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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) 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].
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biosensors-03-00185-f004: (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].

Mentions: Petty’s group reported a turn-on nanocluster probe that has silver clusters initially quenched through hybridization with a quencher strand. As shown in Figure 4(a), the DNA target binds to the NC probe through a competitive process called toehold displacement [80]. While eliminating the need of a guanine-rich enhancer for turning on the fluorescence, this method gives only 2 to 3 fold of fluorescence enhancement upon target binding. Petty and Dickson have previously characterized the near-infrared-emitting silver cluster species (emission maxima around 770 nm) templated within their NC-nucleation sequence, 5′-C3AC3AC3GC3A. Using inductively coupled plasma atomic emission spectroscopy, a stoichiometry of 10 silver atoms per oligonucleotide was determined [63]. Similar to our results, Petty also found that fluorescence enhances through a proportional increase in the number of emissive clusters [80]. As for their turn-on mechanisms, they believe quencher invasion into the 3' region of the NC-nucleation sequence might have driven the silver cluster to a binding site having a different electronic environment, leading to the observed quenching effect. The key advantage of this method lies in the emitter’s near-infrared electronic transition, which enables DNA detection in serum-containing buffers (whose endogenous background fluorescence is low in the near-infrared spectral region). However, it is not clear whether or not the detection scheme shown in Figure 4(a) can be applied to longer DNA targets.


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

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

biosensors-03-00185-f004: (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].
Mentions: Petty’s group reported a turn-on nanocluster probe that has silver clusters initially quenched through hybridization with a quencher strand. As shown in Figure 4(a), the DNA target binds to the NC probe through a competitive process called toehold displacement [80]. While eliminating the need of a guanine-rich enhancer for turning on the fluorescence, this method gives only 2 to 3 fold of fluorescence enhancement upon target binding. Petty and Dickson have previously characterized the near-infrared-emitting silver cluster species (emission maxima around 770 nm) templated within their NC-nucleation sequence, 5′-C3AC3AC3GC3A. Using inductively coupled plasma atomic emission spectroscopy, a stoichiometry of 10 silver atoms per oligonucleotide was determined [63]. Similar to our results, Petty also found that fluorescence enhances through a proportional increase in the number of emissive clusters [80]. As for their turn-on mechanisms, they believe quencher invasion into the 3' region of the NC-nucleation sequence might have driven the silver cluster to a binding site having a different electronic environment, leading to the observed quenching effect. The key advantage of this method lies in the emitter’s near-infrared electronic transition, which enables DNA detection in serum-containing buffers (whose endogenous background fluorescence is low in the near-infrared spectral region). However, it is not clear whether or not the detection scheme shown in Figure 4(a) can be applied to longer DNA targets.

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.