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Review
. 2013 Apr 23;3(2):185-200.
doi: 10.3390/bios3020185.

DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters

Judy M Obliosca  1 , Cong Liu  2 , Robert Austin Batson  3 , Mark C Babin  4 , James H Werner  5 , Hsin-Chih Yeh  6
Affiliations
Review

DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters

Judy M Obliosca et al. Biosensors (Basel). .

Abstract

DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more photostable. Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core. The preparation of DNA/Ag NCs is simple and there is no need to remove excess precursors as these precursors are non-fluorescent. Our recent discovery of the fluorogenic and color switching properties of DNA/Ag NCs have led to the invention of new molecular probes, termed NanoCluster Beacons (NCBs), for DNA detection, with the capability to differentiate single-nucleotide polymorphisms by emission colors. NCBs are inexpensive, easy to prepare, and compatible with commercial DNA synthesizers. Many other groups have also explored and taken advantage of the environment sensitivities of DNA/Ag NCs in creating new tools for DNA/RNA detection and single-nucleotide polymorphism identification. In this review, we summarize the recent trends in the use of DNA/Ag NCs for developing DNA/RNA sensors.

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Figures

Figure 1
Figure 1
(a) Illustration depicting how silver nanoclusters are formed on single-stranded DNA. Silver ions preferentially attach to cytosines on the DNA strand. Addition of NaBH4 reduces these ions, leading to the formation of silver nanoclusters. The number of silver atoms in the cluster drawn here may not represent the real situation, as 10–20 atoms of silver could bind to a DNA strand [61,62,63,64]. (b) DNA microarrays proved to be a useful screening tool to find DNA sequences capable of nucleating Ag NCs of different emission colors. Reprinted with permission from [27]. Copyright (2008) American Chemical Society. (c) It is possible to switch the fluorescence of Ag NCs on and off [29,30] and tune their color [30,31] through interactions with nearby DNA sequences (called enhancers). Adapted with permission from [30]. (d) All DNA/Ag NCs have a common excitation peak between 260 and 270 nm, close to the absorption maxima of nucleobases. Through energy transfer from nucleobases, one can excite all DNA/Ag NCs with a single UV excitation source. Reprinted with permission from [53]. Copyright (2011) American Chemical Society.
Figure 2
Figure 2
Schematic showing the guanine-proximity-induced fluorescence enhancement phenomenon on DNA/Ag NCs and its application in DNA detection—termed NanoCluster Beacons (NCBs). (a) Guanine proximity can dramatically increase the red fluorescence emission of DNA/Ag NCs. A non-emissive silver cluster is first prepared on a cytosine-rich NC-nucleation sequence. Once a guanine-rich enhancer is brought close to the silver cluster through hybridization, a strong red fluorescence emission is observed from the solution, with a bulk enhancement ratio greater than 500 fold. Reprinted with permission from [29]. Copyright (2010) AmericanChemical Society. (b) Representation of the NCB detection scheme. An NCB is composed of an NC probe (carrying a non-emissive Ag cluster) and an enhancer probe (having an enhancer sequence). NCB fluoresces upon binding with a DNA target. In the absence of target, NCB remains dark. Adapted with permission from [30].
Figure 3
Figure 3
(a) The turn-on color of NanoCluster Beacons can be tuned by repositioning the enhancer sequence with respect to the NC-nucleation sequence. Schematic shows the relative positions between the enhancer sequence (lower strand, orange line) and the NC-nucleation sequence (upper strand, blue line). The photo shows the associated emission colors under UV excitation. (b) Chameleon NanoCluster Beacons, which take advantage of the repositioning-induced-color-tuning phenomenon, light up into different colors upon binding with distinct SNP targets. Adapted with permission from [31]. Copyright (2012) AmericanChemical Society.
Figure 4
Figure 4
(a) Representation of a quencher-mediated turn-on probe. After the quencher (black) is displaced by the target (red), fluorescence is enhanced by a proportional increase in the number of emissive clusters in the sample [80]. (b) Representation of a DNA detection assay using DNA/Ag NCs and graphene oxide (GO) nanohybrids. DNA/Ag NCs serves as a reporter while GO is a quencher. Silver clusters templated on the ssDNA are initially quenched by the GO. Once the adsorbed probe hybridizes with a target, the duplex is released from the GO and the fluorescence of the silver cluster is restored [83].
Figure 5
Figure 5
(a) Representation of hybridized DNA structures with a six-cytosine loop as nucleation site for Ag NC synthesis and their use in SNP detection. No fluorescence was observed for the mutant-type duplex after the nucleation process. However, the wild-type duplex produced strong yellow fluorescence emission [32]. (b) Representation of DNA abasic site-directed nucleation of emissive Ag NCs for selective nucleobase recognition [86]. When a cytosine was placed opposite to the abasic site, strong fluorescence emission was seen. On the other hand, when adenine, thymine, or guanine was placed opposite the abasic site, weak fluorescence was observed.
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