First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties

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.

Micro RNA Sensing with Green Emitting Silver Nanoclusters

“…The emission is not excited continuously throughout these regions for both "green" and "red" species but rather with a set of wavelengths: 225, 240, 260, and 274 nm, determined as maxima of the Gaussian fits. Regardless of color, the emission of AgNCs in the visible is universally excited via the DNA bases which agrees well with previously published data [72] and our own observations [2]. Previous studies found that visible emission of DNA templated AgNCs can be excited by both direct excitation into visible band and by UV light into absorption peak of DNA nucleobases [2,69,73].…”

“…Regardless of color, the emission of AgNCs in the visible is universally excited via the DNA bases which agrees well with previously published data [72] and our own observations [2]. Previous studies found that visible emission of DNA templated AgNCs can be excited by both direct excitation into visible band and by UV light into absorption peak of DNA nucleobases [2,69,73]. The tight association of silver nanoclusters with DNA templating bases allows for optical interactions between the DNA template and AgNCs [72].…”

“…We further characterized the properties of AgNC templated with DNA-miR21-probe by employing fluorescence excitation-emission matrix spectroscopy (EEMS). The optical response and the excitation/emission relationship of AgNCs has proven to be a little complicated, hence a better way to represent such responses is through measuring the entire excitation/emission matrix spanning a wide range of wavelengths presented as 2D contour maps [2,70,71]. Figure 2A shows the EEM map for the AgNCs templated on C 12 -loop-miR21-probe with excitation in the range of 220-370 nm while recording the entire emission spectrum in the UV and visible spanning 270-750 nm wavelengths (UV/UV-Vis EEM).…”

“…The continuous density of states, typical for metal structures, breaks up into discrete energy levels in the nanoclusters. The nanoclusters resemble molecular-like behavior with strong fluorescence observed in the wide range of the spectrum, from UV to visible to near IR [1,2]. AgNCs are more stable in photobleaching than widely used organic dyes, quantum dots, or fluorescent proteins [3][4][5].…”

“…Signal changes can be positive when fluorescence is enhanced due to analyte binding or negative when fluorescence is quenched. The ability of the AgNCs to detect short fragments of nucleic acid molecules stems from convenient natural integration of AgNCs into nucleic acid-based nano-assemblies [2]. We dedicated this current study to demonstrating the detection strategy for miR sequences in general and miR-21 in particular.…”