Spectroscopic studies on the thermodynamic and thermal denaturation of the ct-DNA binding of methylene blue.

The ct-DNA binding properties of methylene blue (MB) including binding constant, thermodynamic parameter and thermal denaturation (T(m)) have been systematically studied by spectrophotometric method. The binding of MB to ct-DNA is quite strong as indicated by remarkable hypochromicity, red shift and equilibrium binding constant (K(b)). Van't Hoff plot of 1/T versus lnK(b) suggests that the MB dye binds exothermically to ct-DNA which is characterized by large negative enthalpy and entropy changes. According to polyelectrolyte theory, the charge release (Z) when ct-DNA interacts with MB is +1.09 which corresponds very well to the one positive charge carried by the MB dye. The K(b) at a low concentration of salt is dominated by electrostatic interaction (90%) while that at a high concentration of salt is mostly controlled by non-electrostatic process (85%). However, the stabilization of the DNA binding event in both cases is governed by non-electrostatic process. A moderate stabilization of double helix ct-DNA occurs when the MB dye binds to ct-DNA as indicated by the increase in T(m) of ct-DNA of about 5.5 degrees C in the presence of MB. This suggests that MB dye possibly binds to ct-DNA via electrostatic and intercalation modes.

Synthesis and DNA-binding properties of water-soluble cationic pyropheophorbides derived from chlorophyll a/b.

A series of mono-, di-, tetra- and hexacationic esters of pyropheophorbide a/b have been designed and synthesized to explore the intercalation of their phorbine ring between the base pairs of double-helical DNA and the influence of their peripheral substituents on the DNA interactions. Mono-(1), di-(2, 3) and tetra-(4, 5) cationic pyropheophorbides are soluble as an oligomeric aggregate in HEPES buffer, but hexa-(6) cationic pyropheophorbide is soluble as a monomer at lower concentrations. The interaction of these cationic pyropheophorbide derivatives with DNA has been investigated by DNA unwinding assay, fluorescence energy transfer, and measurements of the melting temperature of the double-helical DNA and visible absorption spectra. Dicationic 2 and 3 bind outside the double-helical DNA without and/or with self-aggregation and with self-aggregation, respectively, because they cannot intercalate between the base-pairs due to their aggregation. On the other hand, tetracationic 4 and 5 and hexacationic 6 intercalate between the base pairs of the double-helical DNA. The binding mode of the cationic pyropheophorbides a/b is strongly dependent on the number and position of the cationic peripheral substituents of the pyropheophorbides.

Enantioselective DNA binding of iron(II) complexes of methyl-substituted phenanthroline.

The enantioselective binding of [Fe(4,7-dmp)(3)](2+) (dmp: 4,7-dimethyl-1,10-phenantroline) and [Fe(3,4,7,8-tmp)(3)](2+) (tmp: 3,4,7,8-tetramethyl-1,10-phenanthroline) to calf-thymus DNA (ct-DNA) has been systematically studied by monitoring the circular dichroism (CD) spectral profile of the iron(II) complexes in the absence and presence of ct-DNA. The effect of salt concentration and temperature on the degree of enantioselectivity of the ct-DNA binding of the iron(II) complexes, i.e. the molar ratio of Delta- to Lambda-enantiomer in the solution or vice versa has been rigorously evaluated. It is noticeable that Delta-[Fe(4,7-dmp)(3)](2+) and Lambda-[Fe(3,4,7,8-tmp)(3)](2+) are preferentially bound to ct-DNA as reflected in their opposite CD spectral profiles. The preferential binding of the Lambda-enantiomer of [Fe(3,4,7,8-tmp)(3)](2+) to ct-DNA compared to that of the Delta-enantiomer is associated with the bulkiness of the ancillary ligands due to substitution of four hydrogen atoms in 1,10-phenanthroline for four methyl groups. The determination of enantiomeric inversion constant (K(inv)) at various salt concentrations has revealed that the degree of enantioselectivity is salt concentration dependent, indicating that electrostatic interaction is involved in the enantioselective binding of the iron(II) complexes to ct-DNA. Although [Fe(4,7-dmp)(3)](2+) and [Fe(3,4,7,8-tmp)(3)](2+) exhibit an opposite pattern in the CD spectra, the degree of their enantioselectivity (K(inv)) is not different from each other significantly. A thermodynamic study on the enantioselective binding of [Fe(4,7-dmp)(3)](2+) to ct-DNA using the van't Hoff plot of In K(inv) versus 1/T has demonstrated that the enthalpy change (Delta H degrees ) in the inversion process from the Lambda- to Delta-enantiomer of [Fe(4,7-dmp)(3)](2+) ct-DNA is positive, indicating that the process is endothermic and thus entropically driven.

Base-specific and enantioselective studies for the DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine.

Base specificity and enantioselectivity for the DNA binding of [Fe(phen)2(dppz)]2+ (phen=1,10-phenanthroline and dppz=dipyrido[3,2-a:2',3'-c]phenazine) have been studied by determining the equilibrium binding constant (Kb) of the iron(II) complex to calf thymus DNA (ct-DNA), poly[(dA-dT)2], poly[(dG-dC)2] and poly[(dI-dC)2] using spectrophotometric titration and by monitoring the CD spectral profile of the iron(II) complex in the presence and absence of different types of DNA using circular dichroism (CD) spectroscopy, respectively. It has been shown that [Fe(phen)2(dppz)]2+ prefers to intercalate into the A-T and I-C sequences of poly[(dA-dT)2] and poly[(dI-dC)2] rather than into the G-C sequences of poly[(dG-dC)2] or into the base pairs of ct-DNA. In contrast to previous reports, it is a surprising observation that the enantioselectivity of the DNA binding for [Fe(phen)2(dppz)]2+ is base-dependent in nature. The Delta-enantiomer of [Fe(phen)2(dppz)]2+ is preferentially intercalated into the base pairs of poly[(dG-dC)2] or ct-DNA as indicated by its CD spectral profiles. On the other hand, the Lambda-enantiomer of [Fe(phen)2(dppz)]2+ is favorably intercalated into poly[(dA-dT)2] or poly[(dI-dC)2] as suggested by the opposite CD spectral profile. This preferential binding of Lambda-[Fe(phen)2(dppz)]2+)for the A-T sequence may be attributed to the fact that the binding site for the A-T sequence is relatively facile and thus the steric effect caused by the ancillary (non-intercalated) phen ligands is alleviated. The degree of enantioselectivity represented by inversion constants (Kinv) decreases as the salt concentration in the solution increases, indicating that electrostatic interaction is also operating in the ct-DNA-binding events of the iron (II) complex.

Binding of tetrakis(pyrazoliumyl)porphyrin and its copper(II) and zinc(II) complexes to poly(dG-dC)2 and poly(dA-dT)2.

Interactions of cationic porphyrins bearing five-membered rings at the meso position, meso-tetrakis(1,2-dimethylpyrazolium-4-yl)porphyrin (MPzP; M is H2, Cu(II) or Zn(II)), with synthetic polynucleotides poly(dG-dC)2 and poly(dA-dT)2 have been characterized by viscometric, visible absorption, circular dichroisim and magnetic circular dichroism spectroscopic and melting temperature measurements. Both H2PzP and CuPzP are intercalated into poly(dG-dC)2 and are outside-bound to the major groove of poly(dA-dT)2, while ZnPzP is outside-bound to the minor groove of poly(dA-dT)2 and surprisingly is intercalated into poly(dG-dC)2. The binding constants of the porphyrin and poly(dG-dC)2 and poly(dA-dT)2 are on the order of 10(6) M(-1) and are comparable to those of other cationic porphyrins so far reported. The process of the binding of the porphyrin to poly(dG-dC)2 and poly(dA-dT)2 is exothermic and enthalpically driven for H2PzP, whereas it is endothermic and entropically driven for CuPzP and ZnPzP. These results have revealed that the kind of the central metal ion of metalloporphyrins influences the characteristics of the binding of the porphyrins to DNA.

DNA-binding properties and photocleavage activity of cationic water-soluble chlorophyll derivatives.

Three cationic water-soluble chlorin e(6) derivatives, that is, 6a-,gammab-,7c-tris(2-trimethylammonioethyl)chlorin e(6) (1), 6a-,gammab-,7c-tris(3-methylpyridiniummethyl)chlorin e(6) (2), and 6a-,gammab-, 7c-tris(2-trimethylammonioethyl)-2-(3-trimethylammonioprop-1-enyl)chlorin e(6) (3), have been designed and synthesized to allow the study of their DNA-binding and -photocleavage activities. The DNA-unwinding assay, measurements of melting temperatures of double-stranded DNA, and the induced CD and visible absorption spectra have revealed that 1 and 3 are intercalated into the base pairs of the double-helical DNA, while 2 is bound to outside the minor groove of the double-helical DNA. The cationic water-soluble chlorin e(6) derivatives effectively cleave the double-helical DNA under photoirradiation and the DNA-photocleavage activity increases in the order 3>1>2. The DNA-binding and -photocleavage characteristics of the three cationic water-soluble chlorin e(6) derivatives are influenced by aspects of their molecular structure, such as the kind, number, and position of the cationic substituents.

Salt-dependent binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine to calf thymus DNA.

The salt-dependent binding of racemic iron(II) mixed-ligand complex containing 1,10-phenanthroline (phen) and dipyrido[3,2-a:2',3'-c]phenazine (dppz), [Fe(phen)2(dppz)]2+ to calf thymus DNA (ct-DNA) has been characterized by UV-VIS spectrophotometric titration. The equilibrium binding constant (Kb) of the iron(II) complex to ct-DNA decreases with the salt concentration in the solution. The slope, SK=(deltalog Kb/deltalog [Na2+]) has been found to be 0.49, suggesting that, in addition to intercalation, considerable electrostatic interaction is also involved in the ct-DNA binding of [Fe(phen)2(dppz)]2+. The calculation of non-electrostatic binding constant (Kt(o)) based on polyelectrolyte theory has revealed that the non-electrostatic contribution to the total binding constant (Kb) increases significantly with the increase in [Na+] and reaches 36% at 0.1 M NaCl. On the other hand, the contribution of the non-electrostatic binding free energy (DeltaGt(o)) to the total binding free energy change (DeltaGo) is considerably large, i.e. 87% at [Na+]=0.1 M, suggesting that the stabilization of the DNA binding is mostly due to the contribution of non-electrostatic process. Moreover, the effect of specific ligand substitutions on DeltaGo has been rigorously evaluated using the quantity DeltaDeltaGt(o), i.e. the difference in DeltaGt(o) relative to that of the parent iron(II) complex, [Fe(phen)3]2+, indicating that each substitution of phen by dip and dppz contributes 7.5 and 17.5 kJ mol(-1), respectively to more favorable ct-DNA binding.

Helicity induction and two-photon absorbance enhancement in zinc(II) meso-meso linked porphyrin oligomers via intermolecular hydrogen bonding interactions.

Helicity has been induced in meso-meso linked oligomers by hydrogen bonding host-guest interactions with cyclic urea. Helical porphyrin arrays thus formed exhibit chirality amplification and enhanced two-photon absorption properties.

Amphiphilic meso-disubstituted porphyrins: synthesis and the effect of the hydrophilic group on absorption spectra at the air-water interface.

Five amphiphilic meso-disubstituted porphyrins bearing one polar group were synthesized, and their monolayer films were prepared. Their limiting molecular areas obtained from pi-A isotherms were 0.5-0.6 nm2, which were smaller than those of the corresponding meso-tetrasubstituted porphyrins. At the air-water interface, the disubstituted porphyrins showed a broad band in visible absorption spectra compared with the solution state, and the red shift of the Soret band exhibited a significant dependence on the kind of hydrophilic groups at the meso positions. Interestingly, the monolayer of the disubstituted porphyrin bearing a carboxyphenyl group (1-CO2H) showed a blue shift of the Soret band by adding cadmium chloride to the subphase, and the spectra varied upon multilayer deposition. The observed phenomena were interpreted by using the exciton theory. The effect of hydrophilic substituents on the absorption spectra of disubstituted porphyrin monolayers is discussed.

An Ideal One-Dimensional Antiferromagnetic Spin System Observed in Hydrogen-Bonded Naphth[2,3-d]imidazol-2-yl Nitronyl Nitroxide Crystal: The Role of the Hydrogen Bond.

A novel stable organic radical, 2-(naphth[2,3-d]imidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazolyl-1-oxyl-3-oxide (4), has been designed, synthesized, and structurally characterized to examine the effects of ring extension on 2-(benzimidazol-2-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazolyl-1-oxyl-3-oxide (2). 4 forms four-centered intramolecular and intermolecular hydrogen bonds, and the hydrogen bonds are repeated along the c-axis to form a one-dimensional chain structure. This hydrogen-bonding motif contrasts that of 2, which forms three-centered intramolecular and intermolecular hydrogen bonds. The magnetic susceptibility measurement of 4 reveals that an antiferromagnetic interaction is dominant between spins, and the magnetic behavior is reproduced by the Bonner-Fisher model with J = -14 cm-1. Because each hydrogen-bonded chain is well isolated, a magnetic interaction pathway was thought to exist along the chain direction. Two interaction pathways have been assumed: (i) through-space interaction between the O atoms of the nitroxide and (ii) through the NH...ON intermolecular hydrogen bond. We have concluded that pathway (i) is predominant, by considering the identical magnetic data between the NH nondeuterated and deuterated samples. The hydrogen bond mainly has a role in crystal scaffolding.

DNA binding of iron(II) complexes with 1,10-phenanthroline and 4,7-diphenyl-1,10-phenanthroline: salt effect, ligand substituent effect, base pair specificity and binding strength.

The DNA binding of iron(II) mixed-ligand complexes containing 1,10-phenanthroline(phen) and 4,7-diphenyl-1,10-phenanthroline(dip), [Fe(phen)(3)](2+), [Fe(phen)(2)(dip)](2+) and [Fe(phen)(dip)(2)](2+) has been characterized by spectrophotometric titration and melting temperature measurements. The salt concentration dependence of the binding constant has allowed us to dissect the DNA-binding constant and free energy change of each iron(II) complex into the nonelectrostatic and polyelectrolyte contributions. A comparison of the nonelectrostatic components in the binding free energy changes among iron(II) complexes has made it possible to rigorously evaluate the contribution of the ligand substituents to the DNA-binding event. The peripheral substitution of phen by two phenyl groups increases the nonelectrostatic binding constant of the iron(II) complex more than 20 times, which is equivalent to approximately 7.5 kJ mol(-1) of more favorable contribution to the DNA binding. In general, the iron(II) complexes studied have higher affinity towards the more facile A-T sequence than the G-C sequence. This preferential binding may be attributed to the steric effect induced by the ancillary part of the ligands in the course of DNA binding. The binding of disubstituted iron(II) complex to DNA is quite strong as reflected in the modest increase in the denaturation temperature (T(m)) of double helical DNA upon the interaction with the iron(II) complex.