Effect of Axial Ligand on the Binding Mode of M-meso-Tetrakis(N-methylpyridinium-4-yl)porphyrin to DNA Probed by Circular and Linear Dichroism Spectroscopies

Interaction of MnTOEtPyP4 porphyrin with DNA

The binding of water-soluble meso-tetra-(4N-oxyethylpyridyl) porphyrin (H2TOEtPyP4) and its manganese (III) derivative (MnTOEtPyP4) with calf thymus DNA have been quantitatively studied using UV/Vis spectrophotometry, Circular Dichroism (CD), thermal melting curves and viscometry. The results show, that porphyrins interact with DNA via one binding mode at low relative concentrations (r) and two binding modes at high values of r. The binding constant (Kb) and stoichiometry (n) were determined from binding isotherms for both porphyrin-DNA complexes. The thermal melting analysis indicates that the double-helical structure of DNA molecules is stabilizing in presence of studied porphyrins. At certain concentrations of porphyrin, two-stage melting curves were observed, which indicates the existence of two different binding modes. Obtained results show that MnTOEtPyP4 associates with DNA duplex via outside binding mode.Communicated by Ramaswamy H. Sarma.

Immobilization of Glucose Oxidase on Glutathione Capped CdTe Quantum Dots for Bioenergy Generation

An efficient immobilization of Glucose oxidase (GOx) on an appropriate substrate is one of the main challenges of developing fuel cells that allow energy to be obtained from renewable substrates such as carbohydrates in physiological environments. The research importance of biofuel cells relies on their experimental robustness and high compatibility with biological organisms such as tissues or the bloodstream with the aim of obtaining electrical energy even from living systems. In this work, we report the use of 5,10,15,20 tetrakis (1-methyl-4-pyridinium) porphyrin and glutathione capped CdTe Quantum dots (GSH-CdTeQD) as a support matrix for the immobilization of GOx on carbon surfaces. Fluorescent GSH-CdTeQD particles were synthesized and their characterization by UV-Vis spectrophotometry showed a particle size between 5–7 nm, which was confirmed by DLS and TEM measurements. Graphite and Toray paper electrodes were modified by a drop coating of porphyrin, GSH-CdTeQD and GOx, and their electrochemical activity toward glucose oxidation was evaluated by cyclic voltammetry, chronoamperometry and electrochemical impedance spectroscopy. Additionally, GOx modified electrode activity was explored by scanning electrochemical microscopy, finding that near to 70% of the surface was covered with active enzyme. The modified electrodes showed a glucose sensitivity of 0.58 ± 0.01 μA/mM and an apparent Michaelis constant of 7.8 mM. The addition of BSA blocking protein maintained the current response of common interferent molecules such as ascorbic acid (AA) with less than a 5% of interference percentage. Finally, the complex electrodes were employed as anodes in a microfluidic biofuel cell (μBFC) in order to evaluate the performance in energy production. The enzymatic anodes used in the μBFC allowed us to obtain a current density of 7.53 mAcm−2 at the maximum power density of 2.30 mWcm−2; an open circuit potential of 0.57 V was observed in the biofuel cell. The results obtained suggest that the support matrix porphyrin and GSH-CdTeQD is appropriate to immobilize GOx while preserving the enzyme’s catalytic activity. The reported electrode arrangement is a viable option for bioenergy production and/or glucose quantification.

Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases

The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.

Sequence selective photoinduced electron transfer of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to various DNAs (calf thymus DNA (Ct-DNA), poly[d(G-C)2], and poly[d(A-T)2]) have been investigated using circular dichroism and linear dichroism measurements. Based on the polarization spectroscopic results, it can be shown that the pyrenyl and porphryin planes are skewed to a large extent for PyTMPyP in an aqueous environment and in the binding site of poly[d(G-C)2]. In this complex, a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties occurs. On the other hand, PET was not observed in the PyTMPyP-poly[d(A-T)2] complex, whereas the fluorescence intensity of TMPyP was enhanced. The molecular planes of the pyrene and porphyrin moieties are almost parallel in the poly[d(A-T)2] and Ct-DNA adducts. Moreover, the generation of 1O2 species occurs only for the PyTMPyP-Ct-DNA and PyTMPyP-poly[d(A-T)2] complexes. We discuss the photophysical properties of PyTMPyP which are attributed to the binding patterns and the sequence of DNA bases.

Relationship between the photoinduced electron transfer and binding modes of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to DNA and its photophysical properties have been investigated using various spectroscopic techniques. The circular dichroism (CD) spectrum of PyTMpyP bound to DNA (PyTMpyP-DNA) showed one negative and two positive bands in the Soret region. The CD signal in the pyrene absorption region was positive. The shape of the CD spectrum does not support an intercalative binding mode of TMpyP, which would typically afford a negative CD band in the absence of the pyrene moiety. Linear dichroism (LD) experiments revealed a very small signal in the Soret region, which also challenges the intercalation of TMpyP into DNA. Upon excitation of the pyrene moiety, the emission intensity of porphyrin in aqueous solution was quenched due to a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties. On the other hand, the emission of porphyrin was markedly enhanced upon binding to DNA, as the PET process from the excited pyrene moiety to TMpyP was suppressed when bound to DNA. The PET process occurs in the timescale of 65 ps, and could be detected by femtosecond transient absorption spectroscopic methods. Two fluorescence decay times were observed for PyTMpyP in aqueous solution (0.78 and 4.8 ns). Both decay times increased upon binding to DNA owing to environment and/or conformational changes in PyTMpyP. The driving force (ΔG) of the PET process was evaluated under conditions of minor and major groove binding. The PET process and photophysical properties of the PyTMpyP dyad were concluded to be influenced by the binding mode.

Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA

Although the transition from B-DNA to the A-form is essential for many biological concerns, the properties of this transition have not been resolved. The B to A equilibrium can be analyzed conveniently because of the significant changes in circular dichroism (CD) and absorption spectrum. CD and linear dichroism (LD) methods were used to examine the binding of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) and its derivatives, Co-TMPyP, with B- and A-calf thymus DNA. B- to A-transitions occurred when the physiological buffer was replaced with a water-ethanol mixture (∼80 v/v %), and the fluorescence emission spectra of TMPyP bound to DNA showed a different pattern under ethanol-water conditions and water alone. The featureless broad emission bands of TMPyP were split into two peaks near at 658 and 715 nm in the presence of DNA under an aqueous solution. In the case of an ethanol-water system, however, the emission bands are split in two peaks near at 648 and 708 nm and 656 and 715 nm with and without DNA, respectively. This may be due to a change in the solution polarity. On the basis of the CD and LD data, TMPyP interacts with B-DNA via intercalation at a low ratio under a low ionic strength, 1 mM sodium phosphate. On the other hand, the interaction with A-DNA (80 v/v % ethanol-water system) occurs in a nonintercalating manner. This difference might be because the structural conformations, such as the groove of A-DNA, are not as deep as in B-DNA and the bases are much more tilted. In the case of Co-TMPyP, porphyrin binds preferably via an outside self-stacking mode with B- and A-DNA.

Interaction between G-Quadruplex and Zinc Cationic Porphyrin: The Role of the Axial Water

The interaction of ligands with G-quadruplexes has attracted considerable attention due to its importance in molecular recognition and anticancer drugs design. Here, we utilize triplet excited state as a sensitive reporter to study the binding interaction of zinc cationic porphyrin (ZnTMPyP4) with three G-quadruplexes, AG3(T2AG3)3, (G4T4G4)2, and (TG4T)4. By monitoring the triplet decay dynamics of ZnTMPyP4 with transient absorption spectroscopy, the coexisted binding modes via π-π stacking of porphyrin macrocycle and the G-quartets are allowed to be identified quantitatively, which involve intercalation (25% and 36%) versus end-stacking (75% and 64%) for AG3(T2AG3)3 and (G4T4G4)2, and end-stacking (23%) versus partial intercalation (77%) for (TG4T)4. It is shown that the steric hindrance of the axial water decreases greatly the percentage of intercalation. Further, a rapid assessment of binding stoichiometry is fulfilled by measuring the triplet decay dynamics under various [G-quadruplex]/[ZnTMPyP4] ratios. The binding stoichiometric ratios of G-quadruplex/ZnTMPyP4 are 1:2 for AG3(T2AG3)3, 1:1 for (G4T4G4)2, and 1:2 for (TG4T)4, which agree well with results obtained by the conventional method of continuous variation analysis. These results reveal a clear scenario of G-quadruplex/ZnTMPyP4 interaction and provide mechanistic insights for the application of anticancer drug designs using G-quadruplex as target.

Fluorescent Phthalocyanine Assembly Distinguishes Chiral Isomers of Different Types of Amino Acids and Sugars

The functions of some natural supramolecular architectures, such as ribosomes, are dependent on the recognition of different types of chiral biomolecules. However, the recognition of different types of chiral molecules (multiobject chiral recognition), such as amino acids and sugars, by independent and identically artificial supramolecular assembly, was rarely achieved. In this article, simple amphiphilic achiral phthalocyanine was found to form supramolecular chiral assemblies with charged water-soluble polymers upon host-guest interactions at the air/water interface. Among these systems, one identical phthalocyanine/poly(l-lysine) assembly not only can distinguish enantiomers of different amino acids but also can recognize several epimers of monose. The chiral recognitions were achieved by comparing either the steady-state fluorescence intensity or fluorescence quenching rate of phthalocyanine/poly(l-lysine) assemblies, before and after interaction with different small chiral molecules. It was demonstrated that the interactions between poly(l-lysine) and different small chiral molecules could change the aggregation of phthalocyanines. And the sensitivity of fluorescence and the excellent multiobject chiral recognition properties of the phthalocyanine/poly(l-lysine) assembly are dependent on the subtle molecular packing mode and the cooperation of different noncovalent interactions.

DNA-Targeted Inhibition of MGMT

The cationic porphyrin 5,10,15,20-tetrakis (diisopropyl-guanidine)-21H,23H-porphine (DIGPor) selectively binds to DNA containing O⁶ -methylguanine (O⁶ -MeG) and inhibits the DNA repair enzyme O⁶ -methylguanine-DNA methyltransferase (MGMT). The O⁶ -MeG selectivity and MGMT inhibitory activity of DIGPor were improved by incorporating Zn^II into the porphyrin. The resulting metal complex (Zn-DIGPor) potentiated the activity of the DNA-alkylating drug temozolomide in an MGMT-expressing cell line. To the best of our knowledge, this is the first example of DNA-targeted MGMT inhibition.

Surface complex of ZnTMPyP4 metalloporphyrin with double-stranded Poly(A)-Poly(U)

This communication presents synthesis and spectral characterization of metalloporphyrin [Zn(X)TMPyP4] (TMPyP4 is 5,10,15,20-tetrakis (N-methylpyridinium-4-yl)porphyrin), and studies its binding onto anionic surface sites of synthetic double stranded polynucleotide Poly(A)-Poly(U). [Zn(X)TMPyP4] binding with Poly(A)-Poly(U) was monitored by UV-Vis absorbance spectroscopy, two fluorescence spectroscopies and 1H NMR in a working aqueous medium of 0.15M ionic strength, pH7.0 and at 25°C. The evidence provided by spectroscopic measurements and multivariate data analysis suggests the use of this metalloporphyrin as a probe for investigation of the polynucleotide surface. In contrast to TMPyP4 intercalation, an outside adsorption of [Zn(X)TMPyP4] induces an attenuation of luminescence intensity and has little influence on the shape of luminescence band. Special attention was paid to the quantitative description of the interaction between neighboring ligands on the Poly(A)-Poly(U) surface. The intrinsic binding constant to an isolated binding site lgKin 5.8±0.1, the cooperativity parameter ω 1.8±0.2, and number of monomers occupied by a ligand n=2 (25°C; pH7.0) were calculated based upon the recently proposed non-linear least-squares fitting procedure. The discovered cooperativity of binding of [Zn(X)TMPyP4] metalloporphyrin to Poly(A)-Poly(U) is significantly lower as compared to free porphyrin TMPyP4, reflecting minimal mutual influence between the nearest neighboring ligands bound with functional PO4(-) groups of the polynucleotide surface.

Effects of guanine bases at the central loop on stabilization of the quadruplex DNAs and their interactions with Meso-tetrakis(N-methylpyridium-4-yl)porphyrin

The thermal stability of the G-quadruplex formed from the thrombin-binding aptamer, 5'G2T2G2TGTG2T2G2, in which the guanine (G) base at the central loop was replaced with an adenine (A) or inosine (I) base, was examined to determine the role of the central G base in stabilizing the quadruplex. Replacement of the central G base by the I base resulted in a slight decrease in thermal stability. On the other hand, the stability of the G-quadruplex decreased to a significant extent when it was replaced with the A base. The optimized structure of the G-quadruplex, which was obtained by a molecular dynamic simulation, showed that the carbonyl group of the C5 position of the central G base could form hydrogen bonds with the G1 amine group at the C7 position on the upper G-quartet. This formation of a hydrogen bond contributes to the stability of the G-quadruplex. The spectral property of meso-tetrakis(N-methylpyridium-4yl)porphyrin (TMPyP) associated with the G-quadruplex was characterized by a moderate red shift and hypochromism in the absorption spectrum, a positive CD signal, and two emission maxima in the fluorescence emission spectrum, suggesting that TMPyP binds at the exterior of the G-quadruplex. Spectral properties were slightly altered when the G base at the central loop was replaced with A or I, while the fluorescence decay times of TMPyP associated with the G-quadruplex were identical. Observed spectral properties removes the possibility of intercalation binding mode for TMPyP. TMPyP binds at the exterior of the quadruplex. Whether it stacks on the central loop or binds at the side of the quadruplex is unclear at this stage.

Effects of deficient of the Hoogsteen base-pairs on the G-quadruplex stabilization and binding mode of a cationic porphyrin

Background

In stabilization of the G-quadruplex, formation of a Hoogsteen base-pair between the guanine (G) bases is essential. However, the contribution of each Hoogsteen base-pair at different positions to whole stability of the G-quadruplex has not been known. In this study, the effect of a deficiency of the Hoogsteen type hydrogen bond in the G-quadruplex stability was investigated. Spectral properties of meso-tetrakis(1-methylpyridinium-4-yl)porphyrin (TMPyP) associated with various G-quadruplexes were also examined.

Methods

The thermal stability of the thrombin-binding DNA aptamer 5′G₁G₂TTG₅G₆TG₈TG₁₀G₁₁TTG₁₄G₁₅ G-quadruplex, in which the guanine (G) base at 1, 2, 5, 6 and 8th positions was replaced with an inosine (I) base, one at a time, was investigated by circular dichroism (CD). The absorption, CD and fluorescence decay curve for the G-quadruplex associated TMPyP were also measured.

Results

The transition from the G-quadruplex to a single stranded form was endothermic and induced by an increase in entropy. The order in stability was 0>8>6>2>5>1, where the numbers denote the position of the replacement and 0 represents no replacements of the G base, suggesting the significant contribution of the G₁ base in the stability of the G-quadruplex. Alteration in the spectral property of TMPyP briefly followed the order in thermal stability.

Conclusions

Replacement of a G base with an I base resulted in destabilization of the G-quadruplex. The missing hydrogen bond at position 1 destabilized the G-quadruplex most efficiently. TMPyP binds near the I base-replaced location namely, the side of the G-quadruplex.

General significance

The Hoogsteen base-pairing is confirmed to be essential in stabilization of G-quadruplex. When G is replaced with I, the latter base is mobile to interact with cationic porphyrin.

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Thermal stability of a quadruplex, 5´G₁G₂TTG₅G₆TG₈TG₉G₁₀TTG₁₁G₁₂ was investigated.

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Replacement of G by I base decreases melting temperature.

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The stability decreased 0>8>6>2>5>1, where numbers denotes the position replaced.

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Replaced I base interacts with a cationic porphyrin, TMPyP.

Photoinduced reduction of manganese(III) meso-tetrakis(1-methylpyridinium-4-yl)porphyrin at AT and GC base pairs

The photoreduction of water-soluble cationic manganese(III) meso-tetrakis(1-methylpyridium-4-yl)porphyrin (Mn(III)(TMPyP)(4+)) bound to a synthetic polynucleotide, either poly[d(A-T)2] or poly[d(G-C)2], was examined by conventional absorption and circular dichroism (CD) spectroscopy, transient absorption, and transient Raman spectroscopy. Upon binding, Mn(III)(TMPyP)(4+) produced a positive CD signal for both polynucleotides, suggesting external binding. In the poly[d(A-T)2]-Mn(III)(TMPyP)(4+) adduct case, an interaction between the bound porphyrin was suggested. The transient absorption spectral features of Mn(III)(TMPyP)(4+) in the presence of poly[d(A-T)2] and poly[d(G-C)2] were similar to those of the photoreduced products, Mn(II)(TMPyP)(4+), whereas Mn(III)(TMPyP)(4+) in the absence of polynucleotides retained its oxidation state. This indicated that both poly[d(A-T)2] and poly[d(G-C)2] act as electron donors, resulting in photo-oxidized G and A bases. The transient Raman bands (ν2 and ν4) that were assigned to porphyrin macrocycles exhibited a large downshift of ~25 cm(-1), indicating the photoreduction of Mn(III) to Mn(II) porphyrins when bound to both polynucleotides. The transient Raman bands for pyridine were enhanced significantly, suggesting that the rotation of peripheral groups for binding with polynucleotides is the major change in the geometry expected in the photoreduction process. These photoinduced changes do not appear to be affected by the binding mode of porphyrin.