Abstract. We have recently reported on the fast and quantitative adsorption of DNA to 13 nm gold nanoparticles (AuNPs) at pH 3. This is in contrast to most traditional methods at neutral pH, where the adsorption is both slow and requires high excess of DNA. Direct application of our protocol to large particles in many cases did not result in particles that are stable at high (0.3 M) salt, and high excess of DNA was still required for the formation of stable particles. In this work we investigate the reasons for this limitation on the basis of kinetics and colloidal stability. Based on our investigation, fast and quantitative modification of large AuNPs is still possible, either by working at high particle concentration, or by using sonication. As we have shown that fast quantitative modification of large particles is possible, the preparation step of reduction and purification of the thiolated DNA becomes the rate limiting step in the whole AuNP-DNA conjugate protocol. However we show that this step is unnecessary when using our current protocol.

Noble metal nanoparticles possess very large scattering cross-sections, which make them useful as tags in biosensing assays with the potential to detect even single binding events. In this study, we investigated the effects of nanoparticle size on the shift in the light scattering spectrum following formation of Au-Au, Ag-Ag or Ag-Au dimers using FDTD simulations. We discuss the use of a color camera to detect these spectral changes for application in a target-induced dimerization sensing assay. Dimerization of Au nanoparticles induced a larger shift in color compared to Ag nanoparticles. Heterodimers composed of 60 nm Ag and 40 nm Au demonstrated an even larger spectral shift and color response compared to the best homodimer pair (80-40 nm Au). The increased spectral shift of the Ag-Au heterodimer was subsequently observed experimentally for the DNA-induced dimerization of nanoparticles, showing that careful selection of nanoparticle size and composition can significantly enhance recognition of nanoparticle dimerization events for use in (color) sensing assays.

Fast modification of large gold nanoparticles with DNA is achieved by using DNA with a polycationic tail. The conjugated DNA is available for specific hybridization, and therefore can be used for DNA-based assays or for constructing nanoparticle superstructures based on DNA hybridization.

DNA-linked 2D and 3D nano-assemblies find use in a diverse set of applications, ranging from DNA-origami in drug delivery and medical imaging, to DNA-linked nanoparticle structures for use in plasmonics and (bio)sensing. However, once these structures have been fully assembled, few options are available to modulate structure geometry. Here, we investigated the use of the polycation spermine to induce DNA collapse in small oligonucleotide-linked (54 bp) gold nanoparticle structures by monitoring shifts in the localized surface plasmon resonance (LSPR) peak and by comparing the data with finite-difference time-domain (FDTD) simulations. Our data shows that low concentrations of spermine can be applied to induce large changes in DNA conformation, leading to a significant reduction in interparticle distance (from ~ 25 to ~ 3 nm) and enhanced plasmonic coupling. The DNA collapse is near-instantaneous and reversible, and its application at low and high DNA densities is demonstrated with surface plasmon resonance imaging (SPRi), showing the potential of spermine to dynamically modulate distances and geometry in DNA-based nano-assemblies.

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