Optically Enhanced, Near-IR, Silver Cluster Emission Altered by Single Base Changes in the DNA Template

Abstract

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 C3AC3AC3TC3A and C3AC3AC3GC3A and both exhibit a trap state with λmax ~ 840 nm and an absorption cross section of 5–6 × 10−16 cm2/molec 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 cm2/molec. Relative to C3AC3AC3TC3A, C3AC3AC3GC3A produces a longer-lived trap state and permits more facile passage back to the emissive manifold. With the C3AC3AC3AC3G template, a spectrally distinct cluster forms having emission at ~900 nm and its trap state has a ~four-fold shorter lifetime. These studies of optically-gated fluorescence bolster the critical role of the nucleobases on 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

“…29,33,36 Base substitutions indicate that the cluster associates with the 3' region of C 3 AC 3 AC 3 GC 3 A, thus the recognition component for DNA binding was appended to this terminus. 30 The cluster bound to C 3 AC 3 AC 3 GC 3 A-duplexes display similar spectra in relation to C 3 AC 3 AC 3 GC 3 A alone, thus supporting integrity of the cluster binding site with the proximal duplex (Figs. 2A/2B and 1S).…”

“…These analogous properties support the formation of the same 10-atom Ag cluster with both templates. 30 The spectral differences indicate that the electronic environment for the cluster depends on the DNA context, and the impact of the nucleobase environment is also evident in the two- to three-fold enhancement in the emission when S B s -TG 3 is replaced by S B (Fig. 2B).…”

“…Fluorescence correlation spectroscopy studies were conducted using diode laser excitation at 690 nm with current and temperature control (LTC100, Thorlabs). 30 A 63× 1.2 NA water immersion microscope objective (Zeiss) was used in a laser epi-illuminated geometry to excite the sample and collect the fluorescence. A long-pass dichroic (Semrock) was used to reflect the laser and transmit cluster emission, which was passed through a long pass filter and coupled into a 50-μm diameter fiber located at the image plane of the microscope.…”

“…32,33 To fully model the correlation function, coupling of a dark electronic state was included in the analysis. 30 Size exclusion chromatography used a 300 × 7.8 mm i.d. column (BioSep, Phenomenex) on an HPLC system (Prominence, Shimadzu) using a 10 mM citrate buffer at pH = 7 with 300 mM NaClO 4 to minimize matrix adsorption.…”

A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

“…Excluding the first 2 Ts, this 10-base sequence is a sub-sequence of several 16-base oligomers known to stabilize fluorescent silver nanoclusters, albeit in homodimer form with near-infrared (nIR) emission. 13,34,35 The shorter wavelength emission of NC22 in its 'off'-state suggests that its cluster contains fewer silver atoms than those nIR-emitting clusters formed by related homodimers. The two distinct AgNCs generated by the 3′-block-NC22 (shown schematically in Fig.…”