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Choi N, Schlücker S. Convergence of Surface-Enhanced Raman Scattering with Molecular Diagnostics: A Perspective on Future Directions. ACS NANO 2024; 18:5998-6007. [PMID: 38345242 DOI: 10.1021/acsnano.3c11370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Molecular diagnostics (MD) is widely employed in multiple scientific disciplines, such as oncology, pathogen detection, forensic investigations, and the pharmaceutical industry. Techniques such as polymerase chain reaction (PCR) revolutionized the rapid and accurate identification of nucleic acids (DNA, RNA). More recently, CRISPR and its CRISPR-associated protein (Cas) have been a ground-breaking discovery that is the latest revolution in molecular biology, including MD. Surface-enhanced Raman scattering (SERS) is a very attractive alternative to fluorescence as the currently most widely used optical readout in MD. In this Perspective, milestones in the development of MD, SERS-PCR, and next-generation approaches to MD, such as Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), are briefly summarized. Our perspective on the future convergence of SERS with MD is focused on SERS-based CRISPR/Cas (SERS-CRISPR) since we anticipate many promising applications in this rapidly emerging field. We predict that major future developments will exploit the advantages of real-time monitoring with the superior brightness, photostability, and spectral multiplexing potential of SERS nanotags in an automated workflow for rapid assays under isothermal, amplification-free conditions.
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Affiliation(s)
- Namhyun Choi
- Physical Chemistry I, Department of Chemistry, and Center of Nanointegration Duisburg-Essen (CENIDE) & Center of Medical Biotechnology (ZMB), University of Duisburg-Essen (UDE), 45141 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry I, Department of Chemistry, and Center of Nanointegration Duisburg-Essen (CENIDE) & Center of Medical Biotechnology (ZMB), University of Duisburg-Essen (UDE), 45141 Essen, Germany
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Lee S, Johnson SN, Ellington TL, Mirsaleh-Kohan N, Tschumper GS. Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions. ACS OMEGA 2018; 3:12936-12943. [PMID: 31458017 PMCID: PMC6645001 DOI: 10.1021/acsomega.8b01895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 06/10/2023]
Abstract
This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.
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Affiliation(s)
- Suhwan
Paul Lee
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Sarah N. Johnson
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Thomas L. Ellington
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Nasrin Mirsaleh-Kohan
- Department
of Chemistry and Biochemistry, Texas Woman’s
University, Denton, Texas 76204, United States
| | - Gregory S. Tschumper
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
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Harroun SG. The Controversial Orientation of Adenine on Gold and Silver. Chemphyschem 2018; 19:1003-1015. [DOI: 10.1002/cphc.201701223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Scott G. Harroun
- Department of Chemistry; Université de Montréal; Montréal Québec H3C 3J7 Canada
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Fato TP, Zhao LJ, Essy KF, Li DW, Long YT. Spectroelectrochemical study of the AMP-Ag +and ATP-Ag +complexes using silver mesh electrodes. Analyst 2018; 143:2342-2348. [DOI: 10.1039/c8an00097b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, electrochemical reaction mechanism of adenosine monophosphate (AMP) and adenosine triphosphate (ATP) on a silver mesh was investigated in acetate buffer using spectroelectrochemical technique.
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Affiliation(s)
- Tano Patrice Fato
- Key Laboratory for Advanced Materials
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Li-Jun Zhao
- Key Laboratory for Advanced Materials
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Kouadio Fodjo Essy
- Key Laboratory for Advanced Materials
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Da-Wei Li
- Key Laboratory for Advanced Materials
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
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Using a silver-enhanced microarray sandwich structure to improve SERS sensitivity for protein detection. Anal Bioanal Chem 2014; 406:1885-94. [PMID: 24577570 DOI: 10.1007/s00216-013-7587-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 01/25/2023]
Abstract
A simple and sensitive method, based on surface-enhanced Raman scattering (SERS), for immunoassay and label-free protein detection is reported. A series of bowl-shaped silver cavity arrays were fabricated by electrodeposition using a self-assembled polystyrene spheres template. The reflection spectra of these cavity arrays were recorded as a function of film thickness, and then correlated with SERS enhancement using sodium thiophenolate as the probe molecule. The results reveal that SERS enhancement can be maximized when the frequency of both the incident laser and the Raman scattering approach the frequency of the localized surface plasmon resonance. The optimized array was then used as the bottom layer of a silver nanoparticle-protein-bowl-shaped silver cavity array sandwich. The second layer of silver was introduced by the interactions between the proteins in the middle layer of the sandwich architecture and silver nanoparticles. Human IgG bound to the surface of this microcavity array can retain its recognition function. With the Raman reporter molecules labeled on the antibody, a detection limit down to 0.1 ng mL(-1) for human IgG is easily achieved. Furthermore, the SERS spectra of label-free proteins (catalase, cytochrome C, avidin and lysozyme) from the assembled sandwich have excellent reproducibility and high quality. The results reveal that the proposed approach has potential for use in qualitative and quantitative detection of biomolecules.
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Calborean A, Buimaga-Iarinca L. DFT simulation of vibrational properties of adenine adsorbed on gold surface: The effect of periodic boundary conditions. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ostovarpour S, Blanch EW. Phosphorylation detection and characterization in ribonucleotides using Raman and Raman optical activity (ROA) spectroscopies. APPLIED SPECTROSCOPY 2012; 66:289-293. [PMID: 22449305 DOI: 10.1366/11-06467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Raman and Raman optical activity (ROA) spectra are presented for adenosine and seven of its derivative ribonucleotides. Both of these spectroscopic techniques are shown to be sensitive to the site and degree of phosphorylation, with a considerable number of marker bands being identified for these ribonucleotides. ROA spectra are shown to provide the most sensitive diagnostic tool for phosphorylation characterization and quantification.
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Affiliation(s)
- Saeideh Ostovarpour
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Lang XF, Yin PG, You TT, Jiang L, Guo L. A DFT investigation of surface-enhanced Raman scattering of adenine and 2'-deoxyadenosine 5'-monophosphate on Ag20 nanoclusters. Chemphyschem 2011; 12:2468-75. [PMID: 21735511 DOI: 10.1002/cphc.201100187] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/19/2011] [Indexed: 11/08/2022]
Abstract
We present a detailed analysis of the surface-enhanced Raman scattering (SERS) of adenine and 2'-deoxyadenosine 5'-monophosphate (dAMP) adsorbed on an Ag(20) cluster by using density functional theory. Calculated Raman spectra show that spectral features of all complexes depend greatly on adsorption sites of adenine and dAMP. The complexes consisting of adenine adsorbed on the Ag(20) cluster through N3 reproduce the measured SERS spectra in silver colloids, and thus demonstrated that adenine interacts with the silver surface via N3. We also investigate the SERS spectrum of adenine at the junction between two Ag(20) clusters and demonstrate that adenine can bind to the clusters through N3 and the external amino group, while dAMP can be adsorbed on the cluster in an end-on orientation with the ribose and phosphate groups near to or away from the silver cluster. In contrast to the adenine-Ag(20) complexes, the dAMP-Ag(20) complexes produce new and strong bands in the low- or high-wavenumber region of the Raman spectra, due to vibrations of the ribose and phosphate groups. Furthermore, the spectrum of dAMP bound to the Ag(20) cluster via N7 approaches the experimental SERS spectra on silver colloids.
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Affiliation(s)
- Xiu-Feng Lang
- School of Chemistry and Environment, Beihang University, Beijing 100191, China
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Sun Y, Xu F, Zhang Y, Shi Y, Wen Z, Li Z. Metallic nanostructures assembled by DNA and related applications in surface-enhancement Raman scattering (SERS) detection. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm11640a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Séquaris JM, Koglin E, Valenta P, W. Nürnberg H. Surface-Enhanced Raman Scattering (SERS) Spectroscopy of Nucleic Acids. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19810850616] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hayazawa N, Watanabe H, Saito Y, Kawata S. Towards atomic site-selective sensitivity in tip-enhanced Raman spectroscopy. J Chem Phys 2006; 125:244706. [PMID: 17199367 DOI: 10.1063/1.2423015] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Depending on each nitrogen atom of adenine molecule to which a silver atom of a metallic tip approaches, tip-enhanced near-field Raman spectroscopy may show a potential to achieve atomic site-selective detection sensitivity. Molecular vibrational calculations show that silver atoms and adenine molecule create several isomers generating specific vibrational modes of each isomer that are shifted or not observable in isolated adenine molecule itself. Here, the authors observe the specific vibrational modes and spectral shifts of isomers experimentally and are in good agreement with their calculations.
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Bell SEJ, Sirimuthu NMS. Surface-Enhanced Raman Spectroscopy (SERS) for Sub-Micromolar Detection of DNA/RNA Mononucleotides. J Am Chem Soc 2006; 128:15580-1. [PMID: 17147354 DOI: 10.1021/ja066263w] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Surface-enhanced Raman (SER) spectra of all the DNA/RNA mononucleotides have been obtained with high sensitivity using citrate-reduced silver colloids aggregated with MgSO4, rather than the more usual halide ions, which were found to prevent enhancement of these compounds. The SERS spectra of adenine, guanine, thymine, cytosine, and uracil were recorded along with their corresponding nucleosides and 5'-deoxynucleotides. For the cytosine series, all three spectra had similar relative band intensities but the spectra of adenine were different from those of adenosine and dAMP, probably due to differences in orientation on the surface. No enhanced bands from the phosphate or sugar groups were observed. There were general similarities between the SERS spectra of the purine mononucleotides and the pyrimidine mononucleotides, but the spectra were sufficiently different to allow each of them to be distinguished. This method can therefore be used for high sensitivity, label-free identification of mononucleotides.
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Affiliation(s)
- Steven E J Bell
- Innovative Molecular Materials Group, School of Chemistry & Chemical Engineering, Queen's University, Belfast BT9 5AG, Northern Ireland.
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Reyes-Goddard JM, Barr H, Stone N. Photodiagnosis using Raman and surface enhanced Raman scattering of bodily fluids. Photodiagnosis Photodyn Ther 2005; 2:223-33. [DOI: 10.1016/s1572-1000(05)00066-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 07/14/2005] [Accepted: 07/15/2005] [Indexed: 10/25/2022]
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14
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Lazorenko-Manevich RM. Adatom Hypothesis as a Predominant Mechanism of Surface Enhanced Raman Scattering: A Review of Experimental Argumentation. RUSS J ELECTROCHEM+ 2005. [DOI: 10.1007/s11175-005-0141-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Giese B, McNaughton D. Surface-Enhanced Raman Spectroscopic Study of Uracil. The Influence of the Surface Substrate, Surface Potential, and pH. J Phys Chem B 2002. [DOI: 10.1021/jp011986h] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernd Giese
- School of Chemistry and Centre for Biospectroscopy, Monash University, Wellington Rd, Clayton, Victoria, Australia
| | - Don McNaughton
- School of Chemistry and Centre for Biospectroscopy, Monash University, Wellington Rd, Clayton, Victoria, Australia
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Giese B, McNaughton D. Surface-Enhanced Raman Spectroscopic and Density Functional Theory Study of Adenine Adsorption to Silver Surfaces. J Phys Chem B 2001. [DOI: 10.1021/jp010789f] [Citation(s) in RCA: 212] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bernd Giese
- School of Chemistry, Monash University, Wellington Rd, Clayton, Victoria, Australia
| | - Don McNaughton
- School of Chemistry, Monash University, Wellington Rd, Clayton, Victoria, Australia
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Yi-Jin Xiao, Ting W, Xun-Qing Wang, Xiao-Xia G. Surface-enhanced near-infrared Raman spectroscopy of nicotinamide adenine dinucleotides on a gold electrode. J Electroanal Chem (Lausanne) 1997. [DOI: 10.1016/s0022-0728(97)00147-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Surface-enhanced Raman spectroscopy of free bilirubin and bilirubin complexes with transition metals iron(II), nickel(II) and cobalt(II). ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0584-8539(94)80141-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Surface enhanced Raman scattering (SERS) of nucleic acids adsrobed on colloidal silver particles. J Mol Struct 1986. [DOI: 10.1016/0022-2860(86)87041-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Applications of surface-enhanced raman scattering (SERS) spectroscopy in biochemistry. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf00593857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Nichols H, Hexter RM. Vibrational frequencies of halogen atoms adsorbed on silver metal surfaces. J Chem Phys 1981. [DOI: 10.1063/1.441252] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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398 - Electrochemical behavior of mono- and oligonucleotides. VIII. Voltammetric studies on the interfacial behaviour of mono-, di- and triphosphate of cytidine. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/0302-4598(80)80036-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ervin K, Koglin E, Sequaris J, Valenta P, Nürnberg H. Surface enhanced Raman spectra of nucleic acid components adsorbed at a silver electrode. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/s0022-0728(80)80446-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Temerk Y, Valenta P, Nürnberg H. Electrochemical behavior of mono- and oligonucleotides. VIII. Voltammetric studies on the interfacial behavior of mono-, Di- and triphosphate of cytidine. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/s0022-0728(80)80300-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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