Calorimetric and thermal analysis studies on the binding of phenothiazinium dye thionine with DNA polynucleotides

Paul, Puja; Hossain, Maidul; Kumar, Gopinatha Suresh

doi:10.1016/j.jct.2011.02.009

Cited by 28 publications

(18 citation statements)

References 44 publications

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“…All the values here are negative and nonspecific binding by small molecules has been usually observed to have small negative DCp o values. Our values are lower than those usually observed for DNA and RNA intercalators or groove binding molecules [64][65][66]. Nevertheless, these small negative values suggest the involvement of some hydrophobic interactions in the binding of the polyamines to DNA.…”

Section: Thermodynamics Of the Interaction By Isothermal Titration Cacontrasting

confidence: 82%

“…Thus, the DG hyd values for the DNA binding of spermine, spermidine, putrescine and cadaverine are (À17.6, À12.8, À6.2 and À3.0) kJ Á mol À1 , respectively. These values are also much lower than that has been reported for many intercalators [64][65][66]. Nevertheless, although electrostatic interaction plays a major role in the binding of polyamines to DNA, these results suggest the importance for the hydrophobic interactions as well.…”

Section: Thermodynamics Of the Interaction By Isothermal Titration Cacontrasting

confidence: 70%

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Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Kabir

Hossain

Kumar

2013

The Journal of Chemical Thermodynamics

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Section: Thermodynamics Of the Interaction By Isothermal Titration Cacontrasting

confidence: 82%

Section: Thermodynamics Of the Interaction By Isothermal Titration Cacontrasting

confidence: 70%

Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Kabir

Hossain

Kumar

2013

The Journal of Chemical Thermodynamics

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“…Negative heat capacity values have been observed for a variety of small molecules and dyes binding to DNA and RNA structures. 28,[33][34][35][36][37][38] A negative ΔC o p value is usually associated with changes in hydrophobic or polar group hydration in the free and the complexed molecules and to a lesser extent from changes in molecular vibrations, 39 and is considered as an indicator of a dominant hydrophobic effect in the binding process. Although a number of factors can influence the heat capacity change on complex formation, change in solvent accessible surface area has been shown to be a large component of ΔC o p .…”

Section: Photochemical and Photobiological Sciences Papermentioning

confidence: 99%

“…These values are well within the range observed for typical DNA and RNA intercalating molecules. 10,[33][34][35]37,44,45 Enthalpy-entropy compensation A significant feature observed in the thermodynamics of dyepoly(A) interactions is the general thermodynamic effect termed the enthalpy-entropy compensation (EEC) phenomenon. Such phenomena may reflect a multiplicity of weak interactions.…”

Section: δGmentioning

confidence: 99%

Photophysical and calorimetric investigation on the structural reorganization of poly(A) by phenothiazinium dyes azure A and azure B

Paul

Kumar

2014

Photochem Photobiol Sci

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Poly(A) has significant relevance to mRNA stability, protein synthesis and cancer biology. The ability of two phenothiazinium dyes azure A (AA) and azure B (AB) to bind single-stranded poly(A) was studied by spectroscopic and calorimetric techniques. Strong binding of the dyes and the higher affinity of AA over AB were ascertained from absorbance and fluorescence experiments. Significant perturbation of the circular dichroism spectrum of poly(A) in the presence of these molecules with formation of induced CD bands in the 300-700 nm region was observed. Strong emission polarization of the bound dyes and strong energy transfer from the adenine base pairs of poly(A) suggested intercalative binding to poly(A). Intercalative binding was confirmed from fluorescence quenching experiments and was predominantly entropy driven as evidenced from isothermal titration calorimetry data. The negative values of heat capacity indicated involvement of hydrophobic forces and enthalpy-entropy compensation suggested noncovalent interactions in the complexation for both the dyes. Poly(A) formed a self-assembled structure on the binding of both the dyes that was more favored under higher salt conditions. New insights in terms of spectroscopic and thermodynamic aspects into the self-structure formation of poly(A) by two new phenothiazinium dyes that may lead to structural and functional damage of mRNA are revealed from these studies.

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“…Phenothiazine dyes typically intercalate between DNA base pairs when the nucleic acid is in excess, but can also occupy groove-bound sites in certain sequences. [30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45] They are known to stack externally on the polyanionic DNA backbone when DNA is in excess, [19][20][21][22][30][31][32] but neither the organization of dyes in the aggregates nor the effects of sequence or dye structure has received significant attention. Methylation of the exocyclic amines has little effect on intercalative binding at high P/D.…”

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confidence: 99%

Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes

Tuite

Nordén

2018

J. Phys. Chem. B

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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)], [poly(dA-dT)], 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)], while thionine aggregates more with [poly(dG-dC)]. 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.

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Calorimetric and thermal analysis studies on the binding of phenothiazinium dye thionine with DNA polynucleotides

Cited by 28 publications

References 44 publications

Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Thermodynamics of the DNA binding of biogenic polyamines: Calorimetric and spectroscopic investigations

Photophysical and calorimetric investigation on the structural reorganization of poly(A) by phenothiazinium dyes azure A and azure B

Structural Heterogeneity in Polynucleotide-Facilitated Assembly of Phenothiazine Dyes

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