DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence–Affinity Relation

Abstract

Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N 26 randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers (k = 1−6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexeshairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.

Effect of Fluorescent Labels on DNA Affinity for Gold Nanoparticles

“…It turned out that heterogeneous G, T and A-rich sequences are mainly selected, while C-rich ONs disappear from the original randomized DNA pool. These results are in line with the well-known range representing the rising affinity of nucleotides to the gold carrier C < T < A < G [ 21 ].…”

“…Our previous studies revealed that incubation conditions, length and composition of ONs influence the kinetics and affinity of their non-covalent adsorption to GNPs surface [ 17 ]. In this study, mixtures of GNPs and all the above-listed ONs were incubated under the same conditions, which provided effective non-covalent adsorption of ONs to the surface of GNPs (17.3 ± 2.1 nm in diameter, DLS data) [ 21 ].…”

“…We extended 20-mer N*-Flu ( Table 2 ) from the 5′-end by the fragments TTTTTT (N*1-Flu) or TTGTTG (N*2-Flu), and compared the values of K L and n , which characterize the efficiency of the formation of associates with GNPs. It was previously shown that both these fragments have an increased affinity for the GNP surface [ 21 ]. However, the introduction of these rather large nucleotide fragments (Δ M w ~1800 Da or 30% elongation) practically did not affect the adsorption parameters of the labeled ONs N*1-Flu and N*2-Flu on GNPs ( Table 2 ).…”

“…Electrophoretic separation of reaction mixtures in an agarose gel is a quick and convenient way to visualize the formation of ON-FD/GNPs. The method allows us to determine the regimes of concentration that provide GNP saturation and to characterize the homogeneity of ON-FD/GNPs [ 17 , 21 , 42 ]. The method also allows us to estimate the relative stability of the associates under nonequilibrium conditions of their movement through the gel matrix under the influence of an electric field.…”

Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles

“…Aptamer selection was performed for AuNP targets using normal or A-rich random ssDNA libraries in two separate screening sessions under otherwise identical selection conditions. Notably, multiple unrelated studies have evaluated binding of one or more particular ssDNA sequences (e.g., polyadenine) to planar gold surfaces and gold nanoparticles. − The choice of employing an A-rich library is based on a prior study that indicated both adenine-rich ssDNA and pure polyadenine induce aggregation of gold nanoparticles during their seeded growth as evidenced by a redshift and overall broadening in the characteristic extinction peak . As detailed previously above, the key differences between the CompELS approach used in the current work and the widely used SELEX process for the selection of aptamers stems from the elimination of intermittent oligonucleotide elution (i.e., intentional dissociation of all target–oligonucleotide complexes each screening round) and amplification (i.e., PCR-based sequence enrichment each screening round) steps during each selection round.…”