Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes

The assembly of stacked dyes on DNA is of interest for electron transfer, light harvesting, sensing, and catalysis applications. A combination of UV/vis absorption, linear dichroism (LD), and circular dichroism (CD) was applied to characterize thoroughly the aggregation with DNA of the phenothiazine dyes methylene blue, azure B, and thionine. Aggregates of each dye with [poly(dG-dC)]₂, [poly(dA-dT)]₂, and calf thymus DNA were explored at high dye:DNA binding ratios, where excess dye groove-binds after all intercalation sites are filled. The organization of the aggregates (dimers, trimers, and multimers) with polydeoxynucleotides displays a structural diversity that depends on DNA sequence, extent of methylation of dye exocyclic amine groups, and ionic strength. The dyes typically form right-handed H-aggregates having negative LD, consistent with stepped stacking along the minor groove. However, aggregates in some dye:DNA aggregates show left-handed chirality or positive LD, indicating unusual modes of aggregation such as formation of adventitious dimers between intercalated and minor groove bound dye. In terms of sequence-dependence, methylene blue shows more extensive aggregation with [poly(dA-dT)]₂, while thionine aggregates more with [poly(dG-dC)]₂. Azure B has distinctive behavior that is unlike either other dyes. Thus, although these phenothiazine dyes possess a common tricyclic framework, the organization of their polynucleotide-facilitated aggregates depends sensitively on the extent of methylation of the exocyclic amines.

Ground and excited state interactions of metalloporphyrin PtTMPyP4 with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2

The ground- and excited-state interactions of Pt(ii) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2 have been investigated using UV/visible, circular dichroism, and steady-state and time-resolved emission spectroscopy. PtTMPyP4 intercalates into [poly(dG-dC)]2 with K∼ 10(6) M(-1). When bound to [poly(dG-dC)]2 in aerated solution there is a six-fold emission enhancement with 18 nm red-shift in emission maximum. Emission lifetimes are biexponential. In the presence of [poly(dA-dT)]2 at least two distinct groove-binding modes are observed, depending on the binding ratio. In [poly(dA-dT)]2 the emission intensity increases by a maximum factor of 17 with no shift in the emission spectrum. Three exponentials were required for lifetime fitting. The lower extent of emission enhancement in the presence of [poly(dG-dC)]2 suggests that a slow electron transfer may take place to guanine, which is significantly less efficient than that previously observed for PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP). The results are compared to those previously recorded with free base H2TMPyP4.

Interaction between methylene blue and calf thymus deoxyribonucleic acid by spectroscopic technologies

Characterization of the interaction between methylene blue (MB) and calf thymus deoxyribonucleic acid (ctDNA) was investigated by UV absorption spectra, fluorescence spectra, fluorescence polarization and fluorescence quenching experiments by ferrocyanide. The above results indicated that the binding modes of MB to ctDNA were relative to the molar ratio gamma (gamma=[DNA]/[MB]). At low gamma ratios (gamma < 4), remarkable hypochromic effect with no shift of lambda(max) in the absorption spectra of MB was observed in the presence of increasing amounts of ctDNA, the fluorescence of MB was efficiently quenched by the ctDNA bases and the fluorescence polarization of MB was slightly increased, which indicated that MB cations bound to phosphate groups of ctDNA by electrostatic interaction and then stacked on the surface of ctDNA helix. While at high gamma ratios (gamma > 6), besides the fluorescence of MB was quenched efficiently by the ctDNA bases, a red shift (about 3 nm) in the absorption spectra of MB was observed and the fluorescence polarization of MB was obviously increased, which indicated the intercalation binding that MB molecules were intercalated into the space of two neighbouring DNA base pairs was the preferred mode. Effects of K(4)Fe(CN)(6) on the fluorescence quenching of the MB-ctDNA system at low and high gamma ratios were also performed. The results showed that at gamma = 1.7, the quenching effect by ferrocyanide was higher than that of pure MB, while at gamma = 13.6 a decreased quenching of the fluorescence intensity was observed as compared with that of pure MB, which further proved the above conclusion. In addition, the mechanisms of the hypochromic effect and the fluorescence quenching were also discussed in detail.

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

The interactions of two phenazine derivatives, one with a neutral chromophore (glycoside) and the other with a cationic one (quaternary salt), with various synthetic single- and double-stranded polynucleotides and natural DNA were studied by fluorescence techniques, conducting measurements of steady-state fluorescence intensity and polarization degree as well as fluorescence lifetime. These dyes show fluorescence quenching upon intercalation into the GC sequences of the double-stranded nucleic acids and an increase in fluorescence emission and lifetime upon incorporation into the AT and AU sequences. GC base pairs in continuous deoxynucleotide sequences were found to be preferred as binding sites for both phenazines, in contrast to AT base pairs. On the contrary, the continuous ribonucleotide GC sequence binds the phenazines more weakly than does the AU sequence. With regard to the interaction of the phenazines with single-stranded polynucleotides, a stacking interaction of the dye chromophores with the nucleic bases was observed. In that case the guanine residue quenches the cationic phenazine fluorescence, while the stacking interaction with the other bases results in an increase in the fluorescence quantum yield. Unlike the cationic dye, the fluorescence of the neutral phenazine was quenched by both purine bases.

Synchronous fluorescence determination of DNA based on the interaction between methylene blue and DNA

The fluorescence intensity of methylene blue (MB) quenched by DNA in the pH range of 6.5-8.0 was studied with synchronous fluorescence technology. A novel method for detecting single-stranded and double-stranded DNA was developed. The decreased fluorescence intensity at 664 nm is in proportion to the concentration of DNA in the range of 0.28-11.0 micromol L(-1) for ctDNA, 0.14-8.25 micromol L(-1) for thermally denatured ctDNA and 0.28-8.25 micromol L(-1) for hsDNA. The detection limits (S/N=3) are 0.11, 0.04 and 0.04 micromol L(-1), respectively. The method is rapid, selective, and the reagents are lower toxic. It has been used for the determination of DNA in synthetic samples with good satisfaction. In addition, the interaction modes between MB and ctDNA and the mechanism of the fluorescence quenching were also discussed in detail. The experimental results from absorption spectra and fluorescence polarization indicate that the possible interaction modes between MB and DNA are the electrostatic binding and the intercalation binding.

Interaction of methylene blue with transfer RNA--a spectroscopic study

The binding of methylene blue (MB) with tRNA was studied using absorption, fluorescence and circular dichroic spectroscopy. In the spectral titration of MB with tRNA, hypochromism was observed in the absorption maximum of the dye in the visible region till P/D = 4 and thereafter the intensity increased with a red shift at P/D > 9, indicating electrostatic and intercalative binding at low and high P/D ratios, respectively. Analysis of absorption data, following Schwarz's procedure, showed that the electrostatic binding is cooperative in nature (cooperatively parameter q = 50) with a binding constant K = 7.77 x 10(3) M-1. A non-linear Scatchard plot was observed for the intercalative binding (at P/D > 4), probably due to a difference in the spectral characteristics of the dye intercalated between the base pairs and that between the bases in the single stranded domains. Quenching of fluorescence was observed for both the binding processes. In the circular dichroism spectra of tRNA-MB complexes at high P/D (approximately 30), nonconservative positive ICD bands were seen at 620 and 680 nm while at low P/D (approximately 2), two conservative negative CD bands at 300 and 660 nm and two bisignate bands with cross overs at 565 and 605 nm were observed. The short wavelength component of the bisignate band at 565 nm is negative while that of the 605-nm band is positive, indicating that the former arises from left handed and the latter from the right handed helical disposition of dye molecules along the tRNA backbone. The changes in the CD spectrum of tRNA on dye binding could be due to a conformational change of the nucleic acid or a negative CD being induced at that region.

Photochemical interactions of methylene blue and analogues with DNA and other biological substrates

The light-induced reactions of methylene blue and related phenothiazinium dyes with biological substrates are described. The properties of the excited states of the dyes, their reactions with nucleic acids and their photosensitised chemical modifications of nucleic acid bases are examined. Reports on phenothiazinium dye-induced damage to proteins, lipids, biological membranes, organelles, viruses, bacteria, mammalian cells and carcinomas are reviewed.