DNA‐binding by Functionalized Gold Nanoparticles: Mechanism and Structural Requirements

Abstract

A family of nanoparticles featuring surfaces of varying hydrophobicity was synthesized. The efficiency of DNA-binding was determined, demonstrating in a fivefold modulation in binding a 37-mer DNA strand. Nanoparticle-binding causes a reversible conformational change in the DNA structure, as demonstrated by circular dichroism and fluorescence experiments. Furthermore, the affinity of the nanoparticle for the DNA can be regulated by external agents, though stability of the complex is observed at relatively high ionic strengths. Gene regulation as a means of controlling disease states or altering cellular activity has become a realistic goal within medicinal chemistry. Exploration of synthetic molecules capable of DNA-binding has resulted in the development of several classes of designed scaffolds. Notable success in the creation of DNA transcription regulators can be traced to the use of substituted polyamides that are highly sequence-selective (1-5). Alternate approaches in the search for molecules appropriate for interaction with DNA sequences have resulted in the identification of systems capable of covalent modification of the target DNA strand (6,7), as well as peptide and saccharide scaffolds that utilize known DNA-binding components to confer activity to unique sequences (8-13). Significant progress has also been made toward understanding DNA reactivity via the detailed analysis of less functionally diverse systems (14-16), including polyamines (17) and cationic dendrimers (18)(19)(20). Consideration of the structure of the DNA strands, as well as its regulation in vivo; however, suggests one additional structure for DNA-binding has not been sufficiently utilized. Histones are a necessary packaging element for DNA within the nucleus. With their large diameter (approximately 6.5 nm) and correspondingly low surface curvature, they are well suited for interacting with and condensing extensive stretches of DNA (21). However, with the exception of dendrimers, which present synthetic challenges (22), none of the major systems under investigation employs a similar shape. Our research focuses on the creation of nanoparticles as scaffolds for DNA-binding.Mixed monolayer-functionalized gold nanoparticles present a promising structure for the development of DNA-regulating molecules ( Figure 1A) (23), and have already been shown to be highly effective transfection vectors (24). In a previous report, we demonstrated that quaternary ammonium-functionalized nanoparticle binds 37-mer DNA in a non-aggregated, stoichiometric fashion with high affinity (25). Centrifugation of the DNA:nanoparticle complexes provided a molar ratio of 3-4 nanoparticles per 37-mer DNA strand, while dynamic light scattering (DLS) of the bound species confirmed that the complexes were not aggregated, but had a specific and small radius in solution of approximately 10 nm. The affinity of the nanoparticles for the DNA segment was demonstrated by their ability to interrupt transcription by T7 RNA polymerase in vitro. As this polymerase has an affinit...

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