Interaction of monomolecular G4-DNA nanowires with TMPyP: evidence for intercalation

Interaction of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with G4-wires composed of approximately 1000 stacked tetrads (Kotlyar, A. B., Borovok, N., Molotsky, T., Cohen, H., Shapir, E., and Porath, D. (2005) Long monomolecular G4-DNA nanowires, Adv. Mater. 17, 1901-1905) was studied. These wires exist in either K (Na)-free or K forms in contrast to short telomeric G-quadruplexes, which are stable only in the presence of monovalent cations. We showed that a stable complex between K-free G4-wires and the porphyrin is formed at a TMPyP to tetrad molar ratio of 0.5. A 19 nm shift and a hypochromicity of 58% in the absorption spectrum, the induced CD of the porphyrin, and efficient energy transfer between TMPyP and K-free G4-wires suggest an intercalative mechanism of TMPyP binding. The K form interacts with TMPyP much weaker than the K-free form of the wires. Binding of TMPyP to the K form is characterized by a small (3 nm) shift of the Soret band, a weak positive induced CD in the Soret region, and the absence of energy transfer between the G-bases and the porphyrin. These parameters reflect a nonintercalative binding of TMPyP to the K form of the wires. We suggest that K ions positioned in the center space between the adjacent tetrads limit the access of TMPyP and other organic molecules to this region, thus enabling only nonintercalative modes of ligand binding to G-quadruplex DNAs.     

Interaction of porphyrin with G-quadruplex structures

Isothermal titration calorimetry (ITC) is a sensitive technique for probing bimolecular processes and can provide direct information about the binding affinity and stoichiometry and the key thermodynamic parameters involved. ITC has been used to investigate the interaction of the ligand H2TMPyP to the two DNA quadruplexes, [d(AGGGT)]4 and [d(TGGGGT)]. Analysis of the ITC data reveals that porphyrin/quadruplex binding stoichiometry under saturating conditions is 1:2 for [d(AGGGT)]4 and 2:1 for [d(TGGGGT)], respectively.     

Interaction between cationic zinc porphyrin and lead ion induced telomeric guanine quadruplexes: evidence for end-stacking

The interaction between small molecules and telomeric quadruplex DNA has received great attention because of its importance in molecular recognition and anticancer drug design. Using UV/vis absorption titration, thermal melting, circular dichroism spectroscopy, and electrospray ionization mass spectrometry, we examined the formation of lead ion induced guanine quadruplexes (Pb-G4) from oligonucleotide AG₃(T₂AG₃)₃ and their interaction with a zinc derivative of 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (Zn-TMPyP). The binding of lead ion to the oligonucleotide was found to have an unusually high affinity and followed a 1:1 stoichiometry, and the resultant Pb-G4 structure was stabilized by Zn-TMPyP binding. Owing to the steric hindrance of the axial ligand of zinc and also the relatively rigid structure of Pb-G4, intercalation of Zn-TMPyP between adjacent guanine quartets is precluded, thus allowing the end-stacking binding mode to be characterized exclusively. In conjunction with a big redshift (more than 8 nm) in the absorption spectrum, we demonstrate that a conservative induced circular dichroism is an important signature for end-stacking of porphyrins on guanine quadruplexes.     

Binding of ethidium bromide to a DNA triple helix. Evidence for intercalation

The interaction of ethidium, a DNA intercalator, with the poly(dA).poly(dT) duplex and the poly (dA).2poly(dT) triplex has been investigated by a variety of spectrophotometric and hydrodynamic techniques. The fluorescence of ethidium is increased when either the duplex or triplex form is present. Binding constants, determined from absorbance measurements, indicate that binding to the triple helical form is substantially stronger than to the duplex, with a larger binding site size (2.8 base triplets compared to 2.4 base pairs). Furthermore, while binding to poly(dA).poly(dT) shows strong positive cooperativity, binding to the triplex is noncooperative. Thermal denaturation experiments demonstrate that ethidium stabilizes the triple helix. Binding to either form induces a weak circular dichroism band in the visible wavelength region, while in the region around 310 nm, there is a band that is strongly dependent on the degree of saturation of the duplex, and which is positive for the duplex but negative for the triplex. Both fluorescence energy transfer and quenching studies provide evidence of intercalation of ethidium in both duplex and triplex complexes. Binding of ethidium leads to an initial decrease in viscosity for both the duplex and triplex structures, followed by an increase, which is greater for the duplex. Taken together, these results strongly suggest that ethidium binds to the poly (dA).2poly(dT) triple helix via an intercalative mechanism.     

Interaction of glutathione and other low-molecular-weight thiols with DNA: evidence for counterion condensation and coion depletion near DNA

The interaction of low-molecular-weight thiols with sonicated DNA was examined using spin filtration to concentrate the DNA. Cationic thiols (WR 1065 and cysteamine) behaved as counterions and were found to have increased concentrations in the DNA retentate relative to the filtrate. Anionic thiols (GSH, 2-mercaptoethanesulfonate, mercaptosuccinate) behaved as coions and were decreased in concentration in the DNA fraction. Concentrations of the uncharged thiol 2-mercaptoethanol were little influenced by DNA. The results demonstrate the importance of counterion condensation and coion depletion in determining the concentrations of charged species near DNA. They provide a rationale for enhanced effectiveness of WR 1065 and cysteamine as radioprotectors compared to neutral and anionic thiols and suggest that anionic thiols such as GSH should be poor radioprotectors of DNA.     

Studies on DNA binding of caffeine and derivatives: evidence of intercalation by DNA-unwinding experiments

Caffeine and derivatives are compounds with pleiotropic effects on the genetic material which are supposed to originate from drugs binding to DNA. Here we show, by using two different topological methods, that methylated oxypurines, at biologically relevant concentrations, unwind DNA in a fashion similar to known intercalators. Methylated oxypurines could be ranked by decreasing unwinding potency: 8-methoxycaffeine greater than 8-ethoxycaffeine greater than 8-chlorocaffeine greater than caffeine greater than theophylline. These findings confirm, with a different assay, interaction of caffeine with DNA and add additional support to an intercalative mode of binding of these drugs to DNA.     

Interaction of cationic porphyrins with DNA: importance of the number and position of the charges and minimum structural requirements for intercalation

Thirty-three porphyrins or metalloporphyrins corresponding to the general formula [meso-[N-methyl-4(or 3 or 2)-pyridiniumyl]n(aryl)4-nporphyrin]M (M = H2, CuII, or ClFeIII), with n = 2-4, have been synthesized and characterized by UV-visible and 1H NMR spectroscopy and mass spectrometry. These porphyrins differ not only in the number (2-4) and position of their cationic charges but also in the steric requirements to reach even temporarily a completely planar geometry. In particular, they contain 0, 1, 2, 3, or 4 meso-aryl substituents not able to rotate. Interaction of these porphyrins or metalloporphyrins with calf thymus DNA has been studied and their apparent affinity binding constants have been determined by use of a competition method with ethidium bromide which was applicable not only for all the free base porphyrins but also for their copper(II) or iron(III) complexes. Whatever their mode of binding may be, their apparent affinity binding constants were relatively high (Kapp between 1.2 x 10(7) and 5 x 10(4) M-1 under our conditions), and a linear decrease of log Kapp with the number of porphyrin charges was observed. Studies of porphyrin-DNA interactions by UV and fluorescence spectroscopy, viscosimetry, and fluorescence energy transfer experiments showed that not only the tetracationic meso-tetrakis[N-methyl-4(or 3)-pyridiniumyl]porphyrins, which both involved four freely rotating meso-aryl groups, but also the corresponding tri- and dicationic porphyrins were able to intercalate into calf thymus DNA. Moreover, the cis dicationic meso-bis(N-methyl-2-pyridiniumyl)diphenylporphyrin, which involved only two freely rotating meso-aryl groups in a cis position, was also able to intercalate. The other meso-(N-methyl-2-pyridiniumyl)n(phenyl)4-nporphyrins, which involved either zero, one, or two trans freely rotating meso-aryl groups, could not intercalate into DNA. These results show that only half of the porphyrin ring is necessary for intercalation to occur.     

Interaction of furazolidone with DNA.

DN forms a complex with furazolidone producing thereby a quenching and a bathochromic shift of the drug absorption pattern. The binding isotherm was a non-linear one indicating involvement of more than one binding process in the formation of the furazolidone - DNA complex. The furazolidone - DNA complex inhibited digestion of DNA by DNAase and stabilized DNA against thermal strand separation by a significant degree.     

The interaction of benzimidazole compounds with DNA: intercalation and groove binding modes.

Benzimidazole compounds (Fig. 1) have been synthesized to study their DNA-binding properties. Results obtained with spectroscopy and viscosity measurements indicate that the binding mode varies from intercalation to groove-binding, depending on the number of benzimidazole rings (conformation and size of compounds).     

Interaction of polypyridyl ruthenium (II) complex containing asymmetric ligand with DNA

A novel asymmetric bidentate ruthenium (II) complex, [Ru(bpy)(2)(PYNI)](2+) (bpy=2,2'-bipyridine, PYNI=2-(2'-pyridyl)naphthoimidazole), has been synthesized and characterized by elemental analysis, ES-MS (electrospray mass spectra) and (1)H NMR. The electrochemical behaviors of this complex were studied by cyclic voltammetry. DNA interaction studies suggest that [Ru(bpy)(2)(PYNI)](2+) binds to calf thymus DNA (CT-DNA) in an intercalative mode. Interestingly, this new Ru(II) complex has also been found to promote cleavage of plasmid pBR 322 DNA from the supercoiled form I to the open circular form II upon irradiation.     

Molecular spectroscopy evidence of berberine binding to DNA: comparative binding and thermodynamic profile of intercalation

Berberine (BH) is an important traditional medicinal herb endowed with diverse pharmacological and biological activities. In this work, the binding characteristics and molecular mechanism of the interaction between the BH and herring sperm DNA were explored by UV-vis absorbance and fluorescence spectroscopy. In the mechanism discussion, fluorescence quenching, absorption spectra, competition experiment, and iodide quenching experiment studies hinted at an intercalative mode of binding for BH to DNA. Fluorescence studies revealed the binding constant (K) of BH-DNA was ～10(4) L·mol(-1). The effects of temperature, chemical denaturants, thermal denaturation, and pH were studied to show the factors of the interaction and provided further support for the intercalative binding mode. The results of thermodynamic parameters ΔG, ΔH, and ΔS at different temperatures indicated that the hydrogen bonds and van der Waals interactions played major roles in the reaction, and the effect of ionic strength indicated that electrostatic attraction between the BH and DNA was also a component of the interaction.     

Interaction of monosulfonate tetraphenyl porphyrin, a competitive inhibitor, with acetylcholinesterase

Monosulfonate tetraphenyl porphyrin (TPPS(1)) forms a 1:1 complex with electric eel acetylcholinesterase (AChE) inducing a loss in TPPS(1) absorbance at 402 nm and the appearance of a new absorbance centered at 442 nm. In the presence of AChE, the fluorescence of TPPS(1) at 652 nm is slightly narrowed, with the maximal 652 nm fluorescence shifted from 407 to 412 nm excitation wavelength. The fluorescence peak of TPPS(1) at 712 nm shifts to 716 nm in the presence of AChE. TPPS(1) is a competitive inhibitor of AChE. The addition of acetylcholine iodide (AChI) or the competitive inhibitor tetracaine to the preformed AChE-TPPS(1) complex results in a loss of the 442 nm absorbance band as the porphyrin is displaced from AChE. The absorbance peak does not decrease in the presence of procaine, a non-competitive inhibitor.     

Interaction of chromium(III) complex of chiral binaphthyl tetradentate ligand with DNA

Since conformation of the molecule plays a vital role in the activity of drug, we have investigated the DNA interaction of a chromium(III) complex with ligands in two conformations. Chromium(III) complexes derived from chiral binaphthyl Schiff base ligands, viz. R- and S-2,2'-bis(salicylideneamino) 1,1'-binaphthyl, have been synthesized and characterized by mass, IR, and electronic spectra. The interaction of these R- and S-binaphthyl Schiff base chromium(III) complexes with CT-DNA was investigated with the goal of examining whether the chirality has an influence on the chromium(III)-DNA binding properties. The difference in chirality of the ligand did not show any striking difference in binding properties. The binding constants for R and S conformers were estimated to be 18 (+/-0.4) x 10(3) and 9.4 (+/-0.3) x 10(3) M(-1), respectively, through spectroscopic titrations. All the experimental results are suggestive that both the isomers are DNA groove binders. The results of steady-state as well as time-resolved fluorescence experiments, however, suggest that the R conformer has restricted mobility when bound to DNA because it is more deeply buried in the groove of DNA compared to the S isomer.     

Interaction of colchicine with DNA molecules.

Colchicine (7.5 X 10-6M or 3.3 X 10-5M) was incubated at pH 7.0, 10.0, or 12.0 with high-molecular DNA from salmon sperm (7 X 10-5M or 3.5 X 10-5M DNA-P) at 40 degrees C. Interaction was monitored by UV spectrophotometry; Amax/Amin ratios, difference and additive spectra, and the quantity of colchicine bound to DNA were presented as functions of time, ionic strength and DNA concentration. Using NMR techniques, delta deltav 1/2/deltac values, chemical shifts and half-line widths of colchicine protons were analyzed as a function of the DNA/colchicine ratio, thus proving the interaction between alkaloid and DNA. An intercalation of the tropolone moiety of colchicine between the nitrogenous bases of DNA is suggested.     

Activation of soluble guanylyl cyclase by four-coordinate metalloporphyrins: evidence for a role for porphyrin conformation

Four-coordinate metalloporphyrins activate soluble guanylyl cyclase. Ni(II)PPIX and Cu(II)PPIX are high affinity activators, with activation constants of 24 and 17 nM, respectively. Both metalloporphyrins remain stably bound to the enzyme, enabling spectroscopic characterization of the Ni(II)- and Cu(II)-reconstituted protein. Electronic absorption and resonance Raman spectroscopy reveal that Ni(II)PPIX remains four coordinate when bound to soluble guanylyl cyclase. Analysis of the vibrational frequencies of the Ni(II)-reconstituted enzyme suggests that the protein imposes a constraining force on the porphyrin, favoring a planar conformation. Spectroscopic data for the Cu(II)-substituted protein are also consistent with four coordination. The intensification of the vibrational modes of the peripheral vinyl groups in both Ni(II)- and Cu(II)-reconstituted soluble guanylyl cyclase are consistent with a substantial influence of the protein on the porphyrin environment. Together these data support a model where activation of soluble guanylyl cyclase correlates with the absence of a metal-to-proximal histidine bond and with decreased conformational freedom for the tetrapyrrole in the activated state.