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Removal of the A₁₀ adenosine in a DNA-stabilized Ag₁₆ nanocluster.

ABSTRACT: The role of the terminal adenosine (A₁₀) on the spectroscopic and structural properties of a previously described DNA-stabilized Ag₁₆ nanocluster (DNA:Ag₁₆NC) is presented. In the original DNA:Ag₁₆NCs (5'-CACCTAGCGA-3'), the A₁₀ nucleobase was involved in an Ag⁺-mediated interaction with an A₁₀ in a neighboring asymmetric unit, and did not interact with the Ag₁₆NC. Therefore, we synthesized AgNCs embedded in the corresponding 9-base sequence in order to investigate the crystal structure of these new DNA-A₁₀:Ag₁₆NCs and analyze the photophysical properties of the solution and crystalline state. The X-ray crystallography and spectroscopic measurements revealed that the 3'-end adenosine has little importance with respect to the photophysics and structure of the Ag₁₆NCs. Additionally, the new crystallographic data was recorded with higher spatial resolution leading to a more detailed insight in the interactions between the nucleotides and Ag atoms.

SUBMITTER: Cerretani C

PROVIDER: S-EPMC9054913 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Ag16B4O10 has been obtained as a coarse crystalline material via hydrothermal synthesis, and was characterized by X-ray single crystal and powder diffraction, conductivity and magnetic susceptibility measurements, as well as by DFT based theoretical analyses. Neither composition nor crystal structure nor valence electron counts can be fully rationalized by applying known bonding schemes. While the rare cage anion (B4O10)8- is electron precise, and reflects standard bonding properties, the silver ion substructure necessarily has to accommodate eight excess electrons per formula unit, (Ag+)16(B3+)4(O2-)10 × 8e-, rendering the compound sub-valent with respect to silver. However, the phenomena commonly associated with sub-valence metal (partial) structures are not perceptible in this case. Experimentally, the compound has been found to be semiconducting and diamagnetic, ruling out the presence of itinerant electrons; hence the excess electrons have to localize pairwise. However, no pairwise contractions of silver atoms are realized in the structure, thus excluding formation of 2e-2c bonds. Rather, cluster-like aggregates of an approximately tetrahedral shape exist where the Ag-Ag separations are significantly smaller than in elemental silver. The number of these subunits per formula is four, thus matching the required number of sites for pairwise nesting of eight excess electrons. This scenario has been corroborated by computational analyses of the densities of states and electron localization function (ELF), which clearly indicate the presence of an attractor within the shrunken tetrahedral voids in the silver substructure. However, one bonding electron pair of s and p type skeleton electrons per cluster unit is extremely low, and the significant propensity to form and the thermal stability of the title compound suggest d10-d10 bonding interactions to strengthen the inter-cluster bonding in a synergistic fashion. With the present state of knowledge, such a particular bonding pattern appears to be a singular feature of the oxide chemistry of silver; however, as indicated by analogous findings in related silver oxides, it is evolving as a general one.

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Removal of the A₁₀ adenosine in a DNA-stabilized Ag₁₆ nanocluster.

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Removal of the A₁₀ adenosine in a DNA-stabilized Ag₁₆ nanocluster.