Jeffrey T. Petty

Base-Directed Formation of Fluorescent Silver Clusters

Small silver clusters that form with short oligonucleotides are distinguished by their strong fluorescence. Previous work showed that red and blue/green emitting species form with the cytosine oligonucleotide dC12. To understand how the bases and base sequence influence cluster formation, the blue/green emitting clusters that form with the thymine-containing oligonucleotides dT12, dT4C4T4, and dC4T4C4 are discussed. With dT12 and dT4C4T4, variations in the solution pH establish that the clusters associate with the N3 of thymine. The small clusters are bound to the larger DNA template, as demonstrated by fluorescence anisotropy, circular dichroism, and fluorescence correlation spectroscopy (FCS) studies. For dT4C4T4, FCS studies showed that approximately 50% of the strands are labeled with the fluorescent clusters. Absorption spectra and the gas dependence of the fluorescence show that nonfluorescent clusters also form following the reduction of the silver cation - oligonucleotide conjugates. Fluorescent cluster formation is favored by oxygen, thus indicating that the DNA-bound clusters are partially oxidized. To elaborate the sequence dependence of cluster formation, dC4T4C4 was studied. Cluster formation depends on the oligonucleotide concentration, and higher concentrations favor a red emitting species. A blue/green emissive species dominates at lower concentrations of dC4T4C4, and it has spectroscopic, physical, and chemical properties that are similar to those of the clusters that form with dT12 and dT4C4T4. These results suggest that cytosine- and thymine-containing oligonucleotides stabilize a preferred emissive silver cluster.

Optically enhanced, near-IR, silver cluster emission altered by single base changes in the DNA template.

Few-atom silver clusters harbored by DNA are promising fluorophores due to their high molecular brightness along with their long- and short-term photostability. Furthermore, their emission rate can be enhanced when co-illuminated with low-energy light that optically depopulates the fluorescence-limiting dark state. The photophysical basis for this effect is evaluated for two near-infrared-emitting clusters. Clusters emitting at ∼800 nm form with C(3)AC(3)AC(3)TC(3)A and C(3)AC(3)AC(3)GC(3)A, and both exhibit a trap state with λ(max) ∼ 840 nm and an absorption cross section of (5-6) × 10(-16) cm(2)/molecule that can be optically depopulated. Transient absorption spectra, complemented by fluorescence correlation spectroscopy studies, show that the dark state has an inherent lifetime of 3-4 μs and that absorption from this state is accompanied by photoinduced crossover back to the emissive manifold of states with an action cross section of ∼2 × 10(-18) cm(2)/molecule. Relative to C(3)AC(3)AC(3)TC(3)A, C(3)AC(3)AC(3)GC(3)A produces a longer-lived trap state and permits more facile passage back to the emissive manifold. With the C(3)AC(3)AC(3)AC(3)G template, a spectrally distinct cluster forms having emission at ∼900 nm, and its trap state has a ∼4-fold shorter lifetime. These studies of optically gated fluorescence bolster the critical role of the nucleobases in both the formation and excited state dynamics of these highly emissive metallic clusters.

DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters.

A bifunctional oligonucleotide integrates in situ synthesis of a fluorogenic silver cluster with recognition of a target DNA sequence. With the template C(3)AC(3)AC(3)GC(3)A, a complex forms with 10 silver atoms that possesses electronic transitions in the near-infrared and that is detected at nanomolar concentrations using diode laser excitation. Pendant to this cluster encoding region, the recognition component binds a target DNA strand through hybridization, and decoupling of these two regions of the composite sensor renders a modular sensor for specific oligonucleotides. A target is detected using a quencher strand that bridges the cluster template and recognition components and disturbs cluster binding, as indicated by static quenching. Competitive displacement of the quencher by the target strand restores the favored cluster environment, and our key finding is that this exchange enhances emission through a proportional increase in the number of emissive clusters. DNA detection is also accomplished in serum-containing buffers by taking advantage of the high brightness of this fluorophore and the inherently low endogenous background in the near-infrared spectral region. Cluster stability in this biological environment is enhanced by supplementing the solutions with Ag(+).

Electron spin resonance investigations of 11B12C, 11B13C, and 10B12C in neon, argon, and krypton matrices at 4 K: Comparison with theoretical results

The first spectroscopic study of the diatomic radical BC is reported which confirms previous theoretical predictions of a 4∑− electronic ground state. The nuclear hyperfine interactions (A tensors) obtained for 11B, 10B, and 13C from the electron spin resonance (ESR) measurements are compared with extensive ab initio CI calculations. The BC molecule is one of the first examples of a small high spin radical for such an in‐depth experimental–theoretical comparison. The electronic structure of BC obtained from an analysis of the nuclear hyperfine interaction (hfi) is compared to that obtained from a Mulliken‐type population analysis conducted on a CI wave function which yields Aiso and Adip results in good agreement with the observed values. The BC radical was generated by the laser vaporization of a boron–carbon mixture and trapped in neon, argon, and krypton matrices at 4 K for a complete ESR characterization. The magnetic parameters (MHz) obtained for 11B13C in solid neon are: g∥ =2.0015(3); g⊥ =2.0020(3)...

Optical sensing by transforming chromophoric silver clusters in DNA nanoreactors

Bifunctional DNA oligonucleotides serve as templates for chromophoric silver clusters and as recognition sites for target DNA strands, and communication between these two components is the basis of an oligonucleotide sensor. Few-atom silver clusters exhibit distinct electronic spectra spanning the visible and near-infrared region, and they are selectively synthesized by varying the base sequence of the DNA template. In these studies, a 16-base cluster template is adjoined with a 12-base sequence complementary to the target analyte, and hybridization induces structural changes in the composite sensor that direct the conversion between two spectrally and stoichiometrically distinct clusters. Without its complement, the sensor strand selectively harbors ~7 Ag atoms that absorb at 400 nm and fold the DNA host. Upon association of the target with its recognition site, the sensor strand opens to expose the cluster template that has the binding site for ~11 Ag atoms, and absorption at 720 nm with relatively strong emission develops in lieu of the violet absorption. Variations in the length and composition of the recognition site and the cluster template indicate that these types of dual-component sensors provide a general platform for near-infrared-based detection of oligonucleotides in challenging biological environments.

Transient infrared absorption spectrum of the ν1 fundamental of trans-DOCO

Using infrared (IR) difference‐frequency laser spectroscopy and 193 nm photolysis of acrylic acid(OD), the rotation–vibration spectrum of the ν1 O–D stretching fundamental of trans‐DOCO radical has been recorded and assigned. The assignment of the spectrum is based on the +0.9% gas phase‐argon matrix shift of the band origins, on the H/D isotopic shifts of the frequencies, and on the chemical reaction rate with O2. The rotational constants confirm that the spectrum is due to the planar trans isomer. The band center is ν0=2684.102 cm−1. Perturbations are observed in the Ka=1 and 6 levels, and information is obtained about the interacting states.

Neon matrix ESR investigation of 69,71GaAs+ generated by the photoionization of laser vaporized GaAs(s)

The first spectroscopic results are reported for the 69,71GaAs+ cation radical generated by photoionizing GaAs (g) produced by the pulsed laser vaporization of GaAs (s). The GaAs+ cation was trapped in neon matrices at 4 K for ESR investigations which show the ground electronic state to be 4Σ− in agreement with previously reported theoretical calculations. Components of the gallium A tensors are 69Ga; A⊥=184.2(2), A∥=270 (30) MHz, and for 71Ga A⊥=234.4(2), A∥=345(35) MHz. The unresolved As hfs was estimated to be less than 8 MHz for the perpendicular direction and the molecular g⊥ value as 1.9978(2) with g∥ presumably∼2.00. These nuclear hyperfine parameters are used to obtain a description of the valence electronic structure for GaAs+ which can be compared with recent MCSCF/CI theoretical results.

A Complementary Palette of NanoCluster Beacons

NanoCluster Beacons (NCBs), which use few-atom DNA-templated silver clusters as reporters, are a type of activatable molecular probes that are low-cost and easy to prepare. While NCBs provide a high fluorescence enhancement ratio upon activation, their activation colors are currently limited. Here we report a simple method to design NCBs with complementary emission colors, creating a set of multicolor probes for homogeneous, separation-free detection. By systematically altering the position and the number of cytosines in the cluster-nucleation sequence, we have tuned the activation colors of NCBs to green (C8–8, 460 nm/555 nm); yellow (C5–5, 525 nm/585 nm); red (C3–4, 580 nm/635 nm); and near-infrared (C3–3, 645 nm/695 nm). At the same NCB concentration, the activated yellow NCB (C5–5) was found to be 1.3 times brighter than the traditional red NCB (C3–4). Three of the four colors (green, yellow, and red) were relatively spectrally pure. We also found that subtle changes in the linker sequence (down to the single-nucleotide level) could significantly alter the emission spectrum pattern of an NCB. When the length of linker sequences was increased, the emission peaks were found to migrate in a periodic fashion, suggesting short-range interactions between silver clusters and nucleobases. Size exclusion chromatography results indicated that the activated NCBs are more compact than their native duplex forms. Our findings demonstrate the unique photophysical properties and environmental sensitivities of few-atom DNA-templated silver clusters, which are not seen before in common organic dyes or luminescent crystals.

Electron spin resonance studies of the methane radical cations (12,13CH+4, 12,13CDH+3, 12CD2H+2, 12CD3H+, 12CD+4) in solid neon matrices between 2.5 and 11 K: Analysis of tunneling

The radical cation of methane isolated in neon matrices exhibits highly unusual electron spin resonance (ESR) spectral features between 2.5 and 11 K. The anomaly has been clarified by invoking large amplitude tunneling motions of the hydrogens among several symmetrically equivalent Jahn–Teller distorted structures. The effect of the tunneling motions upon the ESR spectrum was investigated by an analysis scheme based upon permutation–inversion group theory. All the deuterium substituted cations, i.e., CDH+3, CD2H+2, CD3H+, and CD+4 were also studied. The hyperfine coupling constant of 13C was obtained from the study of 13CDH+3 and 13CH+4. Several independent generation methods were employed during the course of these methane cation studies, including photoionization, electron bombardment, x‐irradiation, and a pulsed laser surface ionization technique.

The generation of 12C31P and 13C31P by reactive laser vaporization for rare gas matrix electron spin resonance studies: Comparison with abinitio theoretical calculations

The 12C31P and 13C31P diatomic radicals have been generated by the laser vaporization reaction between carbon and phosphorus which were pressed into a pellet to form the laser target. This method is applicable to a wide range of nonmetallic systems for generating new reactive intermediates which cannot be done with more conventional approaches. The radicals were isolated in neon and argon matrices at 4 K for detailed ESR investigations. The magnetic parameters (MHz) for neon were: g∥=2.0009(3); g⊥=1.9902(3); A∥(31P)=145.0(3); A⊥(31P)=−269.0(2); A∥(13C)=580.0(3); and A⊥(13C)=422.0(3). The argon A and g tensors were virtually indistinguishable from these neon results. Extensive ab initio theoretical calculations were conducted for CP which yielded nuclear hyperfine A values in close agreement with the experimental results. Valence orbital spin populations extracted from the calculated CI wave functions are compared with those determined directly from the ESR hyperfine parameters for 13C and 31P. The observe...