Optical Sensing by Transforming Chromophoric Silver Clusters in DNA Nanoreactors

Abstract

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 silver atoms that absorb at 400 nm and that 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 silver 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.

Silver Clusters as Both Chromophoric Reporters and DNA Ligands

“…2 and S2). 18,57 All three sensors have similar λ max values, which suggest that thymine modifications are inherently innocuous. However, the number of intervening thymines direct the amount of cluster produced and its extent of conversion, which suggests that the cluster environment is defined by the relative positions of the 5′ and 3′ sensor components.…”

“…Prior studies indicate that this relative amount has a minor impact on the synthetic outcome. 18 This solution was immediately transferred to a high pressure vessel with 500 psi O 2 at room temperature, and after >3 hrs, the sample was diluted three-fold in a buffer supplemented with NaClO 4 to yield a solution with 30 μM oligonucleotide. After adding the complement, the sample was heated to 50 °C for 20 mins and then cooled to room temperature for characterization.…”

Ten-Atom Silver Cluster Signaling and Tempering DNA Hybridization

“…A similar response with H 2 O 2 suggests that these two reagents act as oxidizing agents and selectively destroyed the green but not the more robust violet cluster. 41 Third, the 20-nucleotide template established a preferred cluster environment ( Figure S2 in the Supporting Information). Two abridged derivatives with 15 nucleotides shifted the absorption and diminished the absorbance, whereas two elongated derivatives with 24 and 28 nucleotides recovered the spectrum of the violet cluster.…”

“…Prior studies indicate that the relative amount of BH 4 − has a minor impact on the synthetic outcome. 41 The violet cluster was favored by exposing the solution to 500 psi O 2 at room temperature for 3 h. For mass spectrometry studies, these solutions were dialyzed to achieve 10 2 −10 6 dilution of lower molecular weight species. The dialysis was accomplished using the Vivaspin 20 (Sartorius) at 25°C and 4000 rpm.…”

A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors

“…Furthermore, their sensitivity is also limited due to the incomplete quenching (Tyagi et al 1998). To overcome these shortages, DNA-template silver nanoclusters have been developed as a new class of fluorophores (Guo et al 2009a;Gwinn et al 2008;Han and Wang 2012;LisaáPhipps 2012;Petty et al 2011;Petty et al 2004;Richards et al 2008;Sengupta et al 2008;Sharma et al 2010;Vosch et al 2007;Zheng et al 2007) that have been utilized in the analysis of various biological molecules (Guo et al 2009a;Guo et al 2009b;Lan et al 2011;Lan et al 2010;Yang and Vosch 2011;Zhou et al 2011).…”