DNA-Templated Assembly of Helical Multichromophore Aggregates

Armitage, Bruce A.

doi:10.1201/9781420036992.ch7

Cited by 3 publications

(4 citation statements)

References 64 publications

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“…One is intercalation, first reported by Fiel and co-workers . The others are external (or groove) binding and, under some conditions, outside stacking (or aggregation) along the surface of the DNA host. ,, Because the shape of a porphyrin is not complementary to that of B-form DNA, high-affinity binding always involves a structural reorganization of the host, i.e., an induced fit . External binding, the norm for metalloporphyrins bearing axial ligands, , involves local melting of the DNA structure and formation of a binding pocket to optimize a mix of hydrophobic and electrostatic interactions.…”

Section: Discussionmentioning

confidence: 99%

Accessibility and External versus Intercalative Binding to DNA As Assessed by Oxygen-Induced Quenching of the Palladium(II)-Containing Cationic Porphyrins Pd(T4) and Pd(tD4)

et al. 2014

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Studies reveal that it is possible to design a palladium(II)-containing porphyrin to bind exclusively by intercalation to double-stranded DNA while simultaneously enhancing the ability to sensitize the formation of singlet oxygen. The comparisons revolve around the cations [5,10,15,20-tetra(N-methylpyridinium-4-yl)porphyrin]palladium(II), or Pd(T4), and [5,15-di(N-methylpyridinium-4-yl)porphyrin]palladium(II), or Pd(tD4), in conjunction with A═T and G≡C rich DNA binding sequences. Methods employed include X-ray crystallography of the ligands as well as absorbance, circular dichroism, and emission spectroscopies of the adducts and the emission from singlet oxygen in solution. In the case of the bulky Pd(T4) system, external binding is almost as effective as intercalation in slowing the rate of oxygen-induced quenching of the porphyrin's triplet excited state. The fractional efficiency of quenching by oxygen nevertheless approaches 1 for intercalated forms of Pd(tD4), because of intrinsically long triplet lifetimes. The intensity of the sensitized, steady-state emission signal varies with the system and depends on many factors, but the Pd(tD4) system is impressive. Intercalated forms of Pd(tD4) produce higher sensitized emission yields than Pd(T4) is capable of in the absence of DNA.

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Section: Discussionmentioning

confidence: 99%

Accessibility and External versus Intercalative Binding to DNA As Assessed by Oxygen-Induced Quenching of the Palladium(II)-Containing Cationic Porphyrins Pd(T4) and Pd(tD4)

et al. 2014

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“…Evidence that points to cooperative binding of Zn(tMe 2 D4) includes the difference spectrum in Figure 8 as well as with the bisignate CD spectra exhibited by the adducts formed with [poly(dG-dC)] 2 and [poly(dA-dT)] 2 . In the context of cationic porphyrins, the most commonly recognized form of cooperative binding to DNA is self-stacking on the surface of the host (25,29,79). However, more traditional modes of ligand binding can also exhibit cooperativity when binding involves reorganization of the DNA structure (80).…”

Section: Interactions Of Dna With Zn(tme 2 D4)mentioning

confidence: 99%

“…Uptake of Zn(tMe 2 D4) is very different because binding is a strictly cooperative process and the motif depends on the base content of the DNA host. Heretofore, external stacking has been widely recognized as a binding motif compatible with cooperative uptake of a cationic porphyrin (22,56,79), but cooperative binding may occur whenever substantial structural reorganization is necessary. Recognizing when cooperative binding occurs is important because it impacts everything from competitive binding assays (84) to comparative kinetics studies (85,86).…”

Section: Conclusion and Perspectivementioning

confidence: 99%

DNA Binding Studies of a New Dicationic Porphyrin. Insights into Interligand Interactions

2007

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Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.

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“…It is known that the molecules of DNA, RNA and polynucleotides also represent linear polyanions with intercharge distances corresponding to the thickness of the π-electronic system. They are known as a good scaffold for the self-assembly of cationic porphyrins occurring at low P/D ratios that results in the formation of extended porphyrin aggregates on the polymer exterior [41,42,61,62]. This process induces multiple transformations in porphyrin spectra, such as hypochromism and shift of the Soret absorption band (a blue shift in the case of H-aggregates, and a red shift for J-aggregates); a substantial change in the shape, position and intensity of the dye emission band; and a rise in the fluorescence polarization degree.…”

Section: Discussionmentioning

confidence: 99%

Interaction of a tricationic meso-substituted porphyrin with guanine-containing polyribonucleotides of various structures

Ryazanova

Zozulya

Voloshin

et al. 2016

Methods Appl. Fluoresc.

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The interaction of a tricationic water-soluble meso-(N-methylpyridinium)-substituted porphyrin, TMPyP, derived from classic TMPyP4, with double-stranded poly(G) ⋅ poly(C) and four-stranded poly(G) polyribonucleotides has been studied in aqueous buffered solutions, pH 6.9, of low and near-physiological ionic strengths in a wide range of molar phosphate-to-dye ratios (P/D). To clarify the binding modes of TMPyP to biopolymers various spectroscopic techniques, including absorption and polarized fluorescence spectroscopy, Raman spectroscopy, and resonance light scattering, were used. As a result, two competitive binding modes were revealed. In solution of low ionic strength outside binding of the porphyrin to the polynucleotide backbone with self-stacking prevailed at low P/D ratios (P/D < 3.5). It manifested itself by the substantial quenching of porphyrin fluorescence. Also the formation of large-scale porphyrin aggregates was observed near the stoichiometric binding ratio. The spectral changes observed at P/D > 30 including emission enhancement were supposed to be caused by the embedding of partially stacked porphyrin J-dimers into the polymer groove. TMPyP binding to poly(G) induced a fluorescence increase 2.5 times as large as that observed for poly(G) ⋅ poly(C). In solution of near-physiological ionic strength the efficiency of external porphyrin binding was reduced substantially due to the competitive binding of Na ions with the polymer backbone. The spectroscopic characteristics of porphyrin bound to polynucleotides at different conditions were compared with those for free porphyrin.

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DNA-Templated Assembly of Helical Multichromophore Aggregates

Cited by 3 publications

References 64 publications

Accessibility and External versus Intercalative Binding to DNA As Assessed by Oxygen-Induced Quenching of the Palladium(II)-Containing Cationic Porphyrins Pd(T4) and Pd(tD4)

Accessibility and External versus Intercalative Binding to DNA As Assessed by Oxygen-Induced Quenching of the Palladium(II)-Containing Cationic Porphyrins Pd(T4) and Pd(tD4)

DNA Binding Studies of a New Dicationic Porphyrin. Insights into Interligand Interactions

Interaction of a tricationic meso-substituted porphyrin with guanine-containing polyribonucleotides of various structures

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