Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

Abstract

UV absorption and fluorescence techniques with a thermal denaturation procedure were used in studies of the anchorage of an oligonucleotide hybridization by a covalently tethered nucleoside analogue of an intercalating imidazophenazine derivative (Pzn). The formation by the (dT)(10)Pzn conjugate of the duplex complex with (dA)(15) and the triplex complex with (dA)(15) or poly(dA).poly(dT) was studied in buffered solutions with 0.11 and/or 1M sodium ions at the oligomer strand concentration of 10 microM. Because of the Pzn emission sensitivity to the interaction with adenine bases, a fluorescence technique was found to be effective in the detection of melting transitions. The attached Pzn substantially enhanced the thermal stability of complexes formed by (dT)(10) because of the intercalation mechanism, which increased the temperature of half-dissociation of the duplex by 10-12 degrees C and of the triplexes by approximately 13 degrees C. With the assumption of a two-state model of transition, the thermodynamic parameters for duplex formations were derived. The investigated variant of conjugation has a certain advantage over the widely used attachment via a flexible linker, consisting of a predetermined location of the Pzn chromophore in target sequences that makes it useful as a fluorescent reporter of the hybridization correctness. Molecular modeling was used to construct the geometries of the intercalation sites that turned out to be in conformity with the behavior of the Pzn fluorescence.

Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Four-Stranded Poly(G)

“…1) [25]. Imidazophenazine is known as DNA intercalator [26,27], and we supposed that the attached dye would improve the binding of porphyrin to G4 structures by intercalation into double-stranded regions of telomeric DNA or between guanine quartets. Indeed, TMPyP 3+ -imidazophenazine hybrids and their zinc(II) and manganese(III) complexes efficiently inhibited telomerase and demonstrated antiproliferative activity in vitro at micro-and submicromolar concentrations [28].…”

Noncovalent Interaction of Graphene with Heterocyclic Compounds: Benzene, Imidazole, Tetracene, and Imidazophenazines

“…[36] In the presents tudy,w ec ompare the interaction of the following chromophores:i midazo-[4,5-d]-phenazine (F1)a nd its derivatives (2-methylimidazo-[4,5-d]-phenazine (F2), 2-trifluoromethylimidazo-[4,5-d]-phenazine( F3), and 1,2,3-triazole-[4,5-d]phenazine (F4)( Figure 1) with graphene. Note that these compounds are very perspective in DNA structure studies, [37][38][39][40] and the fluorescences tudy of these dyes [41] shows pH sensitivity of their spectralp roperties. Pre-resonance Raman and IR absorption spectroscopy techniques were applied to study the influence of substitutes in the imidazole ring of F1 on its vibrational structure.…”

Evaluation of the reduction of imidazophenazine dye derivatives under fast‐atom‐bombardment mass‐spectrometric conditions

“…Phenazine derivatives are known to possess antibiotic, antiviral, antiparasitic, and antitumor properties;6–9 they have been used in DNA studies,10 and they have also been employed both in pure and electropolymerized forms11–13 as mediator agents in second‐generation amperometric biosensors13, 14 shuttling electrons between enzymes and electrodes of the sensor. Imidazophenazines are used as fluorescent probes in studies of nucleic acid structure15 and are promising as elements of solar cells, as well as components of pH sensors and biosensors. Considering these applications, we decided to undertake a more detailed study of the reduction of imidazophenazine derivatives under the FAB conditions.…”