In-situ infrared spectroscopic studies of thymine adsorption on a Au(111) electrode

Haiss, Wolfgang; Roelfs, Bernd; Port, Simon N.; Bunge, E.; Baumgärtel, H.; Nichols, Richard J.

doi:10.1016/s0022-0728(98)00243-5

Cited by 59 publications

(58 citation statements)

References 23 publications

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“…The prominent absorbance peak at 1700 cm −1 (included in a broad and intense peak from 1650 to 1750 cm −1 ) is specific to CO stretching vibrations in the free thymine ring, that is, thymine that is not interacting with the surface. The position of this peak is consistent with the ATR measurement shown in Figure 2 and agrees well with experiments performed with thymine in solution 26 or with the adsorption of DNA on gold surfaces. 27 Other features of the IR spectrum can also clearly be attributed to the presence of dTMP, although not just free dTMP.…”

Section: Interaction Of Dtmp With H-terminated Siliconsupporting

confidence: 89%

Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces

et al. 2015

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DNA immobilization on surfaces is crucial to a number of applications. However, detailed understanding of DNA/surface chemistry remains poorly documented, especially on oxide surfaces, due to the complexity of such large molecules. This work focuses on a simpler molecule, 2-deoxythymidine-5-monophosphate (dTMP), which contains all the chemical elements of DNA. It confirms that adsorption of dTMP onto OH-terminated SiO 2 surfaces does not result in a chemical bond (dTMP readily washes off) and instead shows that dTMP chemically adsorbs on Al 2 O 3 surfaces. We combine first-principles calculations, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to determine the bonding configuration of dTMP onto alumina surfaces controllably grown by atomic layer deposition. We demonstrate that dTMP covalently reacts with alumina. Calculations indicate that covalent bonding of all dTMP polar groups (sugar ring, phosphate group, and thymine) is thermodynamically favored. Spectroscopic data and theory-based assignments of vibrational modes show that the bonding takes place primarily through both the thymine and phosphate groups. The reactivity and the tendency for dTMP to lie flat on the surface lead to an irreversible and disorganized dTMP layering. Studies of dTMP adsorption as a function of Al 2 O 3 thickness show that the density of grafted dTMP can be controlled, with measurable amounts even above the Al 2 O 3 monolayer coverage. These findings provide technological directions for DNA-based nanotechnologies to graft DNA on surfaces that would otherwise be unreactive.

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Section: Interaction Of Dtmp With H-terminated Siliconsupporting

confidence: 89%

Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces

et al. 2015

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“…[2][3][4] The structure and properties of adsorbed nucleobase films deduced from electrochemical studies have been confirmed by several in situ spectroscopy techniques, such as subtractively normalized interfacial Fourier-transform infrared spectroscopy (SNIFTIRS), [5] surface-enhanced infrared reflection-absorption spectroscopy with the attenuated total reflection technique (ATR-SEIRAS), [4,6] surface-enhanced Raman spectroscopy (SERS), [7] surface X-ray scattering (SXS), [8] X-ray photoelectron spectroscopy (XPS), [9] and scanning tunnelling microscopy (STM). [9][10][11][12] These techniques, however, were mostly used to obtain information on monolayer films adsorbed on smooth basal planes or single-crystal surfaces with a low density of monotamic steps and hence reduced surface atomic corrugation.…”

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confidence: 85%

Surface‐Structure‐Sensitive Adsorption of Adenine on Gold Electrodes

2005

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Since the earlier work on Hg, and more recently on Ag, Au and Pt single-crystal electrodes, electrochemical studies have shown that DNA bases are strongly adsorbed at the metalsolution interfaces and generally undergo a two-dimensional first-order transition.[1] Although it is well-known that the surface atomic structure, as much as its chemical nature, can play a critical role in the formation of ordered adsorbed monolayers, only few detailed investigations have evaluated the effect of the presence of regular monoatomic steps on the adsorption of nucleobases and nucleosides. [2][3][4] The structure and properties of adsorbed nucleobase films deduced from electrochemical studies have been confirmed by several in situ spectroscopy techniques, such as subtractively normalized interfacial Fourier-transform infrared spectroscopy (SNIFTIRS), [5] surface-enhanced infrared reflection-absorption spectroscopy with the attenuated total reflection technique (ATR-SEIRAS), [4,6] surface-enhanced Raman spectroscopy (SERS), [7] surface X-ray scattering (SXS), [8] X-ray photoelectron spectroscopy (XPS), [9] and scanning tunnelling microscopy (STM). [9][10][11][12] These techniques, however, were mostly used to obtain information on monolayer films adsorbed on smooth basal planes or single-crystal surfaces with a low density of monotamic steps and hence reduced surface atomic corrugation. Although the macroscopic information that can be obtained by electrochemical techniques may not reflect the entire complexity of interfacial phenomena, it has long been used to assess the average systematic effect of surface atomic structure details such as regular monoatomic steps and kinks on, for example, the ionic and organic adsorption, electrocatalysis, under-potential deposition and two-dimensional film condensation.An electrochemical study was therefore initiated to reveal the effect of surface structure regularities, such as monoatomic steps and kinks, on the adsorption of the DNA bases at gold single crystal electrodes. We report here a preliminary overview of the influence of the surface crystallographic orientation on the adsorption of adenine in acid media. Results and DiscussionIn Figure 1 a, the cyclic voltamograms obtained for the Au (111) electrode in the presence and absence of adenine in 0.1 m HClO 4 are compared. The gold surface oxidation is inhibited in the presence of adenine and occurs at higher potential values suggesting that a strongly adsorbed layer is formed. The analysis of the charges involved in the oxidation and reduction processes shows that adenine oxidation is irreversible and concomitant with the gold surface oxidation (Q ox /Q red > 2). The same behavior was also observed for the other gold surfaces under study.The voltamogram obtained for Au (111) in the double layer region, Figure 1 b, as well as the capacitance curve, Figure 1 c, substantiate that a chemisorbed layer of adenine is formed at the more positive potential values (region III). Based on earlier studies on adenine adsorption on Au (111) in acid ...

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“…The position of this peak is consistent with a previous in-situ IR study of thymine adsorption on Au(111) that assigned the carbonyl stretching feature to free thymine in solution (i.e., not adsorbed on the surface). 33 We therefore attribute the 1714 cm -1 feature in our study to thymine bases that are contained in the DNA monolayer but are not interacting strongly with the gold surface (from hereon denoted "nonchemisorbed"). We observe that the position of the main carbonyl peak shifts slightly depending on the valence of the buffer cations: the peak is at ≈1714 cm -1 for monovalent cations and at ≈1718 cm -1 for divalent cations.…”

Section: Xps Analysis Of Dna Filmsmentioning

confidence: 98%

Quantitative Analysis and Characterization of DNA Immobilized on Gold

et al. 2003

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Abstract:We describe the complementary use of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to quantitatively characterize the immobilization of thiolated (dT)25 single-stranded DNA (ssDNA) on gold. When electron attenuation effects are accurately accounted for in the XPS analysis, the relative coverage values obtained by the two methods are in excellent agreement, and the absolute coverage can be calculated on the basis of the XPS data. The evolution of chemically specific spectral signatures during immobilization indicates that at lower coverages much of the DNA lies flat on the surface, with a substantial fraction of the thymine bases chemisorbed. At higher immobilization densities, the (dT) 25 film consists of randomly coiled ssDNA molecules each anchored via the thiol group and at possibly one or two other bases. We use two examples to demonstrate how the quantitative analysis can be applied to practical problems: the effects of different buffer salts on the immobilization efficiency; the immobilization kinetics. Buffers with divalent salts dramatically increase the efficiency of immobilization and result in very high surface densities (>5 × 10 13 / cm 2 ), densities that may only be possible if the divalent counterions induce strong attractive intermolecular interactions. In contrast with previous reports of alkanethiol adsorption kinetics on gold, ssDNA immobilization in 1 M phosphate buffer does not occur with Langmuir kinetics, a result attributable to rearrangement within the film that follows the initial adsorption.

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In-situ infrared spectroscopic studies of thymine adsorption on a Au(111) electrode

Cited by 59 publications

References 23 publications

Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces

Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces

Surface‐Structure‐Sensitive Adsorption of Adenine on Gold Electrodes

Quantitative Analysis and Characterization of DNA Immobilized on Gold

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