Gold Nanoparticles Adsorb DNA and Aptamer Probes Too Strongly and a Comparison with Graphene Oxide for Biosensing

Abstract

Using fluorescently labeled DNA oligonucleotides and nanomaterials for developing biosensors has been extensively reported for gold nanoparticles (AuNPs) and graphene oxide (GO) among others. These materials have vastly different affinities and mechanisms for interacting with DNA, and their analytical performance is likely to be different. In this work, we used several DNA sequences and, respectively, adsorbed them on AuNPs and GO to quench fluorescence. Different from previous work, we used KCN to fully dissolve the AuNPs to calculate the percentage of the desorbed DNA due to the complementary DNA (cDNA) and aptamer target. The desorbed probe DNA from the AuNPs was less than 5% for all of the targets including DNA, adenosine, Hg2+, and lysozyme, indicating a very strong DNA adsorption affinity. Desorption of DNA was achieved by adding HEPES buffer, NaCl, and As­(III), but such desorption was attributed to the adsorption of these molecules or ions by the AuNPs instead of their interaction with the adsorbed DNA. For GO, more probes desorbed with addition of target analytes but so did nonspecific desorption by random DNA and proteins. In summary, AuNPs are unlikely to be a good surface for developing biosensors relying solely on the desorption of probe DNA, while for GO the main problem is nonspecific desorption.

Attaching DNA to Gold Nanoparticles With a Protein Corona

“…On the other hand, previous work showed that non-thiolated DNA can be easily displaced by various anions and small molecules (Liu et al, 2018b;Wu et al, 2019;Zhang et al, 2019;Zong et al, 2019). The reason that BSA cannot displace DNA is attributed its large size making it difficult to penetrate through the DNA layer.…”

Label‐Free Colorimetric Biosensors Based on Aptamers and Gold Nanoparticles: A Critical Review

“…[67][68][69] To test this mechanism, we quantitatively measured the amount of desorbed aptamers in the presence of various target molecules using a few FAM-labeled aptamers (Figure 3). [23] If an aptamer is specifically desorbed, higher fluorescence enhancement would be observed with its target than with other molecules. Based on the fluorescence enhancement, this method was also previously used for developing fluorescent sensors, although the maximal fluorescence enhancement was only about 1-fold.…”

“…[14][15][16] However, adsorbed DNA often loses its hybridization function (except for densely immobilized diblock DNA or other special designs), [14][15][16][17] since DNA adsorption by AuNPs is much stronger than its binding to complementary DNA. [22,23] When a double-stranded DNA is used, the adsorption is kinetically slow since the bases are hidden in the helix. [24,25] This kinetic difference in adsorption was used for developing label-free sensors in 2004 by Li and Rothberg, [25][26][27] where the label-free here referred to the lack of a thiol group.…”

“…Adsorption of nonthiolated DNA can also increase the colloidal stability of AuNPs [14–16] . However, adsorbed DNA often loses its hybridization function (except for densely immobilized diblock DNA or other special designs), [14–17] since DNA adsorption by AuNPs is much stronger than its binding to complementary DNA [22,23] . When a double‐stranded DNA is used, the adsorption is kinetically slow since the bases are hidden in the helix [24,25] .…”

Covalent and Noncovalent Functionalization of Graphene Oxide with DNA for Smart Sensing

“…[ 46 ] Similarly, DNA is also very strongly adsorbed on gold surfaces, making such a sensing mechanism difficult. [ 47 ] In this regard, GO has an appropriate adsorption strength.…”