DNA Sensing by Amplifying the Number of Near-Infrared Emitting, Oligonucleotide-Encapsulated Silver Clusters

Petty, Jeffrey T.; Sengupta, Bidisha; Story, Sandra P.; Degtyareva, Natalya N.

doi:10.1021/ac201321m

Cited by 81 publications

(108 citation statements)

References 53 publications

(134 reference statements)

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“…20,24 To illustrate, hybridizing strands invade cluster binding sites and quench emission, while repositioned complements relieve static quenching. 51 Thus, base pairing overrides cluster association, but the effect is reversible. Hybridization also regulates cluster environments within S1-S2.…”

Section: Discussionmentioning

confidence: 99%

A Silver Cluster–DNA Equilibrium

et al. 2013

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DNA encapsulates silver clusters, and these hybrid nanomaterials form molecular sensors. We discuss a silver cluster-oligonucleotide sensor with four characteristics. First, a specific reporting cluster forms within a single-stranded DNA. This template uses the 5’ cluster domain CCCCAACTCCTT with different 3’ recognition sites for complementary oligonucleotides. The modular composite strand exclusively forms a cluster with λmax = 400 nm and with low emission. Conjugates were chromatographically purified, and their elemental analysis measured a cluster adduct with ~11 silver atoms. Second, hybridization transforms the cluster. Size exclusion chromatography shows that the 3’ recognition sites of the single-stranded conjugates hybridize with their complements. This secondary structural change both shifts cluster absorption from 400 to 490 nm and develops emission at 550 nm. Third, cluster size remains intact. Like their violet predecessors, purified blue-green clusters have ~11 silver atoms. Cluster integrity is further supported by extracting the complement from the blue-green conjugate and reversing the spectral changes. Fourth, the cluster transformation is an equilibrium. Complementary strands generate an isosbestic point and thus directly link single-stranded hosts for the violet cluster and their hybridized analogs for the blue-green cluster. This equilibrium shifts with temperature. A van’t Hoff analysis shows that longer and more stable duplexes favor the blue-green cluster. However, hybridized cluster hosts are less stable than their native DNA counterparts, and stability further degrades when short complements expose nucleobases within S1-S2. Duplex instability suggests that unpaired nucleobases coordinate the violet cluster and favor the single-stranded sensor. A balance between innate hybridization and exogenous folding highlights a distinct feature of silver clusters for sensing – they are both chromophoric reporters and ligands that modulate analyte-sensor interactions.

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Section: Discussionmentioning

confidence: 99%

A Silver Cluster–DNA Equilibrium

et al. 2013

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“…54,55 As in an earlier studies, fluorescence correlation spectroscopy was conducted using diode laser excitation at 690 nm, and cluster concentrations were derived using a solution of Cy7 to calibrate the probe volume. 30 …”

Section: Methodsmentioning

confidence: 99%

“…28,29 A resulting lower background combined with the inherent brightness of silver cluster fluorophores facilitates sensitive detection in complex samples. 27,30–32 Furthermore, optically-based analysis is also attractive because near infrared emitting diode lasers are commercially available for selective cluster excitation. 33 …”

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confidence: 99%

Silver Clusters as Both Chromophoric Reporters and DNA Ligands

et al. 2013

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Molecular silver clusters conjugated with DNA act as analyte sensors. Our studies evaluate a type of cluster-laden DNA strand whose structure and silver stoichiometry changes with hybridization. The sensor strand integrates two functions: the 3′ region binds target DNA strands through base recognition while the 5′ sequence C3AC3AC3TC3A favors formation of a near infrared absorbing and emitting cluster. This precursor form exclusively harbors an ~11 silver atom cluster that absorbs at 400 nm and that condenses its single-stranded host. The 3′ recognition site associates with a complementary target strand, thereby effecting a 330 nm red-shift in cluster absorption and a background-limited recovery of cluster emission at 790 nm. One factor underlying these changes is sensor unfolding and aggregation. Variations in salt and oligonucleotide concentrations control cluster development by influencing DNA association. Structural studies using fluorescence anisotropy, fluorescence correlation spectroscopy, and size exclusion chromatography show that the sensor-cluster conjugate opens and subsequently dimerizes with hybridization. A second factor contributing to the spectral and photophysical changes is cluster transformation. Empirical silver stoichiometries are preserved through hybridization, so hybridized, dimeric near infrared conjugates host twice the amount of silver in relation to their violet absorbing predecessors. These DNA structure and net silver stoichiometry alterations provide insight into how DNA-silver conjugates recognize analytes.

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“…[19][20][21][22][23] On the practical side, by rational incorporation of DNA aptamers, the fluorescence signaling of AgNCs has been successfully coupled with the molecular recognition property of DNA to design biosensors and smart imaging probes. [24][25][26][27][28][29][30][31][32][33][34][35][36] An interesting and useful discovery is that the fluorescence of many NCs is strongly quenched by Hg 2+ , allowing its detection at low nM and even sub-nM concentrations. 20,[37][38][39][40][41][42] Despite its importance in analytical chemistry, our fundamental understanding of NCs is still quite limited.…”

Section: Introductionmentioning

confidence: 99%