucleotide interconversion. The linear conformer population is larger than that of free oligonucleotide. In the core-SRF moiety of the wild-type complex a large spectral change associated with the CO-groups from Asp and/or Glu residues shows that their ionization states and the strength of their interactions decrease as compared to those of mutated non-specific complexes. Structural constraints evidenced on the free core-SRF are released in the wild-type complex and environmental heterogeneities appear in the vicinity of Tyr residues, due to higher water molecule access. The H-bonding configuration of one Tyr OH-group, in average, changes with a net transfer from H-bond acceptor character to a combined donor and acceptor character. A charge repartition distributed on both core-SRF and targeted SRE stabilizes the specific complex, allowing the two partners to experience a variety of conformations.
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Affiliation(s)
- Josef Stepánek
- Laboratoire Acides Nucléiques & Biophotonique, FRE CNRS 3207, Université Pierre et Marie Curie, 5 rue Henri Desbruères, 91030 Evry, France
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34
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Benevides JM, Danahy J, Kawakami J, Thomas GJ. Mechanisms of Specific and Nonspecific Binding of Architectural Proteins in Prokaryotic Gene Regulation. Biochemistry 2008; 47:3855-62. [DOI: 10.1021/bi7009426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James M. Benevides
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Danahy
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Kawakami
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - George J. Thomas
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
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35
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Paramasivan S, Rujan I, Bolton PH. Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding. Methods 2008; 43:324-31. [PMID: 17967702 DOI: 10.1016/j.ymeth.2007.02.009] [Citation(s) in RCA: 422] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 02/14/2007] [Indexed: 10/22/2022] Open
Abstract
Circular dichroism, CD, spectra can be used to gain information about quadruplex structures of DNAs as well as the effects of sequence, cations, chemical modification and ligand binding on quadruplex structure. There is not yet a validated approach to calculate a CD spectrum from a quadruplex structure nor is their one to go from a CD spectrum to a structure. However, it is possible to empirically correlate CD spectra features with quadruplex structural type in many cases. In this article four case studies are presented to indicate the strengths and limitations of CD in investigations of the properties of quadruplex structures formed by telomere repeat sequences. The case studies include determination of the quadruplex structural type present as a function of potassium concentration, the effect of sequence on the equilibrium between quadruplex structural types as a function of potassium concentration, the effect of ligand binding on quadruplex structure and the effect of 5' phosphorylation on quadruplex structural type.
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36
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Pedroso IM, Duarte LF, Yanez G, Burkewitz K, Fletcher TM. Sequence specificity of inter- and intramolecular G-quadruplex formation by human telomeric DNA. Biopolymers 2007; 87:74-84. [PMID: 17549693 DOI: 10.1002/bip.20790] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human telomeric DNA consists of tandem repeats of the sequence 5'-d(TTAGGG)-3'. Guanine-rich DNA, such as that seen at telomeres, forms G-quadruplex secondary structures. Alternative forms of G-quadruplex structures can have differential effects on activities involved in telomere maintenance. With this in mind, we analyzed the effect of sequence and length of human telomeric DNA on G-quadruplex structures by native polyacrylamide gel electrophoresis and circular dichroism. Telomeric oligonucleotides shorter than four, 5'-d(TTAGGG)-3' repeats formed intermolecular G-quadruplexes. However, longer telomeric repeats formed intramolecular structures. Altering the 5'-d(TTAGGG)-3' to 5'-d(TTAGAG)-3' in any one of the repeats of 5'-d(TTAGGG)(4)-3' converted an intramolecular structure to intermolecular G-quadruplexes with varying degrees of parallel or anti-parallel-stranded character, depending on the length of incubation time and DNA sequence. These structures were most abundant in K(+)-containing buffers. Higher-order structures that exhibited ladders on polyacrylamide gels were observed only for oligonucleotides with the first telomeric repeat altered. Altering the sequence of 5'-d(TTAGGG)(8)-3' did not result in the substantial formation of intermolecular structures even when the oligonucleotide lacked four consecutive telomeric repeats. However, many of these intramolecular structures shared common features with intermolecular structures formed by the shorter oligonucleotides. The wide variability in structure formed by human telomeric sequence suggests that telomeric DNA structure can be easily modulated by proteins, oxidative damage, or point mutations resulting in conversion from one form of G-quadruplex to another.
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Affiliation(s)
- Ilene M Pedroso
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101-6129, USA
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37
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Pedroso IM, Duarte LF, Yanez G, Baker AM, Fletcher TM. Induction of parallel human telomeric G-quadruplex structures by Sr(2+). Biochem Biophys Res Commun 2007; 358:298-303. [PMID: 17485073 DOI: 10.1016/j.bbrc.2007.04.126] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 04/18/2007] [Indexed: 11/25/2022]
Abstract
Human telomeric DNA forms G-quadruplex secondary structures, which can inhibit telomerase activity and are targets for anti-cancer drugs. Here we show that Sr(2+) can induce human telomeric DNA to form both inter- and intramolecular structures having characteristics consistent with G-quadruplexes. Unlike Na(+) or K(+), Sr(2+) facilitated intermolecular structure formation for oligonucleotides with 2 to 5 5'-d(TTAGGG)-3' repeats. Longer 5'-d(TTAGGG)-3' oligonucleotides formed exclusively intramolecular structures. Altering the 5'-d(TTAGGG)-3' to 5'-d(TTAGAG)-3' in the 1st, 3rd, or 4th repeats of 5'-d(TTAGGG)(4)-3' stabilized the formation of intermolecular structures. However, a more compact, intramolecular structure was still observed when the 2nd repeat was altered. Circular dichroism spectroscopy results suggest that the structures were parallel-stranded, distinguishing them from similar DNA sequences in Na(+) and K(+). This study shows that Sr(2+), promotes parallel-stranded, inter- and intramolecular G-quadruplexes that can serve as models to study DNA substrate recognition by telomerase.
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Affiliation(s)
- Ilene M Pedroso
- Department of Biochemistry and Molecular Biology, University of Miami, School of Medicine, P.O. Box 016129 (R629), Miami, FL 33101-6129, USA
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38
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Stepanek J, Vincent M, Turpin PY, Paulin D, Fermandjian S, Alpert B, Zentz C. C-->G base mutations in the CArG box of c-fos serum response element alter its bending flexibility. Consequences for core-SRF recognition. FEBS J 2007; 274:2333-48. [PMID: 17403043 DOI: 10.1111/j.1742-4658.2007.05768.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
By binding to the CArG box sequence, the serum response factor (SRF) activates several muscle-specific genes, as well as genes that respond to mitogens. The core domain of the SRF (core-SRF) binds as a dimer to the CArG box C-5C-4A-3T-2A-1T+1T+2A+3G+4G+5 of the c-fos serum response element (SREfos). However, previous studies using 20-mer DNAs have shown that the binding stoichiometry of core-SRF is significantly altered by mutations C-5-->G (SREGfos) and C-5C-4-->GG (SREGGfos) of the CArG box [A Huet, A Parlakian, M-C Arnaud, J-M Glandières, P Valat, S Fermandjian, D Paulin, B Alpert & C Zentz (2005) FEBS J272, 3105-3119]. To understand these effects, we carried out a comparative analysis of the three 20-mer DNAs SREfos, SREGfos and SREGGfos in aqueous solution. Their CD spectra were of the B-DNA type with small differences generated by variations in the mutual arrangement of the base pairs. Analysis by singular value decomposition of a set of Raman spectra recorded as a function of temperature, revealed a premelting transition associated with a conformational shift in the DNA double helices from a bent to a linear form. Time-resolved fluorescence anisotropy shows that the fluorescein reporter linked to the oligonucleotide 5'-ends experiences twisting motions of the double helices related to the interconversion between bent and linear conformers. The three SREs present various bent populations submitted, however, to particular internal dynamics, decisive for the mutual adjustment of binding partners and therefore specific complex formation.
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Affiliation(s)
- Josef Stepanek
- Laboratoire de Biophysique Moléculaire Cellulaire & Tissulaire, Université Pierre et Marie Curie, Evry, France
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Taleb A, Diamond J, McGarvey JJ, Beattie JR, Toland C, Hamilton PW. Raman Microscopy for the Chemometric Analysis of Tumor Cells. J Phys Chem B 2006; 110:19625-31. [PMID: 17004830 DOI: 10.1021/jp061981q] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Raman spectroscopy is recognized as a tool for chemometric analysis of biological materials due to the high information content relating to specific physical and chemical qualities of the sample. Thirty cells belonging to two different prostatic cell lines, PNT1A (immortalized normal prostate cell line) and LNCaP (malignant cell line derived from prostate metastases), were mapped using Raman microscopy. A range of spectral preprocessing methods (partial least-squares discriminant analyses (PLSDAs), principal component analyses (PCAs), and adjacent band ratios (ABRs)) were compared for input into linear discriminant analysis to model and classify the two cell lines. PLSDA and ABR were able to correctly classify 100% of cells into benign and malignant groups, while PLSDA correctly classified a greater proportion of individual spectra. PCA was used to image the distribution of various biochemicals inside each cell and confirm differences in composition/distribution between benign and malignant cell lines. This study has demonstrated that PLSDAs and ABRs of Raman data can identify subtle differences between benign and malignant prostatic cells in vitro.
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Affiliation(s)
- Ahcene Taleb
- Biomedical Imaging and Informatics Research Group, Department of Pathology, Queen's University Belfast, Grosvenor Road, Belfast BT12 6BL, Northern Ireland, United Kingdom.
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Rujan IN, Meleney JC, Bolton PH. Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium. Nucleic Acids Res 2005; 33:2022-31. [PMID: 15817566 PMCID: PMC1074753 DOI: 10.1093/nar/gki345] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The circular dichroism, CD, spectra of the telomere repeats of vertebrates, d(TTAGGG), indicate that parallel type quadruplex structures or disordered single-stranded structures are formed in low salt. Anti-parallel quadruplex structures are favored in the presence of high concentrations, 140 mM, of sodium. External loop, also known as propeller, parallel type structures are favored in the presence of high concentrations, 100 mM, of potassium in the presence of either 5 or 140 mM sodium. The cation dependence of the CD spectra of the vertebrate telomere repeat DNAs is distinctly different from that of the telomere repeats of Tetrahymena and Oxytricha as well as that of the thrombin binding aptamer. These results indicate that the external loop structures may be present in vertebrate telomeres under the conditions of high potassium and low sodium concentration found in nuclei.
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Affiliation(s)
| | | | - Philip H. Bolton
- To whom correspondence should be addressed. Tel: +1 860 685 2668; Fax: +1 860 685 2211;
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41
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Breuzard G, Millot JM, Riou JF, Manfait M. Selective interactions of ethidiums with G-quadruplex DNA revealed by surface-enhanced Raman scattering. Anal Chem 2004; 75:4305-11. [PMID: 14632150 DOI: 10.1021/ac034123o] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes formed between G-quadruplex (G4)-conformed oligonucleotides and four ethidium derivatives were studied by surface-enhanced Raman spectroscopy (SERS) to detail the topology of complexes that support a G4 stabilization. Ethidium bromide (EB), which presents a weak ability to stabilize oligonucleotides in G4 conformation, displayed no SERS intensity modification when bound to G4, as compared with the free EB. Three ethidium derivatives have been selected due to their higher ability to stabilize G4 than EB. Bound with G4-conformed oligonucleotides, SERS intensity of these three ethidiums decreased by factors of about 6, 3.5, and 15. The high SERS quenching was interpreted as a loss of accessibility of silver colloids for G4-bound ethidiums. This could represent a new selective parameter useful to identify G4-stabilizing molecules. To apraise the role of the oligonucleotide sequence on the interaction mode, complexes were formed with eight G4-conformed oligonucleotides in which the three loops were either 5'-TTA-3' or 5'-AAA-3'. Spectra of ethidiums were sensitive to both lateral loops, opposite to the 3' and 5' G4 ends. The sequence of these loops are believed to be selective in the interaction mode of ethidiums for G4.
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Affiliation(s)
- Gilles Breuzard
- Unité MéDIAN CNRS UMR 6142, IFR53, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims, France
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42
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Phan AT, Modi YS, Patel DJ. Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) Sequence interconverts between asymmetric dimeric G-quadruplexes in solution. J Mol Biol 2004; 338:93-102. [PMID: 15050825 PMCID: PMC4690524 DOI: 10.1016/j.jmb.2004.02.042] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 02/17/2004] [Accepted: 02/18/2004] [Indexed: 10/26/2022]
Abstract
Recently, the two-repeat human telomeric d(TAGGGTTAGGGT) sequence has been shown to form interconverting parallel and antiparallel G-quadruplex structures in solution. Here, we examine the structures formed by the two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) sequence, which differs from the human sequence only by one G-for-A replacement in each repeat. We show by NMR that this sequence forms two novel G-quadruplex structures in Na+-containing solution. Both structures are asymmetric, dimeric G-quadruplexes involving a core of four stacked G-tetrads and two edgewise loops. The adjacent strands of the G-tetrad core are alternately parallel and antiparallel. All G-tetrads adopt syn.syn.anti.anti alignments, which occur with 5'-syn-anti-syn-anti-3' alternations along G-tracks. In the first structure (head-to-head), two loops are at one end of the G-tetrad core; in the second structure (head-to-tail), two loops are located on opposite ends of the G-tetrad core. In contrast to the human telomere counterpart, the proportions of the two forms here are similar for a wide range of temperatures; their unfolding rates are also similar, with an activation enthalpy of 153 kJ/mol.
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Affiliation(s)
- Anh Tuân Phan
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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Abstract
The telomere is a nucleoprotein complex located at the ends of eukaryotic chromosomes. It is essential for maintaining the integrity of the genome. It is not a linear structure and, for much of the cell cycle, telomeric DNA is maintained in a loop structure, which serves to protect the vulnerable ends of chromosomes. Many of the key proteins in the telomere have been identified, although their interplay is still imperfectly understood and structural data are only available on a few. Telomeric DNA itself comprises simple guanine-rich repeats for most of its length, culminating in a short overhang of single-stranded sequence at the extreme 3' ends. This can, at least in vitro, fold into a wide variety of four-stranded quadruplex structures, many of whose arrangements are being revealed by crystallographic and NMR studies.
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Affiliation(s)
- Stephen Neidle
- Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, WC1N 1AX, London, UK.
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