Structure and Formation of Luminescent Centers in Light-Up Ag Cluster-Based DNA Probes

Abstract

Fluorescent beacons based on silver (Ag) clusters for DNA/RNA detection represent a new type of turn-on probe that fluoresces upon hybridization to target nucleobase sequences. Physical–chemical mechanisms of their fluorescence activation still remain poorly understood. We studied in detail the fluorescence activation of dark Ag clusters induced by interactions of Ag–DNA complexes with different DNA sequences. In all cases, the final result depends neither on the location of the precursors (dark clusters) nor on their spectral properties. The reaction of fluorescence activation is a process similar to the growth of fluorescent silver clusters on dsDNA matrices. In both cases, reactants are dark clusters and two adjacent DNA strands. The latter form a double-stranded template for cluster nucleation. We found the optimized structure of a green fluorescent Ag4 +2 cluster assembled on a C3/C3 DNA dimer in two different ssDNA pairs using QM modeling. The calculated absorption spectra match nicely the experimental ones, which proves the optimized structures. We conclude that apparent fluorescence activation in the studied systems results from reassembling Ag clusters on the new dsDNA template formed upon hybridization with the target. The suggested mechanism of “fluorescence activation” offers a way to design new light-up DNA probes. Two DNA strands making up the dsDNA template providing a high yield of bright Ag clusters can be used as the halves with the “stick” tails hybridizing with the base sequence of the target DNA. In this way, we have designed a light-up Ag cluster probe for β-actin mRNA.

Optical, structural, and biological properties of silver nanoclusters formed within the loop of a C-12 hairpin sequence

“…A limited number of studies have shown resolved structures of AgNCs including X-ray crystallography 8,9 and computational reports. 34 Further studies are expected to uncover more details of structural control and reproducibility, making it possible to regulate properties of the nanoclusters both wanted (fluorescence wavelength and intensity) and unwanted (stability).…”

“…It has been recently suggested that the core of the "luminescent" cluster may be different from the size of the full AgNC. 34 Further visualization of molecular orbitals involved in the visible transitions conrmed the highly delocalized properties of the AgNC@hpC 12 . Fig.…”

“…32 Both experimental and computational studies have already contributed to our understanding of the shape and size of the AgNC@DNA within the templating DNA sequence. 33,34 However, structural details of the AgNC@DNA are still missing despite a few X-ray crystallography studies identifying the exact structures of different AgNC@DNA. 8,9 Computational studies can bridge the gap in experimental techniques which still cannot reach the level of materials comprised of only a few atoms.…”

Migration of Excitation Energy in Furocoumarins

“…Using the software package, you can determine the important characteristics of the electronic states of polyatomic molecules: the energies and nature of molecular orbitals, the energies and wave functions of singlet and triplet electronically excited states, the oscillator strength and polarization of electronic transitions, the distribution of the electron density on the atoms and bonds of the molecule, the dipole moments in ground and excited states, rate constants of radiative and nonradiative processes involving electronically excited states of molecules, as well as absorption spectra from excited singlet and triplet states ( Artyukhov et al, 2008 ; Alfimov et al, 2014 ; Artyukhov et al, 1997 ; Plotnikov, 1979 ; Pomogaev and Artyukhov, 2001 ). Moreover, this software set has achieved success in solving the problems of large molecules photonics ( Plotnikov, 1979 ; Artyukhov and Pomogaev, 2000 ; Bocharnikova et al, 2019 ; Liano et al, 2003 ; Reveguk et al, 2020 ; Tchaikovskaya et al, 2020 ). The methodology for studying the spectral-luminescent properties of complex molecules was described in ( Alfimov and Plotnikov, 2014 ; Bocharnikova et al, 2020 ).…”

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA–Silver Cluster Chromophores

“…Nucleobases preferentially coordinate silvers but with different affinities, so a particular pattern of nucleobase ligands encodes the cluster spectra. ,,,− Second, DNA structure shapes binding sites. A single-stranded oligonucleotide can both encapsulate a cluster and hybridize with a complement. ,− Complementary base pairs block cluster binding sites on nucleobases and force a DNA-bound cluster to reorganize, which can enhance emission by ≲10 3 fold. Third, a flexible DNA wraps around a cluster to give compact and emissive conjugates because hinge sites allow the oligonucleotide to fold. − Fourth, DNA strands assemble around a shared cluster.…”