A silver cluster-DNA equilibrium

Jeffrey T. Petty, Orlin O. Sergev, David A. Nicholson, Peter M. Goodwin, Banabihari Giri, D. Ryan McMullan

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)9868-9876
Number of pages9
JournalAnalytical Chemistry
Volume85
Issue number20
DOIs
StatePublished - Oct 15 2013

Fingerprint

Silver
DNA
Sensors
Oligonucleotides
Atoms
Size exclusion chromatography
Single-Stranded DNA
Nanostructured materials
Ligands
Composite materials
Chemical analysis
Temperature

ASJC Scopus subject areas

  • Analytical Chemistry

Cite this

Petty, J. T., Sergev, O. O., Nicholson, D. A., Goodwin, P. M., Giri, B., & McMullan, D. R. (2013). A silver cluster-DNA equilibrium. Analytical Chemistry, 85(20), 9868-9876. https://doi.org/10.1021/ac4028559

A silver cluster-DNA equilibrium. / Petty, Jeffrey T.; Sergev, Orlin O.; Nicholson, David A.; Goodwin, Peter M.; Giri, Banabihari; McMullan, D. Ryan.

In: Analytical Chemistry, Vol. 85, No. 20, 15.10.2013, p. 9868-9876.

Research output: Contribution to journalArticle

Petty, JT, Sergev, OO, Nicholson, DA, Goodwin, PM, Giri, B & McMullan, DR 2013, 'A silver cluster-DNA equilibrium', Analytical Chemistry, vol. 85, no. 20, pp. 9868-9876. https://doi.org/10.1021/ac4028559
Petty JT, Sergev OO, Nicholson DA, Goodwin PM, Giri B, McMullan DR. A silver cluster-DNA equilibrium. Analytical Chemistry. 2013 Oct 15;85(20):9868-9876. https://doi.org/10.1021/ac4028559
Petty, Jeffrey T. ; Sergev, Orlin O. ; Nicholson, David A. ; Goodwin, Peter M. ; Giri, Banabihari ; McMullan, D. Ryan. / A silver cluster-DNA equilibrium. In: Analytical Chemistry. 2013 ; Vol. 85, No. 20. pp. 9868-9876.
@article{adc30a9edd3e4ea58b544e2d10153c6a,
title = "A silver cluster-DNA equilibrium",
abstract = "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.",
author = "Petty, {Jeffrey T.} and Sergev, {Orlin O.} and Nicholson, {David A.} and Goodwin, {Peter M.} and Banabihari Giri and McMullan, {D. Ryan}",
year = "2013",
month = "10",
day = "15",
doi = "10.1021/ac4028559",
language = "English (US)",
volume = "85",
pages = "9868--9876",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "20",

}

TY - JOUR

T1 - A silver cluster-DNA equilibrium

AU - Petty, Jeffrey T.

AU - Sergev, Orlin O.

AU - Nicholson, David A.

AU - Goodwin, Peter M.

AU - Giri, Banabihari

AU - McMullan, D. Ryan

PY - 2013/10/15

Y1 - 2013/10/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84886918327&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84886918327&partnerID=8YFLogxK

U2 - 10.1021/ac4028559

DO - 10.1021/ac4028559

M3 - Article

C2 - 24032398

AN - SCOPUS:84886918327

VL - 85

SP - 9868

EP - 9876

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 20

ER -