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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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Zhong Y, Wu J, Pan X, Liu B, Wang L. Aptamer-functionalized polydiacetylene biosensor for the detection of three foodborne pathogens. ANAL SCI 2024; 40:199-211. [PMID: 37856010 DOI: 10.1007/s44211-023-00445-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]
Abstract
Rapid, simple and sensitive screening of foodborne pathogens is of great significance to ensure food safety. In this study, an aptamer-functionalized polydiacetylene (Apta-PDA) biosensor was developed for the detection of E. coli O157:H7, S. typhimurium or V. parahaemolyticus. First, aptamers responding to the target bacteria were modified on the surface of magnetic beads by covalent binding to form MBs-oligonucleotide conjugates for bacterial enrichment. Then, an Apta-PDA biosensor was obtained by connecting the aptamers to the PDA nanovesicles using the carbodiimide method. Molecular recognition occurred in the presence of the target bacteria, whereby the aptamer folded into a sequence-defined unique structure, resulting in an MBs-Apta/bacteria/Apta-PDA sandwich structure. Due to the optical properties of PDA, the blue-red transition of the detection system could be observed by the naked eye and quantified by the colorimetric response percentage (CR%). Under optimized conditions, the detection limits of E. coli O157:H7, S. typhimurium and V. parahaemolyticus were 39, 60 and 60 CFU/ml, respectively, with a selectivity of 100% and a reaction time of 30 min. Compared with the gold standard method, the accuracy of the three target bacteria detection reached 98%, 97.5% and 97%, respectively, and the sensitivity and specificity were both greater than 90%. The entire detection process was rapid and easy to execute without any special equipment, making this technology particularly suitable for resource-poor laboratories or regions.
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Affiliation(s)
- Yuhong Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China.
| | - Jiaqi Wu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310059, People's Republic of China
| | - Xiaoyan Pan
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
| | - Bo Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
| | - Lin Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, People's Republic of China
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Yu CN, Hiramatsu H. Resonance Hyper-Raman Spectroscopy of Nucleotides and Polynucleotides. J Phys Chem B 2022; 126:9309-9315. [PMID: 36326439 DOI: 10.1021/acs.jpcb.2c05673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We applied 532 nm-excited two-photon resonance hyper-Raman (RHR) spectroscopy to nucleotides (dA, dG, dT, and dC) to obtain fundamental knowledge about their spectral patterns. The RHR spectrum of each nucleotide exhibited various modes of the purine and pyrimidine rings, showing the ability to acquire the structural information on the chromophore. The band positions of the RHR spectrum and the 266 nm-excited one-photon UV-resonance Raman (UVRR) spectrum were identical, while the intensity patterns differed. The peak assignments of the RHR bands were given by analogy to the UVRR spectrum. In examining the polynucleotides, which form a double-stranded helix through intermolecular hydrogen bonds, some RHR bands were found to be available as structural markers. Moreover, several overtone and combination bands were detected above 2000 cm-1. The frequencies of dA and dG were accounted for by considering the involvement of the vibration of dA at 1579 cm-1 and that of dG at 1482 cm-1, respectively. Multiple vibronically active modes were seen for dT and dC. HR spectroscopy offers unique information on the fundamental, combination, and overtone modes of dA and dG, of which the multiple electronic states are involved in the resonance process.
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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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5
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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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Sofińska K, Wilkosz N, Szymoński M, Lipiec E. Molecular Spectroscopic Markers of DNA Damage. Molecules 2020; 25:E561. [PMID: 32012927 PMCID: PMC7037412 DOI: 10.3390/molecules25030561] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage.
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Affiliation(s)
| | | | | | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland; (K.S.); (N.W.); or (M.S.)
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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Mendoza-Figueroa JS, Badillo-Ramírez I, Kvarnheden A, Rosas-Ramírez DG, Rodríguez-Negrete EA, Méndez-Lozano J, Saniger JM, Soriano-García M. The Peptide AmPep1 Derived from Amaranth Recognizes the Replication Hairpin of TYLCV Disturbing Its Replication Process in Host Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9241-9253. [PMID: 31369258 DOI: 10.1021/acs.jafc.9b02526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antiviral compounds targeting viral replicative processes have been studied as an alternative for the control of begomoviruses. Previously, we have reported that the peptide AmPep1 has strong affinity binding to the replication origin sequence of tomato yellow leaf curl virus (TYLCV). In this study, we describe the mechanism of action of this peptide as a novel alternative for control of plant-infecting DNA viruses. When AmPep1 was applied exogenously to tomato and Nicotiana benthamiana plants infected with TYLCV, a decrease in the synthesis of the two viral DNA strands (CS and VS) was observed, with a consequent delay in the development of disease progress in treated plants. The chemical mechanism of action of AmPep1 was deduced using Raman spectroscopy and molecular modeling showing the formation of chemical interactions such as H bonds and electrostatic interactions and the formation of π-π interactions between both biomolecules contributing to tampering with the viral replication.
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Affiliation(s)
- José S Mendoza-Figueroa
- Departmento de Química de Biomacromoleculas, Instituto de Química , Universidad Nacional Autónoma de México , 04510 Mexico City , Mexico
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología , Universidad Nacional Autónoma de México , Circuíto Exterior S/N, Ciudad Universitaria , 04510 Mexico City , Mexico
| | - Anders Kvarnheden
- Department of Plant Biology , Swedish University of Agricultural Sciences , 75651 Uppsala , Sweden
| | - Daniel G Rosas-Ramírez
- Departmento de Química de Biomacromoleculas, Instituto de Química , Universidad Nacional Autónoma de México , 04510 Mexico City , Mexico
| | - Edgar A Rodríguez-Negrete
- CONACYT, Department of Agrobiotechnology, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional-Sinaloa , Instituto Politécnico Nacional , Guasave , 81049 Sinaloa , Mexico
| | - Jesús Méndez-Lozano
- Department of Agrobiotechnology, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional-Sinaloa , Instituto Politécnico Nacional , Guasave , 81049 Sinaloa , Mexico
| | - José M Saniger
- Instituto de Ciencias Aplicadas y Tecnología , Universidad Nacional Autónoma de México , Circuíto Exterior S/N, Ciudad Universitaria , 04510 Mexico City , Mexico
| | - Manuel Soriano-García
- Departmento de Química de Biomacromoleculas, Instituto de Química , Universidad Nacional Autónoma de México , 04510 Mexico City , Mexico
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Li Y, Lv J, Gu Q, Hu S, Li Z, Jiang X, Ying Y, Si G. Metadevices with Potential Practical Applications. Molecules 2019; 24:E2651. [PMID: 31336634 PMCID: PMC6680820 DOI: 10.3390/molecules24142651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
Metamaterials are "new materials" with different superior physical properties, which have generated great interest and become popular in scientific research. Various designs and functional devices using metamaterials have formed a new academic world. The application concept of metamaterial is based on designing diverse physical structures that can break through the limitations of traditional optical materials and composites to achieve extraordinary material functions. Therefore, metadevices have been widely studied by the academic community recently. Using the properties of metamaterials, many functional metadevices have been well investigated and further optimized. In this article, different metamaterial structures with varying functions are reviewed, and their working mechanisms and applications are summarized, which are near-field energy transfer devices, metamaterial mirrors, metamaterial biosensors, and quantum-cascade detectors. The development of metamaterials indicates that new materials will become an important breakthrough point and building blocks for new research domains, and therefore they will trigger more practical and wide applications in the future.
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Affiliation(s)
- Yafei Li
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Jiangtao Lv
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Qiongchan Gu
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Sheng Hu
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Zhigang Li
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Xiaoxiao Jiang
- College of Information Science and Engineering, Northeastern University, Shenyang 110004, China
| | - Yu Ying
- College of Information & Control Engineering, Shenyang Jianzhu University, Shenyang 110168, China.
| | - Guangyuan Si
- Melbourne Centre for Nanofabrication, Clayton, Victoria 3168, Australia.
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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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Raman Spectroscopy and Aptamers for a Label-Free Approach: Diagnostic and Application Tools. JOURNAL OF HEALTHCARE ENGINEERING 2019; 2019:2815789. [PMID: 31183028 PMCID: PMC6512054 DOI: 10.1155/2019/2815789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 01/04/2023]
Abstract
Raman spectroscopy is a powerful optical technique based on the inelastic scattering of incident light to assess the chemical composition of a sample, including biological ones. Medical diagnostic applications of Raman spectroscopy are constantly increasing to provide biochemical and structural information on several specimens, being not affected by water interference, and potentially avoiding the constraint of additional labelling procedures. New strategies have been recently developed to overcome some Raman limitations related, for instance, to the need to deal with an adequate quantity of the sample to perform a reliable analysis. In this regard, the use of metallic nanoparticles, the optimization of fiber optic probes, and other approaches can actually enhance the signal intensity compared to spontaneous Raman scattering. Moreover, to further increase the potential of this investigation technique, aptamers can be considered as a valuable means, being synthetic, short, single, or double-stranded oligonucleotides (RNAs or DNAs) that fold up into unique 3D structures to specifically bind to selected molecules, even at very low concentrations, and thus allowing an early diagnosis of a possible disease. Due to the paramount relevance of the topic, this review focuses on the main Raman spectroscopy techniques combined with aptamer arrays in the label-free mode, providing an overview on different applications to support healthcare management.
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Thrombin Assessment on Nanostructured Label-Free Aptamer-Based Sensors: A Mapping Investigation via Surface-Enhanced Raman Spectroscopy. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5293672. [PMID: 29750159 PMCID: PMC5884298 DOI: 10.1155/2018/5293672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 01/27/2023]
Abstract
Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal. The study presents the fabrication and characterization of a label-free aptamer sensor designed using a gold-coated silicon nanostructured substrate to map the target molecule by means of surface-enhanced Raman spectroscopy (SERS). As a proof, thrombin was used as a model at four different concentrations (i.e., 0.0873, 0.873, 8.73, and 87.3 nM). SERS mapping analysis was carried out considering each representative band of the aptamer-thrombin complex (centered at 822, 1140, and 1558 cm−1) and then combining them in order to acquire a comprehensive and unambiguous measure of the target. In both cases, a valuable correlation was evaluated, even if the first approach can suffer from some limitations in the third band related to lower definition of the characteristic peak compared to those in the other two bands.
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13
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Manukyan A, Tekin A. The intermolecular dimer potential for guanine. J Chem Phys 2017; 147:154311. [DOI: 10.1063/1.4998792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artür Manukyan
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey
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14
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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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15
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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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16
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Ou L, Chen Y, Su Y, Zou C, Chen Z. Detection of Genomic DNA Damage from Radiated Nasopharyngeal Carcinoma Cells Using Surface-Enhanced Raman Spectroscopy (SERS). APPLIED SPECTROSCOPY 2016; 70:1821-1830. [PMID: 27703049 DOI: 10.1177/0003702816671073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/09/2015] [Indexed: 05/19/2023]
Abstract
Structural changes and chemical modifications in DNA during interactions with X-ray radiation are still not clear within 48 h of incubation. We investigate genomic DNA from the radiated CNE2 cell line within 48 h of incubation using surface-enhanced Raman spectroscopy (SERS). Multivariate methods including principal component analysis (PCA) and random forest are proposed to explore the statistical significance before and after radiation. Our results show that intensities of several bands change after radiation, which indicates backbone damage and base-unstacking. Biological effects from DNA damage repairing process may be simultaneously stimulated and different from incubation time. Under doses of 10 Gy (with 24 and 48 h of incubation) and 20 Gy (with 48 h of incubation), the relative contents of C against T and A against G deviate obviously from the control level. Statistical results strengthen significantly the idea that modification in DNA bases is associated with the disruption of base-stacking in the DNA duplex. Our findings provide vital information for radiation-induced the DNA damage at the molecular level, which may provide insight into the effect and mechanism of anticarcinogens in tumor therapy.
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Affiliation(s)
- Lin Ou
- Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Yang Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Ying Su
- Laboratory of Radiobiology, Fujian Provincial Tumor Hospital, Fuzhou, China
| | - Changyan Zou
- Laboratory of Radiobiology, Fujian Provincial Tumor Hospital, Fuzhou, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
- Laboratory of Radiobiology, Fujian Provincial Tumor Hospital, Fuzhou, China
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17
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Sun K, Huang Q, Meng G, Lu Y. Highly Sensitive and Selective Surface-Enhanced Raman Spectroscopy Label-free Detection of 3,3',4,4'-Tetrachlorobiphenyl Using DNA Aptamer-Modified Ag-Nanorod Arrays. ACS APPLIED MATERIALS & INTERFACES 2016; 8:5723-5728. [PMID: 26849392 DOI: 10.1021/acsami.5b12866] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
An improved label-free approach for highly sensitive and selective detection of 3,3',4,4'-tetrachlorobiphenyl (PCB-77), a type of polychlorinated biphenyl, via surface-enhanced Raman spectroscopy (SERS) using DNA aptamer-modified Ag-nanorod arrays as the effective substrate is reported. The devised system consists of Ag-nanorod (Ag-NR) arrays with the PCB-77 binding aptamers anchored covalently to the Ag surfaces through a thiol linker. The aptamers are made of single-stranded DNA (ssDNA) oligomers, with one end standing on the Ag surface, and upon conjugation with PCB-77, the ssDNA molecules can change their conformation to hairpin loops, so that the Raman intensity of guanines at the other end of the DNA strand increases accordingly. As such, the intensity ratio I(656 cm(-1))/I(733 cm(-1)) increases concomitantly with the increase of the concentration of PCB-77, making the quantitative evaluation of trace amounts of PCB-77 attainable. Moreover, it is found that the DNA aptamer-based Ag-NR arrays can be more responsive with a lower and optimal density of the DNA molecules modified on the substrate surface, and the best sensitivity for detection of PCB-77 can be achieved with the lower detection limit approaching 3.3 × 10(-8) M. This work therefore demonstrates that the design of aptamer-modified Ag-NRs can be used as a practically promising SERS substrate for label-free trace detection of persistent organic pollutants (POPs) in the environment.
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Affiliation(s)
| | - Qing Huang
- University of Science and Technology of China , Hefei, Anhui 230026, People's Republic of China
| | - Guowen Meng
- University of Science and Technology of China , Hefei, Anhui 230026, People's Republic of China
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18
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Manukyan A, Tekin A. First principles potential for the cytosine dimer. Phys Chem Chem Phys 2015; 17:14685-701. [DOI: 10.1039/c5cp00553a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new first principles potential for the cytosine dimer.
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Affiliation(s)
- Artür Manukyan
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| | - Adem Tekin
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
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19
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Lu Y, Huang Q, Meng G, Wu L, Jingjing Z. Label-free selective SERS detection of PCB-77 based on DNA aptamer modified SiO₂@Au core/shell nanoparticles. Analyst 2014; 139:3083-7. [PMID: 24776730 DOI: 10.1039/c4an00197d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A label-free approach to selective detection of 3,3',4,4'-tetrachlorobiphenyl (PCB77) using aptamer modified silica-Au/core-shell nanoparticles (denoted as SiO2@Au core/shell NPs) through surface enhanced Raman scattering (SERS) spectroscopy was proposed. The devised system consisted of SiO2@Au core/shell NPs fixed on the amino-silane functionalized glass slides with the PCB77-binding aptamers attached covalently to the gold surfaces through a thiol linker. The aptamers made of single-stranded DNA (ssDNA) oligomers with one end standing on the Au surface changed the conformation upon conjugation with PCB77, which correspondingly caused the spectral response of the ssDNA oligomers. The intensity ratio I(660 cm(-1))/I(736 cm(-1)) decreased with the amount of PCB77 added, which thus allowed us to measure trace amounts of PCB77 in a selective and quantitative way. This work therefore demonstrates that the design of aptamer-modified SiO2@Au core/shell NPs can be utilized for label-free SERS detection of persistent organic pollutants (POPs) in the environment.
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Affiliation(s)
- Yilin Lu
- Key Laboratory of Ion Beam Bio-engineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, PR China.
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20
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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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21
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Panikkanvalappil SR, Mahmoud MA, Mackey MA, El-Sayed MA. Surface-enhanced Raman spectroscopy for real-time monitoring of reactive oxygen species-induced DNA damage and its prevention by platinum nanoparticles. ACS NANO 2013; 7:7524-33. [PMID: 23952174 DOI: 10.1021/nn403722x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have successfully demonstrated the potential of surface-enhanced Raman spectroscopy (SERS) in monitoring the real time damage to genomic DNA. To reveal the capabilities of this technique, we exposed DNA to reactive oxygen species (ROS), an agent that has been implicated in causing DNA double-strand breaks, and the various stages of free radical-induced DNA damage have been monitored by using SERS. Besides this, we showed that prompt DNA aggregation followed by DNA double-strand scission and residual damage to the DNA bases caused by the ROS could be substantially reduced by the protective effect of Pt nanocages and nearly cubical Pt nanopartcles. The antioxidant activity of Pt nanoparticles was further confirmed by the cell viability studies. On the basis of SERS results, we identified various stages involved in the mechanism of action of ROS toward DNA damage, which involves the DNA double-strand scission and its aggregation followed by the oxidation of DNA bases. We found that Pt nanoparticles inhibit the DNA double-strand scission to a significant extent by the degradation of ROS. Our method illustrates the capability of SERS technique in giving vital information about the DNA degradation reactions at molecular level, which may provide insight into the effectiveness and mechanism of action of many drugs in cancer therapy.
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Affiliation(s)
- Sajanlal R Panikkanvalappil
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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22
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Sengupta B, Pahari B, Blackmon L, Sengupta PK. Prospect of bioflavonoid fisetin as a quadruplex DNA ligand: a biophysical approach. PLoS One 2013; 8:e65383. [PMID: 23785423 PMCID: PMC3681855 DOI: 10.1371/journal.pone.0065383] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/24/2013] [Indexed: 01/30/2023] Open
Abstract
Quadruplex (G4) forming sequences in telomeric DNA and c-myc promoter regions of human DNA are associated with tumorogenesis. Ligands that can facilitate or stabilize the formation and increase the stabilization of G4 can prevent tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, steady state and time-resolved fluorescence measurements provide important structural and dynamical insights into the free and bound states of the therapeutically potent plant flavonoid fisetin (3,3',4',7-tetrahydroxyflavone) in a G4 DNA matrix. The excited state intra-molecular proton transfer (ESPT) of fisetin plays an important role in observing and understanding the binding of fisetin with the G4 DNA. Differential absorption spectra, thermal melting, and circular dichroism spectroscopic studies provide evidences for the formation of G4 DNA and size exclusion chromatography (SEC) proves the binding and 1∶1 stoichiometry of fisetin in the DNA matrix. Comparative analysis of binding in the presence of EtBr proves that fisetin favors binding at the face of the G-quartet, mostly along the diagonal loop. Time resolved fluorescence anisotropy decay analysis indicates the increase in the restrictions in motion from the free to bound fisetin. We have also investigated the fingerprints of the binding of fisetin in the antiparallel quadruplex using Raman spectroscopy. Preliminary results indicate fisetin to be a prospective candidate as a G4 ligand.
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Affiliation(s)
- Bidisha Sengupta
- Department of Chemistry, Tougaloo College, Tougaloo, Mississippi, United States of America
| | - Biswapathik Pahari
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal, India
| | - Laura Blackmon
- Department of Chemistry, Tougaloo College, Tougaloo, Mississippi, United States of America
| | - Pradeep K. Sengupta
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, West Bengal, India
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23
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Panikkanvalappil SR, Mackey MA, El-Sayed MA. Probing the Unique Dehydration-Induced Structural Modifications in Cancer Cell DNA Using Surface Enhanced Raman Spectroscopy. J Am Chem Soc 2013; 135:4815-21. [DOI: 10.1021/ja400187b] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sajanlal R. Panikkanvalappil
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Megan A. Mackey
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Mostafa A. El-Sayed
- Laser Dynamics Laboratory,
School of Chemistry and
Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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24
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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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