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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.


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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].
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biosensors-03-00185-f002: 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].

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)

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

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

biosensors-03-00185-f002: 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].
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.


Related in: MedlinePlus