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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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2
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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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3
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In situ SERS probing of nano-silver coated individual yeast cells. Biosens Bioelectron 2013; 49:536-41. [DOI: 10.1016/j.bios.2013.05.053] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/20/2013] [Accepted: 05/30/2013] [Indexed: 01/05/2023]
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4
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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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5
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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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6
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Takamura K, Kusu F. Electro-optical reflection methods for studying bioactive substances at electrode-solution interfaces--an approach to biosurface behavior. METHODS OF BIOCHEMICAL ANALYSIS 2006; 32:155-214. [PMID: 3553854 DOI: 10.1002/9780470110539.ch3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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7
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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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8
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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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9
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Polarography of DNA. Retrospective View. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1871-0069(05)01001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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11
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Wu S, Huang J, Li C, Liang Y. Fourier transform surface-enhanced Raman scattering of single-layer nucleolipid Langmuir–Blodgett films on silver island film substrates. J Colloid Interface Sci 2004; 270:309-14. [PMID: 14697695 DOI: 10.1016/j.jcis.2003.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Surface-enhanced Raman scattering (SERS) spectra of four amphiphilic nucleolipids in single-layer Langmuir-Blodgett (LB) films deposited on silver island film substrates from pure water and complementary nucleotide-containing subphase and corresponding powder normal Raman spectra were obtained. The analysis of these spectra indicates that the SERS effect is mainly caused by a charge-transfer mechanism, and only the nucleobase headgroup moieties and complementary bases combined with them through hydrogen bonds, which are directly in contact with the silver island film substrates, could be enhanced. For the amphiphilic nucleolipids with the identical nucleobase headgroups, the SERS spectra of the LB films are similar, implying that the orientations of these nucleobase moieties on the silver substrates are analogous. However, the nucleobase takes different orientations on the silver substrates before and after complementary binding. The nucleobases in the LB films deposited from pure water are nearly lying flat on the silver surface, while the complementary binding pairs transferred from the air/water interface tend to take an end-on orientation on the metal surface.
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Affiliation(s)
- Sanxie Wu
- Key Laboratory for Mesoscopic Chemistry of Ministry of Education, Nanjing University, 210093 Nanjing, People's Republic of China
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12
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Li C, Huang J, Liang Y. Spectroscopic studies on molecular recognition capabilities of a nucleolipid bearing thymine headgroup to adenosine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:1587-1593. [PMID: 11471710 DOI: 10.1016/s1386-1425(01)00392-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Langmuir-Blodgett (LB) films of octadecanoyl ester of 1-(2-carboxyethyl) thymine deposited from pure water and aqueous adenosine subphases were investigated by ultraviolet-visible (UV-vis), Fourier transform infrared-attenuated total reflection (FTIR-ATR), and Fourier transform surface-enhanced Raman scattering (FT-SERS) spectroscopy. The obtained spectral results indicate that the adenosine molecules in the subphase can be transferred onto solid substrates by LB techniques as a result of the formation of base pairs at the air/water interface. UV-vis spectra alternations indicated that, with increasing adenosine concentration in subphase, more adenosine molecules were recognized by nucleolipid monolayer and were transferred onto the quartz substrates. The closed-packing of the constituent molecules facilitates the photodimerization of the thymine moieties in the headgroup under ultraviolet irradiation. FTIR-ATR results suggest that the hydrocarbon chains of nucleolipid in the LB films deposited from pure water and aqueous adenosine take on a close-packed all trans conformation. By analyzing the FT-SERS spectra results, it can be deduced that the orientation of nucleobase in the headgroup is different before and after the recognition effect occurred. For LB film deposited from pure water, the nucleobases are lying flat on the silver substrates; whereas for LB film deposited from aqueous adenosine, the base pairs take an end-on adsorption on silver substrate.
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Affiliation(s)
- C Li
- Lab of Mesoscopic Materials and Chemistry and State Key Laboratory of Coordination Chemistry, Nanjing University, People's Republic of China
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14
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Shen H, Xia J, Yang H, Luo Y. Hydrolysis of oligodeoxynucleotide phosphodiester linkages. ACTA ACUST UNITED AC 2001. [DOI: 10.1007/bf02879534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Fan C, Song H, Hu X, Li G, Zhu J, Xu X, Zhu D. Voltammetric response and determination of DNA with a silver electrode. Anal Biochem 1999; 271:1-7. [PMID: 10360998 DOI: 10.1006/abio.1999.4102] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A current from DNA was obtained using a silver electrode with low overpotentials for the first time. Experimental results revealed that the voltammetric response of DNA was attributed to the redox reactions of purine bases. It was also shown that such a method provided a convenient and practical way to determine DNA. A linear dependence of the peak currents on ssDNA concentrations was observed in the range 0.5-2.5 microg/mL. The relative standard deviation was 3.5% for six successive determinations at 0.5 microg/mL. The detection limit was 50 ng/mL. Influence of the structure and the length of the nucleic acids on their electrochemical behavior was discussed. In view of the merits of the silver electrode, this technique might provide new possibilities for further electrochemical research and determination of nucleic acids.
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Affiliation(s)
- C Fan
- Department of Biochemistry and National Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, People's Republic of China
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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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17
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Lecomte S, Baron MH. Surface-enhanced raman spectroscopy investigation of fluoroquinolones-DNA-DNA gyrase-Mg2+ interactions. II. Interaction of pefloxacin with Mg2+ and DNA. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/(sici)1520-6343(1997)3:1<31::aid-bspy3>3.0.co;2-v] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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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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19
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Electrical communication between horse heart cytochrome c and electrodes in the presence of DNA or RNA. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0022-0728(90)87168-j] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Seibert M, Cotton TM, Metz JG. Surface-enhanced Raman scattering spectroscopy: Probing the lumenal surface of Photosystem II membranes for evidence of manganese. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1988. [DOI: 10.1016/0005-2728(88)90187-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Combining surface enhanced Raman scattering (SERS) and high-performance thin-layer chromatography (HPTLC). J Mol Struct 1988. [DOI: 10.1016/0022-2860(88)80068-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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The effects of protonation on the surface-enhanced Raman scattering from ATP molecules adsorbed on the Ag electrode. Chem Phys Lett 1987. [DOI: 10.1016/0009-2614(87)80905-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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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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24
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Taniguchi I, Umekita K, Yasukouchi K. Surface-enhanced raman scattering of nicotinamide adenine dinucleotide (NAD+) adsorbed on silver and gold electrodes. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0022-0728(86)90127-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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25
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Abstract
Adsorption of nucleic acids at a silver electrode polarized to -0.6 to -0.1 V (vs. Ag/AgCl) was investigated by means of surface enhanced Raman scattering (SERS) spectroscopy. Single-stranded polyriboadenylic acid and thermally denaturated DNA adsorbed at the silver electrode yield two intense bands at 734 and 1335 cm-1 on the SERS spectra. These bands, assigned to the vibrations of adenine residue rings, were much less intense if the SERS spectra were recorded for double-helical complex polyadenylic X polyuridylic acid and native DNA. Moreover, the courses of alkaline denaturation of DNA and its digestion by deoxyribonuclease I were observed by SERS spectroscopy. The results were interpreted as support for the view that intact double-helical segments of nucleic acids are not denatured or destabilized due to their adsorption at the positively charged and roughened surface.
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26
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27
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Séquaris JM, Fritz J, Lewinsky H, Koglin E. Surface enhanced raman scattering spectroscopy of methylated guanine and dna. J Colloid Interface Sci 1985. [DOI: 10.1016/0021-9797(85)90315-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Séquaris JM, Koglin E, Malfoy B. Inner and outer complexes of Pt-coordination compounds with DNA probed by SERS spectroscopy. FEBS Lett 1984; 173:95-8. [PMID: 6540207 DOI: 10.1016/0014-5793(84)81024-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Surface enhanced Raman scattering (SERS) spectroscopy has been used to study the interfacial behaviour of DNA modified by cis-Pt(NH3)2Cl2, (cis-DDP) and [Pt-(dien)Cl]Cl bidentate and monodentate platinum coordination compounds, respectively. Two stereochemical configurations of Pt-DNA complexes can be deduced from the adsorption behaviour of the Pt adducts. The antitumoral inactive [Pt-(dien)Cl] Cl forms an outer complex whereas the antitumoral active cis-DDP favours an inner complex.
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29
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Klukanová H, Studničková M, Kováŕ J. Cathodic stripping voltammetry of adenine nucleotides, polyriboadenylic acid and nicotinamide adenine dinucleotide coenzymes at the dropping mercury electrode. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/0302-4598(84)87010-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Taniguchi I, Iseki M, Toyosawa K, Yamaguchi H, Yasukouchi K. Purines as new promoters for the voltammetric response of horse heart cytochrome c at a gold electrode. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/s0022-0728(84)80221-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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32
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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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33
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Miles R. In situ characterization of electrode-electrolyte interfaces using spectroscopic techniques. SURF INTERFACE ANAL 1983. [DOI: 10.1002/sia.740050202] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Soriaga MP, Wilson PH, Hubbard AT, Benton CS. Orientational transitions of aromatic molecules adsorbed on platinum electrodes. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0022-0728(82)80024-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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38
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Subnanogram colloid surface-enhanced Raman spectroscopy (SERS) of methylated guanine on silica gel plates. ACTA ACUST UNITED AC 1982. [DOI: 10.1007/bf00466947] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Koglin E, Séquaris JM, Valenta P. Surface enhanced raman spectroscopy of nucleic acid bases on Ag electrodes. J Mol Struct 1982. [DOI: 10.1016/0022-2860(82)85050-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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