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

Obliosca JM, Liu C, Batson RA, Babin MC, Werner JH, Yeh HC - Biosensors (Basel) (2013)

Bottom Line: Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA. jmobliosca@utexas.edu.

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.

No MeSH data available.


(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.
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biosensors-03-00185-f001: (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.

Mentions: Compared to gold nanoclusters, silver nanoclusters are brighter [34] and can be easily synthesized by using a number of ligands as stabilization agents (also called “encapsulation agents” or “templates”), including zeolites [41,42], PAMAM [40,43], PMMA [44], polyacrylate [45,46], poly(NIPAM-AA-HEA) microgels [47], sugar molecules [48], mercaptosuccinic acid [49], lipoic acid [50], thiol ligands [51], peptides [52] and DNA [24,26,28]. Among the different Ag NCs synthesized, ssDNA-templated silver nanoclusters (DNA/Ag NCs, Figure 1(a)) have become the center of research focus due to three key advantages. First, the fluorescence emission of DNA/Ag NCs can be tuned throughout the visible and near-IR range by simply programming the template sequences (Figure 1(b)). A complementary palette of DNA/Ag NC fluorophores has been produced [27,28]. Second, fluorescence of Ag NCs can be switched on and off [29,30] or color tuned [30,31] through interactions with a nearby DNA sequence (called an enhancer, see the next section) (Figure 1(c), Figure 2(a)). These emerging properties allow DNA/Ag NCs to be used not only as fluorescent tags but as sensors/indicators, leading to a variety of new biosensing opportunities, especially in DNA/RNA detection. Third, all DNA/Ag NCs share a similar UV excitation feature, regardless of the location of their visible excitation peaks (Figure 1(d)) [53]. In other words, it is possible to use a single UV source to excite all silver cluster species templated on DNA for multiplexed detection.


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

Obliosca JM, Liu C, Batson RA, Babin MC, Werner JH, Yeh HC - Biosensors (Basel) (2013)

(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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263537&req=5

biosensors-03-00185-f001: (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.
Mentions: Compared to gold nanoclusters, silver nanoclusters are brighter [34] and can be easily synthesized by using a number of ligands as stabilization agents (also called “encapsulation agents” or “templates”), including zeolites [41,42], PAMAM [40,43], PMMA [44], polyacrylate [45,46], poly(NIPAM-AA-HEA) microgels [47], sugar molecules [48], mercaptosuccinic acid [49], lipoic acid [50], thiol ligands [51], peptides [52] and DNA [24,26,28]. Among the different Ag NCs synthesized, ssDNA-templated silver nanoclusters (DNA/Ag NCs, Figure 1(a)) have become the center of research focus due to three key advantages. First, the fluorescence emission of DNA/Ag NCs can be tuned throughout the visible and near-IR range by simply programming the template sequences (Figure 1(b)). A complementary palette of DNA/Ag NC fluorophores has been produced [27,28]. Second, fluorescence of Ag NCs can be switched on and off [29,30] or color tuned [30,31] through interactions with a nearby DNA sequence (called an enhancer, see the next section) (Figure 1(c), Figure 2(a)). These emerging properties allow DNA/Ag NCs to be used not only as fluorescent tags but as sensors/indicators, leading to a variety of new biosensing opportunities, especially in DNA/RNA detection. Third, all DNA/Ag NCs share a similar UV excitation feature, regardless of the location of their visible excitation peaks (Figure 1(d)) [53]. In other words, it is possible to use a single UV source to excite all silver cluster species templated on DNA for multiplexed detection.

Bottom Line: Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA. jmobliosca@utexas.edu.

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.

No MeSH data available.