Distinct structural interactions of polyadenine and polythymine on gold nanoparticles: from single strands to duplexes

Abstract

Motivated by potential applications in fields such as medicine or materials science, various methodologies have been developed for the preparation of so-called spherical nucleic acids, based on oligonucleotides and metal nanoparticles. Despite optimization through various parameters such as loading efficiency or nanoconjugate stability, much remains to be known regarding the actual conformations of oligonucleotides and their interactions with the nanoparticle surface. We employed a combination of spectroscopic techniques and liquid transmission electron microscopy to analyze the interactions and conformations adopted by polyAdenine (polyA) and polyThymine (polyT) chains in contact with gold nanoparticles (AuNPs). These studies revealed the presence of AuNP@polyA dimers, with polyA strands forming duplexes, whereas polyT forms isolated strands on the AuNPs. The presence or absence of polyA duplexes on AuNPs can be modulated by external stimuli such as temperature or NaCl. This study contributes to understanding the interactions and secondary structure of oligonucleotides on AuNPs.

Scheme 1. (a) Graphical illustration of secondary structures of polyA at different pH values. (b) Graphical illustration of AuNP@polyA, at different DNA concentrations on the gold surface.

Fig. 1. (a) Schematic illustration of the formation of AuNP@polyA duplexes on AuNPs. (b) CD spectra of AuNP@polyA at pH = 7 and free polyA strands at both pH = 3 and pH = 7. (c) UV-vis spectra of AuNP@citrate and AuNP@polyA.

Fig. 2. (a) HAADF-STEM images of AuNP@polyA in a liquid environment, showing the presence of dimers and individual particles. (b) Two-component Gaussian mixture model (GMM) showing the presence of AuNP@polyA duplexes and single AuNP@polyA.

Fig. 3. Scatter plots of the trajectories of the center position of AuNP@polyA. The center position of each particle is tracked across a time series of HAADF-STEM images with an electron dose of 20 e⁻ per Ų per frame (a) and 50 e⁻ per Ų per frame (b). When the electron dose is low, AuNP@polyA dimers move as stable units (a), whereas for the higher electron dose the polyA structure might be disrupted by the high energy electron beam, ultimately leading to fusion of AuNPs (b).

Fig. 4. EDX spectra and elemental maps for AuNP@polyA under dry conditions, confirming the presence of N and P (from polyA) around AuNPs.

Fig. 5. (a) Schematic illustration of AuNP@polyT conjugates. (b) UV-vis spectra of AuNP@citrate and AuNP@polyT. (c) CD spectra of AuNP@polyT at pH = 7 (black), polyT (red) at pH = 7 and polyT (pink) at pH = 3. (d) Representative liquid-phase TEM image of AuNP@polyT.

Fig. 6. (a) Schematic illustration of the behavior of AuNP@polyA duplexes in the presence of added NaCl. (b) Fluorescence spectra of AuNP@FAM-polyA before and after addition of NaCl (100 mM). (c) CD spectra of AuNP@polyA at different NaCl concentrations, as labeled.

Fig. 7. CD spectra at different temperatures for AuNP@polyA (a) and AuNP@polyT (b).

Fig. 8. (a) CD spectra of AuNP@polyA prepared at different polyA/AuNP ratios. (b) Correlation between the number of polyA strands on AuNPs and CD intensity at 265 nm.