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The use of DNA as a scaffold for nanoclusters is particularly interesting due to its structural versatility and easy integration with aptamers. In their structure, aptamers often contain non-canonical forms of DNA, i.e., G-quadruplexes (GQs). Four-stranded GQs are used to construct nanomachines and biosensors for monitoring changes in the concentration of potassium ions. In the present study, we continue our work related to the synthesis of silver nanoclusters formed on a bifunctional DNA template. By attaching a cytosine-rich domain (C12) to a G-quadruplex-forming sequence—human telomeric (Tel22) or thrombin-binding aptamer (TBA)—we constructed bifunctional templates for fluorescent silver nanoclusters (C12) with the ability to detect potassium ions (GQs). The changing localization of the C12 domain from the 3′ to 5′ end of the oligonucleotide was a successful way to improve the fluorescence properties of the obtained fluorescent probes. The best performance as a probe for potassium ions was exhibited by C12Tel22-AgNCs, with an LOD of 0.68 mM in PBS. The introduction of the fluorescent cytosine analog tC leads to an LOD of 0.68 mM in PBS and 0.46 mM in Tris-acetate. Additionally, we performed AFM, TEM, DLS analysis, and cellular studies to further investigate the structural properties and behavior of the Tel22C12-AgNCs in biological contexts.

We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius σ = 5.0 Å was chosen on the basis of a comparison of the calculated translational diffusion coefficients ( D T) and the rotational relaxation times ( τ R) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D T and τ R of tRNA Phe. Better agreement with the experimental data was achieved for slightly larger σ = 5.7 Å. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D T of small proteins were used to establish the optimum value of σ = 4.5 Å for amino acids. The lack of experimental data on τ R for proteins restricted the tests to the translational diffusion properties.

The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.

We analyze the structure of napin (BngNAP1), a storage protein (m.w. 14.5 kDa) from Brassica napus. On the basis of the results of 1H NMR spectroscopy and dynamic light scattering (DLS) studies, the overall shape and secondary structure of the molecule are estimated.