Fluorescence and binding properties of phenazine derivatives in complexes with polynucleotides of various base compositions and secondary structures

Zozulya, Victor; Blagoi, Y.-U. P.; Löber, G.; Voloshin, Igor; Winter, Stefan; Makitruk, V. L.; Shalamay, A. S.

doi:10.1016/s0301-4622(96)02247-8

Cited by 38 publications

(26 citation statements)

References 13 publications

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“…Thus, on binding of the free Pzn to poly(A), when its chromophore came into close contact with polynucleotide bases, the fluorescence was quenched more than 10-fold. 23 In the investigated (dA) 15 ⅐(dT) 10 Pzn duplex the contact of the attached chromophore with adenine planes took place to a considerable extent, which resulted in the fluorescence intensity decreasing by ϳ3.5 times. By contrast, the contact in the poly(dA)⅐poly(dT)⅐(dT) 10 Pzn triplex complex was rather weak; therefore, feeble fluorescence quenching (ϳ30%) had occurred.…”

Section: Discussionmentioning

confidence: 97%

“…was suggested 23 that the fluorescence of Pzn is quenched by the adenine by means of an electron transfer mechanism. 28 The stacking interaction of the Pzn chromophore with adenine bases is needed so that fluorescence quenching can occur.…”

Section: Discussionmentioning

confidence: 99%

“…23 The Pzn absorption spectrum shows a UV band with a maximum at 262 nm, one band in the visible range with a maximum at 384 nm, and a broad long-wave shoulder extending up to 500 nm. It was insignificantly changed with the attachment of Pzn to the end of (dT) 10 .…”

Section: Spectroscopic Properties Of (Dt) 10 Pzn Conjugatementioning

confidence: 99%

“…The fluorescence quenching was caused by the interaction of the Pzn chromophore with adenine bases, whose quenching ability was demonstrated earlier. 23 The quenching effect is dependent on the ionic strength, which is seen from the different low-temperature levels reached by the fluorescence intensity for the duplex systems with 0.11 and 1M Na ϩ ions. On heating up to certain temperatures, the emission intensity of the duplex or triplex samples became identical to that of the free (dT) 10 Pzn, which is evidence of the complete dissociation of the complexes.…”

Section: Fluorescence Melting Studiesmentioning

confidence: 99%

“…The absorption data were obtained with a Specord UV/VIS spectrophotometer (Carl Zeiss, Jena), and the fluorescent data were found with a laboratory spectrofluorimeter equipped with a photon counting electronic device system. 23 These instruments were interfaced to a personal computer for data collection. The absorbance and fluorescence were measured in the same 0.2-cm path length quartz cuvette.…”

Section: Optical Techniques Of Thermal Denaturationmentioning

confidence: 99%

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Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

et al. 2003

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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.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Spectroscopic Properties Of (Dt) 10 Pzn Conjugatementioning

confidence: 99%

Section: Fluorescence Melting Studiesmentioning

confidence: 99%

Section: Optical Techniques Of Thermal Denaturationmentioning

confidence: 99%

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Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

et al. 2003

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

et al. 2016

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Noncovalent functionalization of graphene with organic molecules offers a direct route to multifunctional modification of this nanomaterial, leading to its various possible practical applications. In this work, the structures of hybrids formed by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2-F4) with graphene and the corresponding interaction energies are studied by using the DFT method. Special attention is paid to the hybrids where the attached molecule is located along the graphene zigzag (GZZ ) and armchair (GAC ) directions. The interaction energies corresponding to the graphene hybrids of the F1-F4 compounds for the two directions are found to be distinct, while tetracene (being a symmetrical molecule) shows a small difference between these binding energies. It is found that the back-side CH3 and CF3 groups have an important influence on the arrangements of F1 derivatives on graphene and on their binding energies. The contribution of the CF3 group to the total binding energy of the F3 molecule with graphene is the largest (3.4 kcal mol(-1) ) (the GZZ direction) while the CH3 group increases this energy of F2 only by 2.0 kcal mol(-1) (the GAC direction). It is shown that replacing the carbons with other atoms or adding a back-side group enables one to vary the polarizability of graphene.

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Spectroscopic Studies on Binding of Cationic Pheophorbide-a Derivative to Model Polynucleotides

et al. 2008

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Fluorescence and binding properties of phenazine derivatives in complexes with polynucleotides of various base compositions and secondary structures

Cited by 38 publications

References 13 publications

Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

Anchorage of oligonucleotide hybridization by tethered phenazine nucleoside analogue

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

Spectroscopic Studies on Binding of Cationic Pheophorbide-a Derivative to Model Polynucleotides

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