DNA Templates for Fluorescent Silver Clusters and I-Motif Folding

Abstract

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.

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

“…The mobile phase was buffered at pH = 6.5 with 10 mM citrate/ citric acid that was supplemented with 300 mM NaClO 4 to minimize solute interactions with the stationary phase. 47,48 To assess hydrodynamic radii, size standards were based on thymine oligonucleotides dT 10 , dT 15 , dT 20 , and dT 30 . 20,49 For sample isolation, timing between the absorption spectrometer (SPD-M20A) and the fraction collection (FRC-10A) was determined using a concentrated solution of dye.…”

“…The electron-rich nucleobases coordinate silver atoms and restrain cluster growth, and the primary sequence and secondary structure of DNA strands define specific cluster binding sites. 19,20 A resulting suite of chromophores is spectrally diverse and optically bright. They absorb and emit throughout the visible to near-infrared region from 400−900 nm and have extinction coefficients of ∼10 5 M −1 cm −1 , fluorescence quantum yields of ∼40%, and fluorescence lifetimes of ∼1 ns.…”

Biomediated Atomic Metal Nanoclusters: Synthesis and Theory

“…The formation of AgNCs stabilized by HP-DNA begins when Ag + cations from the silver precursor AgNO 3 bind preferentially to DNA bases of the HP-DNA as opposed to the sugar-phosphate backbone. After the reduction step using NaBH 4 , the cytosine bases are able to form a tight bond with the Ag atoms by direct interaction with the N 3 of the cytosine, producing stable AgNCs with excellent fluorescence emission [34,68]. Conversely, gold precursors produce AuCl 4 À anions,…”

“…Metal nanoclusters can be synthesized in a variety of ways ranging from purely synthetic to fully biostabilized with several methods that fall somewhere in between [1,2,10,12,13,31,34,35,50,68]. Traditional chemical reduction and polymer etching techniques for gold nanocluster synthesis require the addition of harsh and environmentally unfriendly reducing agents such as sodium borohydride and tetrabutylammonium borohydride.…”

Catalytic Performance of Ag Nanoparticles Templated by Polymorphic DNA

“…DNA has particular advantages to produce Ag nanomaterials [15][16][17], because of its unique self-assembly and mechanical properties, as well as the high affinity with Ag ? cations.…”