Noncovalent Adsorption of Single-Stranded and Double-Stranded DNA on the Surface of Gold Nanoparticles

Abstract

Understanding the patterns of noncovalent adsorption of double-stranded nucleic acids (dsDNA) on gold nanoparticles (GNPs) was the aim of this study. It was found that the high-affinity motifs in DNA can and do act as an “anchor” for the fixation of the whole molecule on the GNP (up to 98 ± 2 single-stranded (ss)DNA molecules per particle with diameter of 13 ± 2 nm). At the same time, the involvement of an “anchor” in the intramolecular DNA interaction can negatively affect the efficiency of the formation of ss(ds)DNA–GNP structures. It has been shown that the interaction of GNP with DNA duplexes is accompanied by their dissociation and competitive adsorption of ssDNAs on GNP, wherein the crucial factor of DNA adsorption efficiency is the intrinsic affinity of ssDNA to GNP. We propose a detailed scheme for the interaction of dsDNA with GNPs, which should be taken into account in studies of this type. Researchers focused on this field should accept the complicated nature of such objects and take into account the many competing processes, including the processes of adsorption and desorption of DNA on gold as well as the formation of secondary structures by individual DNA strands.

Label-Free DNA Biosensor Based on Reduced Graphene Oxide and Gold Nanoparticles

“…Next, the incubations of the sensor with 1 nM, 10 nM, 50 nM, and 100 nM DNA targets determined successive increases in current intensity, which can be explained by the formation of dsDNA with each addition of a DNA target. In agreement with the previous findings [ 31 ], we may assume that the newly formed dsDNA easily detaches from the surface, thus favoring the redox process of [Fe(CN) 6 ] 3–/4– species. The impedimetric measurements ( Figure 9 B) were in agreement with the CV results and showed an increase in Rct following the adsorption of the DNA probe at the AuNPs-RGO/SPCE interface, which impeded the redox process of the negatively charged [Fe(CN) 6 ] 3–/4– .…”

“…Among these, the electrochemical synthesis of Au nanostructures has been widely employed because it offers several advantages over chemical synthesis, including the ability to control the size, shape, morphology, and growth rate by modulating the applied potential or current and via the electrolyte concentration [ 27 , 28 , 29 ]. Several studies have demonstrated that single-stranded (ss) oligonucleotides possess a more pronounced affinity for gold nanoparticles than their corresponding double-stranded (ds) helix [ 30 , 31 ]. Li and Rothberg mentioned that the underlying adsorption mechanism of ssDNA on gold is electrostatic and exploited the difference in the electrostatic properties of ssDNA and dsDNA in DNA detection by a colorimetric assay [ 30 ].…”

Label-Free DNA Biosensor Based on Reduced Graphene Oxide and Gold Nanoparticles

“…Next, the incubations of the sensor with 1 nM, 10 nM, 50 nM, and 100 nM DNA targets determined successive increases in current intensity, which can be explained by the formation of dsDNA with each addition of a DNA target. In agreement with the previous findings [31], we may assume that the newly formed dsDNA easily detaches from the surface, thus favoring the redox process of [Fe(CN) 6 ] 3-/4species. The impedimetric measurements (Figure 9B) were in agreement with the CV results and showed an increase in Rct following the adsorption of the DNA probe at the AuNPs-RGO/SPCE interface, which impeded the redox process of the negatively charged [Fe(CN) 6 ] 3-/4-.…”

Recent Advances in DNA Nanomaterials

“…ssDNA forms multipoint contacts with AuNP, and the nucleotide sequence, its length, the presence of modifications in DNA, the ionic strength and pH of the medium during incubation, the temperature, and reaction time of the association significantly affect the efficiency of the observed adsorption of cDNA to the surface of AuNP. It is shown that the adsorption of various DNA structures (dsDNA, ssDNA with a hairpin structure, and self-complementary ssDNA) on AuNP really differs significantly from nanoparticles [132].…”

“…According to a number of studies, it is this interaction that determines the binding strength of NA with AuNP. The second difference is that ssDNA has a much more mobile structure, whereas dsDNA has a rigid structure that prevents direct interaction of nitrogenous bases with the surface of nanoparticles [132].…”