The Coordination Chemistry of DNA Nucleosides on Gold Nanoparticles as a Probe by SERS

Abstract

The DNA nucleosides (dA, dC, dG, dT) bound to gold nanoparticles (~13 nm) in aqueous solution has been studied as a probe by the SERS and their coordination structures have been proposed on the basis of them. According to UV-Visible absorption of gold nanoparticles after modifying with DNA nucleosides, the rates of absorption of dA, dC, and dG were much faster than that of dT as monitored by the aggregation kinetics at 700 nm. These data indicated that the nucleosides dA, dC, and dG had a higher affinity for the gold nanoparticles surface than nucleoside dT. As the result of SERS spectra, the binding modes of each of the nucleosides on gold nanoparticles have been assigned. A dA binds to gold nanoparticles via a N(7) nitrogen atom of the imidazole ring, which the C(6)-NH 2 group also participates in the coordination process. In the case of dC, it binds to the gold surface via a N(3) nitrogen atom of the pyrimidine ring with a partial contribution from the oxygen of C(2)=O group. A coordination of dG to the gold surfaces is also proposed. Although the dG has the two different nitrogens of a pyrimidine ring and the amino group, the N(1) nitrogen atom of a pyrimidine ring has a higher affinity after the hydrogen migrates to the amino group. Conversely, dT binds via the oxygen of the C(4)=O group of the pyrimidine ring. Accordingly, these data suggest that the nitrogen atom of the imidazole or the pyrimidine ring in the DNA nucleosides will bind more fast to the gold nanoparticles surfaces than the oxygen atom of the carbonyl group.

Optimization of Surface-Enhanced Raman Spectroscopy Conditions for Implementation into a Microfluidic Device for Drug Detection

“…The LODs are dependent not only on the plasmonic efficiency of the substrate but also on the binding affinity of the chemical to that substrate. Several studies examining the binding of nitrogen-containing compounds to different metals, including Ag and Au, have been conducted. − Acioli and Srinivas studied nucleobase binding to Ag and Au. The authors found that (i) both Ag and Au bind the nucleobases through a nitrogen site and (ii) an Au surface had twice the binding energy of an Ag surface.…”

Distinction of nucleobases – a tip-enhanced Raman approach

“…For the band assignment the spectral features were compared with those of SERS and Raman spectra of adenine derivates (deoxyadenosine (dA) [27], deoxyadenosine monophosphate (AMP) [28] and single stranded adenine homopolymer (poly(dA)) [29]).…”

“…An example is the band at 1251 cm −1 in spectrum 3. It can be attributed to the (C 8 –H, N 9 –H) deformation, the (N 7 –C 8 ) stretching of adenine [35], a ring mode of adenine or cytosine [37], the (C 8 –N 9 ) stretching of guanine [27] or the in-plane ring stretching of thymine [35]. …”

Hydrogen bonds in the nucleobase-gold complexes: Photoelectron spectroscopy and density functional calculations

“…[10][11][12] The DNA nucleosides bound to gold nanoparticles in aqueous solution were studied with surface-enhanced Raman scattering. 13 The temperatureprogrammed desorption experiments show that the heat of desorption of DNA bases from gold thin film decreases in the order of G > A > C > T. 8 The base-dependent competitive adsorption of single-stranded DNA on polycrystalline Au films indicates that the adsorption affinity to gold surface decreases in the order of A > C ≥ G > T. 14 On the other hand, the isothermal titration calorimetry studies on the binding of DNA bases to gold nanoparticles show that the strength of nucleobase-gold interaction decreases in the a) Author to whom correspondence should be addressed. Electronic mail: zhengwj@iccas.ac.cn.…”