QM/MM-MD dissociation of Ag+ and H+ mediated cytosine pairs: Monomers and dimers

Silver(I)-Mediated 2D DNA Nanostructures

Structural DNA nanotechnology enables the self-organization of matter at the nanometer scale, but approaches to expand the inorganic and electrical functionality of these scaffolds remain limited. Developments in nucleic acid metallics have enabled the incorporation of site-specific metal ions in DNA duplexes and provide a means of functionalizing the double helix with atomistic precision. Here a class of 2D DNA nanostructures that incorporate the cytosine-Ag+-cytosine (dC:Ag+:dC) base pair as a chemical trigger for self-assembly is described. It is demonstrated that Ag+-functionalized DNA can undergo programmable assembly into large arrays and rings, and can be further coassembled with guanine tetraplexes (G4). It is shown that 2D DNA lattices can be assembled with a variety of embedded nanowires at tunable spacing. These results serve as a foundation for further development of self-assembled, metalated DNA nanostructures, with potential for high-precision DNA nanoelectronics with nanometer pitch.

Nonradiative Deactivation of the Fluorescent Ag16-DNA and Ag10-DNA Emitters: The Role of Water

The luminescent quantum yield of silver-cluster emitters stabilized by short oligonucleotides (AgN-DNA) may be efficiently tuned by replacing nucleobases in their stabilization DNA matrices with analogues. In the present study, we proposed a valuable and straightforward theoretical methodology for assessing the photophysical behaviors emerging in AgN-DNA emitters after excitation. Using green Ag10-DNA and near-IR Ag16-DNA emitters we demonstrate how point guanine/inosine replacement could affect the photophysical rate constants of radiative/nonradiative processes. The main deactivation channel of the fluorescence of Ag16-DNA is intersystem crossing, which is in line with experimental data, whereas for Ag10-DNA the calculations overestimate the intersystem crossing rate possibly due to pure solvent contributions.

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

RATIONALE

Cytosine and its conjugates are prone to form protonated, triply-bonded dimers. Therefore, the nucleic-acid cytosine-rich sequence forms the four-stranded noncanonical secondary structure known as the intercalated motif (i-motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.

METHODS

To obtain the precursor ion fragmentation curve, the plot of SY against Ecomδ , the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q-TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6-31G(d,p).

RESULTS

The precursor ion fragmentation curve allowed the rating of the gas-phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas-phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine-deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine-cytosine nucleoside dimers but not in the formation of cytosine dimers.

CONCLUSIONS

The results obtained for nucleoside dimers indicated that the SY method may reflect the i-motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine-cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i-motif stabilities. Cytosine tautomer containing C2-OH… N(2H)-C4 moiety may be involved in the formation of protonated cytosine-cytosine nucleoside dimers.

Chemical reduction of Ag+ to Ag employing organic electron donors: evaluation of the effect of Ag+-mediated cytosine-cytosine base pairing on the aggregation of Ag nanoparticles

Ag⁺-mediated base pairing is valuable for synthesising DNA-based silver nanoparticles (AgNPs) and nanoclusters (AgNCs). Recently, we reported the formation of a [Ag(cytidine)₂]⁺ complex in dimethyl sulfoxide (DMSO), which facilitated the evaluation of the effect of cytosine-Ag⁺-cytosine (C-Ag⁺-C) base pairing on the degree of AgNP aggregation in solution. As an aprotic solvent, DMSO was expected to dissolve the [Ag(cytidine)₂]⁺ complex, and powerful reducing agents, such as organic electron donors. In this study, the chemical reduction of a cytidine/Ag⁺ system using a powerful reducing agent tetrakis(dimethylamino)ethylene (TDAE) was investigated. ¹H/¹³C/¹⁵N NMR spectroscopic evidence was obtained to identify the iminium dication (TDAE²⁺), which is an oxidised form of TDAE. The results were compared with those obtained using another organic electron donor, tetrathiafulvalene (TTF), which exhibits a relatively lower reduction activity than TDAE. AgNPs prepared via redox reaction between [Ag(cytidine)₂]⁺ and organic electron donors (TDAE and TTF) were characterised using UV-Vis spectroscopy and nanoparticle tracking analysis. It was found that the formation of C-Ag⁺-C base pairing inhibited the aggregation of AgNPs in solution. In addition, in the presence of cytidine, the total concentration of the AgNP solution was affected by the reduction activity of the reducing agent.

Effect of cytosine-Ag+-cytosine base pairing on the redox potential of the Ag+/Ag couple and the chemical reduction of Ag+ to Ag by tetrathiafulvalene

The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.