Abstract
Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence—an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence—twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single “basic” templating element, (dC)12, emit in “red”. The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in “green”. A new population of “blue” emitting clusters forms only when ssDNA templating sequence is placed on the 5′ end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure—a first step towards a larger assembly.
Highlights
The field of nucleic acid (NA) nanotechnology has brought various designs of materials and devices created with facilitation of nucleic acids both DNA and RNA [1,2,3,4]
One of the questions that we address with this study is, what would be the properties of AgNCs when they are assembled into larger networks using DNA as an architectural element? The effects needed to be probed are the close proximity of the DNA on the optical properties of templated AgNCs such as double-stranded core, loose ends of nucleic acids, and other structural elements used in the field of DNA nanotechnology [48]
We have shown the possibility of combining silver nanoclusters into larger assemblies of nucleic acids using a simple design containing a single-stranded template and a double-stranded core
Summary
The field of nucleic acid (NA) nanotechnology has brought various designs of materials and devices created with facilitation of nucleic acids both DNA and RNA [1,2,3,4]. Additional flexibility is added by the architectural elements of NA that employ tertiary interactions, such as kissing loops [6,7], loop receptor interactions [8], paranemic motifs [9], G-quadruplexes [10], and i-motifs [11], just to name a few. All these combined properties of NA provide a remarkable control over the versatile molecular structures that they can be programmed to assemble. NA nanotechnology opens large prospects for practical applications of novel materials design, diagnostics, and nanomedicine
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