Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes

Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.

Understanding the ancillary ligand effect on luminescent cyclometalated Ir(III) complex as a reporter for 2-acetylaminofluorene DNA(AAF-dG) adduct

Mutagenic agents such as aromatic amines undergo metabolic activation and produce DNA adducts at C8 position of guanine bases. N-2-acetylaminofluorene (AAF) generates different mutational outcomes when placed at G₁, G₂, and G₃ of a NarI sequence (-G₁G₂CG₃CC/T-). These outcomes are dictated by the conformations adopted by these adducts. Detection of such lesions is of considerable interest owing to their hazardous effects. Here, we report the synthesis of three cyclometalated [Ir(L)₂dppz]⁺ complexes (L = 2-phenylpyridine (ppy) 1; benzo[h]quinoline (bhq) 2; 2-phenylquinoline (pq) 3; dppz = dipyrido[3,2-a:2',3'-c]phenazine) and their interaction with AAF adducted NarI DNA. Remarkably, complexes 1 and 2 displayed dominant ³LC transition characteristic of polar environment despite binding to the adducted sites. On the other hand, complex 3 binds to NarI sequences and behaves as a luminescent reporter for AAF-modified DNA. The results reported here emphasize that molecular light switching phenomenon can be stimulated by switching ancillary ligands and might act as potential probes for covalent-DNA defects.

Inhibition of Aβ peptide aggregation by ruthenium(II) polypyridyl complexes through copper chelation

Alzheimer's disease (AD) is known as a complex multifactorial syndrome and both metal chelators and amyloid β peptide (Aβ) inhibitors show promise against AD. Herein, four small hybrid compounds have been designed and synthesized utilizing 8-hydroxyquinoline, pyridine or imidazole as chelators and benzimidazole as the recognition moiety for AD treatment. These conjugates can capture Cu²⁺ from Aβ and become dimers upon Cu²⁺ coordination and show high efficiency for both Cu²⁺ elimination and Aβ assembly inhibition. Besides, these designed complexes can inhibit the production of Aβ-induced reactive oxygen species (ROS), protect mitochondria from damage, and improve the survival rate of neuron cells. Our work provides a new strategy to combine hydrophobic interaction and metal ion chelation to design amyloid inhibitors.

Structural insights into the recognition of DNA defects by small molecules

Studies on the binding interaction of small molecules and nucleic acids have been explored for their biological applications. With excellent photophysical/chemical properties, numerous metal complexes have been studied as structural probes for nucleic acids. The recognition of DNA defects is of high importance due to their association with various types of cancers. Small molecules that target DNA defects in a specific and selective manner offer a new avenue for developing novel drugs and diagnostic tools. Transition metal complexes have been studied as probes for abasic sites and DNA/RNA mismatches. By changing the ligand structure or metal center, the probing efficiency of the metal complexes varies towards the defects. In this perspective, we have discussed mainly the structural requirement of metal complexes as probes for abasic sites, mismatches, and covalent DNA adducts, followed by the challenges and future directions.

Exploring the potential of highly charged Ru(II)- and heteronuclear Ru(II)/Cu(II)-polypyridyl complexes as antimicrobial agents

The antimicrobial potential of two ruthenium(II) polypyridyl complexes, [Ru(phen)₂L1]²⁺ and [Ru(phen)₂L2]²⁺ (phen = 1,10-phenanthroline) containing the 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridilophane (L1) and the 4,4'-bis-[methylen-(1,4,7,10-tetraazacyclododecane)]-2,2' bipyridine (L2) units, is herein investigated. These peculiar polyamine frameworks afford the formation of highly charged species in solution, influence the DNA-binding and cleavage properties of compounds, but they do not undermine their singlet oxygen sensitizing capacities, thus making these complexes attractive ¹O₂ generators in aqueous solution. L1 and L2 also permit to stably host Fenton -active Cu²⁺ ion/s, leading to the formation of mixed Ru²⁺/Cu²⁺ forms capable to further strengthen the oxidative damages to biological targets. Herein, following a characterization of the Cu²⁺ binding ability by [Ru(phen)₂L2]²⁺, the water-octanol distribution coefficients, the DNA binding, cleavage and ¹O₂ sensitizing properties of [Ru(phen)₂L2]²⁺ and [Cu₂Ru(phen)₂L2]⁶⁺ were analysed and compared with those of [Ru(phen)₂L1]²⁺ and [CuRu(phen)₂L1]⁴⁺. The antimicrobial activity of all compounds was evaluated against B. subtilis, chosen as a model for gram-positive bacteria, both under dark and upon light-activation. Our results unveil a notable phototoxicity of [Ru(phen)₂L2]²⁺ and [Cu₂Ru(phen)₂L2]⁶⁺, with MIC (minimal inhibitory concentrations) values of 3.12 μM. This study highlights that the structural characteristics of polyamine ligands gathered on highly charged Ru(II)-polypyridyl complexes are versatile tools that can be exploited to achieve enhanced antibacterial strategies.

Single-Molecule MicroRNA Electrochemiluminescence Detection Using Cyclometalated Dinuclear Ir(III) Complex with Synergistic Effect

The realization of electrochemiluminescence (ECL) detection at the single-molecule level is a longstanding goal of ECL assay that requires a novel ECL probe with significantly enhanced luminescence. Here, the synergistic effect of electrochemiluminescence (ECL) is observed unprecedentedly in a new cyclometalated dinuclear Ir(III) complex [Ir₂(dfppy)₄(imiphenH)]PF₆ (1·PF₆, PF₆^- = hexafluorophosphate) in which two {Ir(dfppy)₂}⁺ units are bridged by an imiphenH^- ligand. The ECL intensity from complex 1·PF₆ is 4.4 and 28.7 times as high as that of its reference mononuclear complexes 2 and 3·PF₆, respectively. Theoretical calculation reveals that the S₀ to S₁ excitation is a local excitation in 1·PF₆ with two electron-coupled Ir(III) centers, which contributes to the enhanced ECL. The synergistic effect of ECL in 1·PF₆ can be used to detect microRNA 21 at the single-molecule level (microRNA 21: UAGCUUAUCAGACUGAUGUUGA), with detectable ECL emission from this complex intercalated in DNA/microRNA 21 duplex as low as 90 helix molecules. The finding of the synergistic effect of ECL will not only provide a novel strategy for the modulation of ECL intensity but also enable the detection of microRNA at the single-molecule level.

Selective recognition of DNA defects by cyclometalated Ir(iii) complexes

Three different cyclometalated Ir(iii) complexes selectively bind to DNA defects.

Coumarin centered copper(ii) complex with appended-imidazole as cancer chemotherapeutic agents against lung cancer: molecular insight via DFT-based vibrational analysis

Synthesis and structural characterization of the novel copper complex, DFT based vibrational analysis, DNA binding studies. In vitro cytotoxicity against A549 cancer cell lines and estimation of GSH, ROS, LPO levels, have been reported.