DNA Templates for Fluorescent Silver Clusters and I-Motif Folding

When compared with silver nanoparticles, silver clusters comprised of ?101 atoms are distinguished by their strong fluorescence, and DNA directs and stabilizes particular types of clusters via base-specific interactions. Two main observations considered in this paper are the pH dependence of the fluorescence and the folded conformation of the oligonucleotide?cluster conjugates. Two i-motif forming oligonucleotides (dTA2C4)4 and (dC4A2)3C4 coordinate red and green emissive species, and these fluorescent species are favored in slightly acidic and basic solutions, respectively. The red emission is highest at pH 6, at which the i-motif forms of the oligonucleotides are also stable. When assessed by size exclusion chromatography, the oligonucleotide and cluster conjugate have similar global structures, which indicate that the DNA strands are similarly organized at this pH. The green emission is highest at pH 8?9. In these basic solutions, the oligonucleotide alone is unfolded, yet the green and red cluster?oligonucleotide conjugates have similar shapes. The pH-dependent fluorescence and the compact shapes of the cluster?oligonucleotide conjugates suggest that protons dominate DNA folding for the red emissive species, while the green emissive clusters themselves determine the shape of their DNA matrix. These studies provide the basis for understanding how specific base arrangements and environmental factors influence the formation of this new class of fluorescent nanomaterials. When compared with silver nanoparticles, silver clusters comprised of ?101 atoms are distinguished by their strong fluorescence, and DNA directs and stabilizes particular types of clusters via base-specific interactions. Two main observations considered in this paper are the pH dependence of the fluorescence and the folded conformation of the oligonucleotide?cluster conjugates. Two i-motif forming oligonucleotides (dTA2C4)4 and (dC4A2)3C4 coordinate red and green emissive species, and these fluorescent species are favored in slightly acidic and basic solutions, respectively. The red emission is highest at pH 6, at which the i-motif forms of the oligonucleotides are also stable. When assessed by size exclusion chromatography, the oligonucleotide and cluster conjugate have similar global structures, which indicate that the DNA strands are similarly organized at this pH. The green emission is highest at pH 8?9. In these basic solutions, the oligonucleotide alone is unfolded, yet the green and red cluster?oligonucleotide conjugates have similar shapes. The pH-dependent fluorescence and the compact shapes of the cluster?oligonucleotide conjugates suggest that protons dominate DNA folding for the red emissive species, while the green emissive clusters themselves determine the shape of their DNA matrix. These studies provide the basis for understanding how specific base arrangements and environmental factors influence the formation of this new class of fluorescent nanomaterials