Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides.

Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.

Synthesis and Biological Evaluation of Novel Amino and Amido Substituted Pentacyclic Benzimidazole Derivatives as Antiproliferative Agents.

Newly designed pentacyclic benzimidazole derivatives featuring amino or amido side chains were synthesized to assess their in vitro antiproliferative activity. Additionally, we investigated their direct interaction with nucleic acids, aiming to uncover potential mechanisms of biological action. These compounds were prepared using conventional organic synthesis methodologies alongside photochemical and microwave-assisted reactions. Upon synthesis, the newly derived compounds underwent in vitro testing for their antiproliferative effects on various human cancer cell lines. Notably, derivatives 6 and 9 exhibited significant antiproliferative activity within the submicromolar concentration range. The biological activity was strongly influenced by the N atom's position on the quinoline moiety and the position and nature of the side chain on the pentacyclic skeleton. Findings from fluorescence, circular dichroism spectroscopy, and thermal melting assays pointed toward a mixed binding mode-comprising intercalation and the binding of aggregated compounds along the polynucleotide backbone-of these pentacyclic benzimidazoles with DNA and RNA.

Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential.

The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect.

Photoluminescent Gold/BSA Nanoclusters (AuNC@BSA) as Sensors for Red-Fluorescence Detection of Mycotoxins.

The BSA-encapsulated gold nanoclusters (AuNC@BSA) have drawn considerable interest and demonstrated applications as biological sensors. In this study, we demonstrated that the red-emitting AuNC@BSA prepared using a modified procedure fully retained the binding of standard BSA-ligands (small molecule drugs), significantly improving fluorescence detection in some cases due to the red-emission property. Further, we showed that AuNC@BSA efficiently bind a series of aflatoxin-related mycotoxins as well as the aliphatic mycotoxin FB1, reporting interactions in the nanomolar range by instantaneous emission change at 680 nm. Such red emission detection is advantageous over current detection strategies for the same mycotoxins, based on complex mass spectrometry procedures or, eventually (upon chemical modification of the mycotoxin), by fluorescence detection in the UV range (<400 nm). The later technique yields fluorescence strongly overlapping with the intrinsic absorption and emission of biorelevant mixtures in which mycotoxins appear. Thus, here we present a new approach using the AuNC@BSA red fluorescence reporter for mycotoxins as a fast, cheap, and simple detection technique that offers significant advantages over currently available methods.

Optical microstructures based on surface-selective growth of Ag nanoparticles on thermally poled soda-lime glass.

Glass is important as a substrate for coatings in a wide range of applications or as a substrate for the fabrication of optical micro/nano structures. Coating by wet chemistry methods often demands modifications of the glass surface properties involving several steps. In addition, the micro/nano structuring is usually a several-step process. New methods that are simpler and more efficient are being proposed. One of them is glass poling that has been used to obtain surface relief on glass and, together with electric field assisted dissolution, for metal nanostructures in glass/metal systems. In this work, we demonstrate that poling increases the susceptibility of the glass surface for coating with Ag nanoparticles synthesized in situ by silver salt reduction. It is shown that a selectively poled glass surface can be used as a template to obtain optical microstructures consisting of Ag nanoparticles in only three simple steps. As a proof-of-concept, the method is used to fabricate diffraction gratings with an optical response that can be tuned by adjusting the Ag concentration. This approach is more versatile than the standard structuring by electric field assisted dissolution, as it does not require application of an elevated temperature once the coating is formed, which might change or destroy the properties of the thermally sensitive coating species or morphologies.

Structural and computational analysis of intermolecular interactions in a new 2-thiouracil polymorph.

The crystallization and characterization of a new polymorph of 2-thiouracil by single-crystal X-ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (A) crystallizes in the triclinic space group P\overline{1}, while that described herein (B) crystallizes in the monoclinic space group P21/c. Periodic DFT calculations showed that the energies of polymorphs A and B, compared to the gas-phase geometry, were -108.8 and -29.4 kJ mol-1, respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O...H and S...H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N-H...O and N-H...S types were found in polymorph A, whereas in polymorph B, only those of the N-H...O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak-to-medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4-10.2 and 4.9-9.2 kJ mol-1 for polymorphs A and B, respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5-4.1 and 3.1-5.5 kJ mol-1 for polymorphs A and B, respectively, as shown by QTAIM analysis.

The DFT local reactivity descriptors of α-tocopherol.

The calculations of local reactivity descriptors, the electron donor Fukui function f(-)(r), the average local ionization energy I(r), the Fukui function dual descriptor f((2))(r), and the electron acceptor Fukui function f(+)(r) for α-tocopherol, the main biologically active form of vitamin E for antioxidant reactions in phospholipid membranes, is presented. The calculations are performed at B3LYP/6-311++G** level of theory in the gas-phase. The obtained results indicate that the most preferred sites for donating electron in a reaction with radical or oxidizing molecule are associated mostly with π electrons above and below the aromatic part of the α-tocopherol chromanol ring. The most reactive sites for accepting electrons are associated with the leaving H(9) atom in the extension of the phenolic OH bond on the α-tocopherol chromanol ring plane, in the place where the formation of H-bond of the precursor complex between approaching reactive oxygen radical and phenolic OH group of α-tocopherol could be expected. The separated reactive sites in α-tocopherol suggest that the proton and electron, along with the hydrogen atom transfer (HAT) process, could also be transferred to different proton and electron acceptors as in bidirectional proton coupled electron transfer (PCET) reactions. The results presented in this paper suggest that large charge redistribution and significant π-π interactions may be expected in antioxidant reactions of α-tocopherol.