16 research outputs found
A Segregated, Partially Oxidized, and Compact Ag\u3csub\u3e10\u3c/sub\u3e Cluster within an Encapsulating DNA Host
Silver clusters develop within DNA strands and become optical chromophores with diverse electronic spectra and wide-ranging emission intensities. These studies consider a specific cluster that absorbs at 400 nm, has low emission, and exclusively develops with single-stranded oligonucleotides. It is also a chameleon-like chromophore that can be transformed into different highly emissive fluorophores. We describe four characteristics of this species and conclude that it is highly oxidized yet also metallic. One, the cluster size was determined via electrospray ionization mass spectrometry. A common silver mass is measured with different oligonucleotides and thereby supports a Ag10 cluster. Two, the cluster charge was determined by mass spectrometry and Ag L3-edge X-ray absorption near-edge structure spectroscopy. Respectively, the conjugate mass and the integrated white-line intensity support a partially oxidized cluster with a +6 and +6.5 charge, respectively. Three, the cluster chirality was gauged by circular dichroism spectroscopy. This chirality changes with the length and sequence of its DNA hosts, and these studies identified a dispersed binding site with ∼20 nucleobases. Four, the structure of this complex was investigated via Ag K-edge extended X-ray absorption fine structure spectroscopy. A multishell fitting analysis identified three unique scattering environments with corresponding bond lengths, coordination numbers, and Debye-Waller factors for each. Collectively, these findings support the following conclusion: a Ag10+6 cluster develops within a 20-nucleobase DNA binding site, and this complex segregates into a compact, metal-like silver core that weakly links to an encapsulating silver-DNA shell. We consider different models that account for silver-silver coordination within the core
A silver cluster-DNA equilibrium
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\u27 cluster domain CCCCAACTCCTT with different 3\u27 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\u27 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\u27t 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
Near-Infrared Silver Cluster Optically Signaling Oligonucleotide Hybridization and Assembling Two DNA Hosts
Silver
clusters with ∼10 atoms form within DNA strands,
and the conjugates are chemical sensors. The DNA host hybridizes with
short oligonucleotides, and the cluster moieties optically respond
to these analytes. Our studies focus on how the cluster adducts perturb
the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide
with two components: a 5′-cluster domain that complexes silver
clusters and a 3′-recognition site that hybridizes with a target
oligonucleotide. The single-stranded sensor encapsulates an ∼11
silver atom cluster with violet absorption at 400 nm and with minimal
emission. The recognition site hybridizes with complementary oligonucleotides,
and the violet cluster converts to an emissive near-infrared cluster
with absorption at 730 nm. Our key finding is that the near-infrared
cluster coordinates two of its hybridized hosts. The resulting tertiary
structure was investigated using intermolecular and intramolecular
variants of the same dimer. The intermolecular dimer assembles in
concentrated (∼5 μM) DNA solutions. Strand stoichiometries
and orientations were chromatographically determined using thymine-modified
complements that increase the overall conjugate size. The intramolecular
dimer develops within a DNA scaffold that is founded on three linked
duplexes. The high local cluster concentrations and relative strand
arrangements again favor the antiparallel dimer for the near-infrared
cluster. When the two monomeric DNA/violet cluster conjugates transform
to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate
silver. We propose that these correlated changes in DNA structure
and silver stoichiometry underlie the violet to near-infrared cluster
transformation
Silver clusters as both chromophoric reporters and DNA ligands
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 change with hybridization. The sensor strand integrates two functions: the 3\u27 region binds target DNA strands through base recognition while the 5\u27 sequence C(3)AC(3)AC(3)TC(3)A 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\u27 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
A Segregated, Partially Oxidized, and Compact Ag<sub>10</sub> Cluster within an Encapsulating DNA Host
Silver
clusters develop within DNA strands and become optical chromophores
with diverse electronic spectra and wide-ranging emission intensities.
These studies consider a specific cluster that absorbs at 400 nm,
has low emission, and exclusively develops with single-stranded oligonucleotides.
It is also a chameleon-like chromophore that can be transformed into
different highly emissive fluorophores. We describe four characteristics
of this species and conclude that it is highly oxidized yet also metallic.
One, the cluster size was determined via electrospray ionization mass
spectrometry. A common silver mass is measured with different oligonucleotides
and thereby supports a Ag<sub>10</sub> cluster. Two, the cluster charge
was determined by mass spectrometry and Ag L<sub>3</sub>-edge X-ray
absorption near-edge structure spectroscopy. Respectively, the conjugate
mass and the integrated white-line intensity support a partially oxidized
cluster with a +6 and +6.5 charge, respectively. Three, the cluster
chirality was gauged by circular dichroism spectroscopy. This chirality
changes with the length and sequence of its DNA hosts, and these studies
identified a dispersed binding site with ∼20 nucleobases. Four,
the structure of this complex was investigated via Ag K-edge extended
X-ray absorption fine structure spectroscopy. A multishell fitting
analysis identified three unique scattering environments with corresponding
bond lengths, coordination numbers, and Debye–Waller factors
for each. Collectively, these findings support the following conclusion:
a Ag<sub>10</sub><sup>+6</sup> cluster develops within a 20-nucleobase
DNA binding site, and this complex segregates into a compact, metal-like
silver core that weakly links to an encapsulating silver–DNA
shell. We consider different models that account for silver–silver
coordination within the core
Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization
Silver clusters with ∼10 atoms
are molecules, and specific
species develop within DNA strands. These molecular metals have sparsely
organized electronic states with distinctive visible and near-infrared
spectra that vary with cluster size, oxidation, and shape. These small
molecules also act as DNA adducts and coordinate with their DNA hosts.
We investigated these characteristics using a specific cluster-DNA
conjugate with the goal of developing a sensitive and selective biosensor.
The silver cluster has a single violet absorption band (λ<sub>max</sub> = 400 nm), and its single-stranded DNA host has two domains
that stabilize this cluster and hybridize with target oligonucleotides.
These target analytes transform the weakly emissive violet cluster
to a new chromophore with blue-green absorption (λ<sub>max</sub> = 490 nm) and strong green emission (λ<sub>max</sub> = 550
nm). Our studies consider the synthesis, cluster size, and DNA structure
of the precursor violet cluster-DNA complex. This species preferentially
forms with relatively low amounts of Ag<sup>+</sup>, high concentrations
of the oxidizing agent O<sub>2</sub>, and DNA strands with ≳20
nucleotides. The resulting aqueous and gaseous forms of this chromophore
have 10 silvers that coalesce into a single cluster. This molecule
is not only a chromophore but also an adduct that coordinates multiple
nucleobases. Large-scale DNA conformational changes are manifested
in a 20% smaller hydrodynamic radius and disrupted nucleobase stacking.
Multidentate coordination also stabilizes the single-stranded DNA
and thereby inhibits hybridization with target complements. These
observations suggest that the silver cluster-DNA conjugate acts like
a molecular beacon but is distinguished because the cluster chromophore
not only sensitively signals target analytes but also stringently
discriminates against analogous competing analytes
Silver Clusters as Both Chromophoric Reporters and DNA Ligands
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 change with hybridization. The sensor strand
integrates two functions: the 3′ region binds target DNA strands
through base recognition while the 5′ sequence C<sub>3</sub>AC<sub>3</sub>AC<sub>3</sub>TC<sub>3</sub>A 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