Quantification of nucleobases/gold nanoparticles interactions: energetics of the interactions through apparent binding constants determination

Abstract

We explore the possibilities of quantifying the interaction of both adenine and thymine with non-functionalized, anionic citrate gold nanoparticles (AuNPs). Following the plasmon absorbance band's red shifts, dependent of the AuNPs aggregation state, apparent binding free energies of the system are obtained for the sum of the two processes (nucleobase interaction plus nanoparticle aggregation). A deconvolution procedure confirms those results. Those apparent binding free energies are, in both cases, in good agreement with previous studies indicating an increased reactivity for adenine. Moreover, density functional theory (DFT) calculations were carried out both to model the structures and to theoretically support and help understand the observed experimental stability of adenine as compared to thymine over gold nanoparticles. Theoretical results indicate the N atom in the amino group of adenine adopts a pyramidal sp hybridization character, stabilizing the interaction with Au as compared to thymine.

SERS, XPS and DFT Study of Xanthine Adsorbed on Citrate-Stabilized Gold Nanoparticles

“…This is due to their peculiar properties, which can be summarized as: (1) marked chemical and physical stability; (2) high biocompatibility; (3) efficient surface functionalization with organic and biological ligands; and (4) enhanced optical responses related to surface plasmons. In particular, the use of gold nanoparticles in diagnostics, especially for the detection of DNA/RNA chains and their nucleobases [7,8,9], is getting more and more interest. The most common procedure for obtaining stable aqueous suspensions of gold nanoparticles is the reduction of tetrachloroauric acid by sodium citrate [10,11].…”

The Controversial Orientation of Adenine on Gold and Silver

“…Conversely, the computational studies discussed in Sections 2.2 and 2.4 have reported significantly different conclusions from each other . These discrepancies, at least for this field, highlight the importance of using computational tools to help interpret experimental measurements of physical phenomena, rather than relying on them exclusively.…”

“…Therefore, despite its interesting approach, this study apparently omitted a crucial consideration in reaching its conclusions for adenine adsorption. Other recent theoretical investigations have proposed planar adsorption, [242 , 243] by N1/N10, [244 ] and by sp 3 hybridization of the amino group . Elsewhere, a DFT study reported that the preferred binding site for gold–adenine interaction follows the order N1 > N7 > N3, but for silver–adenine it is N3 > N1 > N7; with differences also observed for cationic and anionic variants of the nucleobase .…”

Nucleoside–AuCl4− interactions as studied by electrospray ionization mass spectrometry

“…When we deal with the interaction between a nucleic acid and any chemical individuum, the key question is which of the nucleobases is the most prone to interact with this chemical individuum. For example, this problem has been widely studied in detail for the interactions between nucleic acids and gold nanoparticles . The matter has also been studied for the interactions between nucleobases and simple gold anions, namely Au − and Au 2 − .…”