What Controls the Melting Properties of DNA-Linked Gold Nanoparticle Assemblies?*

Abstract

We report a series of experiments and a theoretical model designed to systematically define\nand evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that\ncontribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures.\nThese variables include the size of the nanoparticles, the surface density of the oligonucleotides on the\nnanoparticles, the dielectric constant of the surrounding medium, target concentration, and the position of\nthe nanoparticles with respect to one another within the aggregate. The experimental data may be\nunderstood in terms of a thermodynamic model that attributes the sharp melting to a cooperative mechanism\nthat results from two key factors: the presence of multiple DNA linkers between each pair of nanoparticles\nand a decrease in the melting temperature as DNA strands melt due to a concomitant reduction in local\nsalt concentration. The cooperative melting effect, originating from short-range duplex-to-duplex interactions,\nis independent of DNA base sequences studied and should be universal for any type of nanostructured\nprobe that is heavily functionalized with oligonucleotides. Understanding the fundamental origins of the\nmelting properties of DNA-linked nanoparticle aggregates (or monolayers) is of paramount importance\nbecause these properties directly impact one's ability to formulate high sensitivity and selectivity DNA\ndetection systems and construct materials from these novel nanoparticle materials.