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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 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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biosensors-03-00185-f005: (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.

Mentions: Several methods (in addition to cNCBs [31]) have been developed to use DNA/Ag NCs to detect single-nucleotide polymorphisms (SNPs). In work done by Wang’s group, identification of the SNPs responsible for sickle cell anemia was achieved using a probe with a six-cytosine, NC-nucleation loop (Figure 5(a)) [32]. The probe was first hybridized with the wild-type and the mutant-type targets (T to A substitution), forming two different duplexes. After performing NC-nucleation process on these duplexes, almost no fluorescence was observed from the mutant-type duplex, whereas the wild-type duplex produced a strong yellow fluorescence emission. However, unlike cNCBs, this method differentiates single-nucleotide variants by the level of fluorescence intensity. It requires nanocluster synthesis process to take place after probe/target hybridization is completed, leading to a longer assay time. Moreover, it is not clear whether or not such a method can be generally applied to a wide variety of target sequences and still obtain similar discrimination results.


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

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

biosensors-03-00185-f005: (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.
Mentions: Several methods (in addition to cNCBs [31]) have been developed to use DNA/Ag NCs to detect single-nucleotide polymorphisms (SNPs). In work done by Wang’s group, identification of the SNPs responsible for sickle cell anemia was achieved using a probe with a six-cytosine, NC-nucleation loop (Figure 5(a)) [32]. The probe was first hybridized with the wild-type and the mutant-type targets (T to A substitution), forming two different duplexes. After performing NC-nucleation process on these duplexes, almost no fluorescence was observed from the mutant-type duplex, whereas the wild-type duplex produced a strong yellow fluorescence emission. However, unlike cNCBs, this method differentiates single-nucleotide variants by the level of fluorescence intensity. It requires nanocluster synthesis process to take place after probe/target hybridization is completed, leading to a longer assay time. Moreover, it is not clear whether or not such a method can be generally applied to a wide variety of target sequences and still obtain similar discrimination results.

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.