Evidences of adenine–thymine Interactions at gold electrodes interfaces as provided by in-situ infrared spectroscopy (original) (raw)
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Surface-Structure-Sensitive Adsorption of Adenine on Gold Electrodes
ChemPhysChem, 2005
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. 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. 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), surface-enhanced infrared reflection-absorption spectroscopy with the attenuated total reflection technique (ATR-SEIRAS), surface-enhanced Raman spectroscopy (SERS), surface X-ray scattering (SXS), X-ray photoelectron spectroscopy (XPS), and scanning tunnelling microscopy (STM). 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.
In situ infrared study of adenine adsorption on gold electrodes in acid media
Electrochimica Acta, 2012
In situ external reflection infrared reflection spectroscopy (IRRAS) and surface-enhanced infrared reflection absorption spectroscopy under attenuated total reflection conditions (ATR-SEIRAS) have been used to study the adsorption of adenine at Au(1 1 1) and gold thin-film electrodes in 0.1 M HClO 4 solutions in deuterium oxide and in water. The existence of protonated and deprotonated adenine molecules at the electrode surface has been proved from the comparison of the spectra for adsorbed adenine with those obtained for dissolved adenine. In all cases, characteristic band frequencies are observed for the enhanced ring stretching band in D 2 O and also the bending band of the amino group in H 2 O. Both signals appear at higher wavenumbers for the protonated species. In acid media, deprotonation of adsorbed adenine is induced by increasing positive potentials and/or adenine coverage leading to the same adsorbed species as previously reported in basic media, namely chemically adsorbed adenine with a tilted orientation of the molecular plane on the electrode. Co-adsorption of water and perchlorate anions is detected in the case of the acid media, indicating the involvement of these species in the stabilization of the organic film. Time-resolved experiments at negative potentials and low adenine concentrations have shown also the physical adsorption of protonated adenine and have allowed the monitoring of the adsorption of the protonated and unprotonated forms as a function of time. Adsorption of unprotonated adenine is slower but is favored at the equilibrium at the electrode surface even if the pH of the media is three units lower than the pK a of adenine in solution.
Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study
Biointerphases, 2013
Background: The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine. Methods: We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold.
Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 2018
Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orien...
The Journal of Physical Chemistry C, 2009
Understanding the interactions of biomolecules with noble metal surfaces is critical to our development of functional biomedical nanodevices and accurate biosensors. Here we use surface enhanced Raman spectroscopy (SERS) and surface enhanced infrared absorption spectroscopy (SEIRA) on Au nanoshell substrates to study the interactions of adenine and two adenine derivatives, thiolated polyadenine single-stranded DNA (polyA) and adenosine monophosphate (AMP), with Au surfaces. pH-dependent conformational changes of these molecular species adsorbed on Au nanoshell surfaces were observed using SERS, and confirmed with SEIRA. The combined SERS-SEIRA spectra show significant pH dependence, consistent with adenine protonation and reduced Au-adenine binding at low pH. The spectra are also consistent with adenine binding "end-on" to the Au surface via a ring nitrogen, with the bond to the external NH 2 group aligned near the surface normal. For AMP, spectral evidence indicates binding through either a ring nitrogen and/or the external NH 2 group. Density functional calculations on adenine and comparisons with the literature allow us to assign the observed spectral features and to gain insight to the local binding geometry of the adsorbates.
Electrochimica Acta, 2016
The adsorption of thymine on gold electrodes has been studied by ATR-SEIRAS in situ spectroscopy at three pH values (1, 7 and 12), in order to analyse the tautomeric equilibrium of deprotonated thymine in the adsorbed state. The anionic form which is deprotonated in nitrogen N1 (N1 tautomer) and the one deprotonated in nitrogen N3 (N3 tautomer) are considered. The spectroscopic results have been interpreted in the light of DFT ab-initio calculations of both tautomeric forms adsorbed on gold surfaces. The basis sets 6-311 + +G(d,p) for C, H, O and N atoms and LANDL2DZ for Au atoms have been used. The electrode surface has been simulated as an unreconstructed Au(111) surface of 19 atoms. The preponderance of each tautomer of adsorbed thymine as a function of pH has been inferred from the analysis of the spectral signals in the 1500-1800 cm À1 wavenumber region related mostly to stretching modes of the carbonyl groups. It has been found that the adsorbed N3 tautomer predominates in the case of adsorption from acid media while the N1 tautomer predominates in the adsorption from basic media but the adsorption of both forms have been distinguished in the experiments from neutral media. Moreover, the plausible changes in the orientation of the two adsorbed tautomers with the electric field have been determined by analysing the relative intensities of the characteristic CH stretching signals in the 2800-3300 cm À1 spectral region. It is proposed that the N3 tautomer undergoes changes in the interaction sites with the metal and in the molecular plane orientation on the electrode as the electric potential is increased, but the N1 tautomer molecule keeps the interaction sites while the molecular plane slightly rotates to facilitate the electrostatic interaction with the field.
The journal of physical chemistry. B, 2015
Among the low-index single-crystal gold surfaces, the Au(110) surface is the most active toward molecular adsorption and the one with fewest electrochemical adsorption data reported. Cyclic voltammetry (CV), electrochemically controlled scanning tunneling microscopy (EC-STM), and density functional theory (DFT) calculations have been employed in the present study to address the adsorption of the four nucleobases adenine (A), cytosine (C), guanine (G), and thymine (T), on the Au(110)-electrode surface. Au(110) undergoes reconstruction to the (1 × 3) surface in electrochemical environment, accompanied by a pair of strong voltammetry peaks in the double-layer region in acid solutions. Adsorption of the DNA bases gives featureless voltammograms with lower double-layer capacitance, suggesting that all the bases are chemisorbed on the Au(110) surface. Further investigation of the surface structures of the adlayers of the four DNA bases by EC-STM disclosed lifting of the Au(110) reconstruc...
Kinetic studies of HRP adsorption on ds-DNA immobilized on gold electrode surface by EIS and SPR
Journal of the Brazilian Chemical Society, 2010
Este trabalho descreve a construção de um filme de multicomponentes via método layer-bylayer (LbL) e a análise cinética da interação da enzima peroxidase de raiz forte (HRP) sobre a camada de ds-DNA de timo de bezerro formada numa superfície de ouro modificada. As técnicas de ressonância de plásmon de superfície (SPR) e a espectroscopia de impedância eletroquímica (EIE) foram usadas para caracterizar a construção do filme sobre a superfície de ouro. A ressonância de plásmon de superfície forneceu informações essenciais para o estudo e caracterização da interação proteína e ácido nucléico. Este método não necessita de marcador e monitora as interações em tempo real. Os estudos cinéticos obtidos por SPR da formação do filme de HRP sobre o ds-DNA apresentaram valores de 24,7 L mol-1 s-1 e 1,2×10-3 s-1 para k a e k d , respectivamente. A energia livre de Gibbs obtida para o sistema foi de-23,1 kJ mol-1. Os resultados obtidos mostram que a interação das moléculas da enzima sobre o ds-DNA é cinética e termodinamicamente favoráveis e a interação entre as camadas ocorre principalmente pela atração de cargas opostas. This paper describes the construction of a multicomponent film via layer-by-layer (LbL) method and the kinetic analysis of the interaction between horseradish peroxidase (HRP) enzyme on calf thymus double-stranded DNA layer on a modified gold surface. Surface plasmon resonance (SPR) and electrochemical impedance spectroscopy (EIS) are used to characterize the successful construction of the film on the gold surface. Surface plasmon resonance provided essential information for the study and characterization of protein and nucleic acid interaction and this method is label-free and monitors the interactions in real time. The kinetic studies determined by SPR of the horseradish peroxidase film formation on ds-DNA layer showed values of 24.7 L mol-1 s-1 and 1.2×10-3 s-1 for k a and k d , respectively. The Gibbs free energy obtained for the system was-23.1 kJ mol-1. The results obtained show that the interaction of the enzymes molecules on ds-DNA is kinetically and thermodynamically favourable and the interaction among the layers probably occurs mainly by attraction of opposite charges.
SERS, XPS, and DFT Study of Adenine Adsorption on Silver and Gold Surfaces
The Journal of Physical Chemistry Letters, 2012
The adsorption of adenine on silver and gold surfaces has been investigated combining density functional theory calculations with surface-enhanced Raman scattering and angle-resolved X-ray photoelectron spectroscopy measurements, obtaining useful insight into the orientation and interaction of the nucleobase with the metal surfaces.
For the first time, we used electrochemical shell-isolated nanoparticle-enhanced Raman spectroscopy (EC-SHINERS) technique to in-situ characterize the adsorption behaviour of four DNA bases (adenine, guanine, thymine, and cytosine) on atomically flat Au(111) electrode surfaces. The spectroscopic results of the various molecules reveal similar features, such as the adsorption-induced reconstruction of Au(111) surface and the drastic Raman intensity reduction of the ring breathing modes after the lifting reconstruction. As a preliminary study of the photo-induced charge transfer (PICT) mechanism, the in-situ spectroscopic results obtained on single crystal surfaces are excellently illustrated with electrochemical data.