Electronic structures, DNA-binding and related properties of complexes [Ru(bpy)2L]2+ (L=ip, pip, hpip)

Photoinduced Electron Transfer between DNA and Water-Soluble Porphyrins

Photophysical properties of five kinds of porphyrins (H₂TMPyP, ZnTMPyP, PdTMPyP, H₂TPPS, and ZnTPPS) complexed with model DNAs (ctDNA and dGMP) have been investigated using steady-state absorption, circular dichroism (CD), and femtosecond transient absorption spectroscopy. Upon addition of ctDNA (or dGMP), larger hypochromism and red shifts are observed for H₂TMPyP and PdTMPyP compared to the other samples. The steady-state measurements have suggested that the binding modes of H₂TMPyP-ctDNA and PdTMPyP-ctDNA are partial intercalation and full intercalation, respectively, while ZnTMPyP-ctDNA shows outside groove binding. No significant interaction was observed between both H₂TPPS and ZnTPPS with two kinds of DNA. Upon excitation of the porphyrins into the higher excited state S₂ (Soret band), the appearance of the transient absorption from ∼500 to ∼620 nm at about 0.05 ps in H₂TMPyP-ctDNA, H₂TMPyP-dGMP, and PdTMPyP-dGMP indicates the occurrence of the electron transfer (ET) from guanine to H₂TMPyP and PdTMPyP. The forward ET are extremely fast (k_f ≥ 1.0 × 10¹³ s^-1), and the backward ET rates are ∼5.6 × 10¹² and ∼4.0 × 10¹² s^-1, respectively. The complexation with DNA may lead to the shorter lifetime of the fluorescence of H₂TMPyP and PdTMPyP.

DNA groove-binding and acid-base properties of a Ru(II) complex containing anthryl moieties

DNA groove binders have been poorly studied as compared to the intercalators. A novel Ru(II) complex of [Ru(aeip)₂(Haip)](PF₆)₂ {Haip = 2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline and aeip = 2-(anthracen-9-yl)-1-ethyl-imidazo[4,5-f][1, 10]phenanthroline} is synthesized and characterized by elemental analysis, ¹H NMR spectroscopy and mass spectrometry. The complex is evidenced to be a calf-thymus DNA groove binder with a large intrinsic binding constant of 10⁶ M^-1 order of magnitude as supported by UV-visible absorption spectral titrations, salt effects, DNA competitive binding with ethidium bromide, DNA melting experiment, DNA viscosity measurements and density functional theory calculations. The acid-base properties of the complex studied by UV-Vis spectrophotometric titrations are reported as well.

Photoinduced Electron Transfer between Anionic Corrole and DNA

The interaction between a water-soluble anionic Ga(III) corrole [Ga(tpfc)(SO3Na)2] and calf thymus DNA (ct-DNA) has been investigated by using femtosecond transient absorption spectroscopy. A significant broadening from 570 to 585 nm of positive absorption band of the blend of Ga(tpfc)(SO3Na)2 and ct-DNA (Ga(tpfc)(SO3Na)2-ctDNA) has been observed from 0.15 to 0.50 ps after photoexcitation of Ga(tpfc)(SO3Na)2 into the Soret band. The control experiment has been performed on the model DNA ([poly(dG-dC)]2) rich in guanine bases, which exhibits a similar spectral broadening, whereas it is absent for [poly(dA-dT)]2 without guanine bases. The molecular orbital calculation shows that HOMO of Ga(tpfc)(SO3Na)2 is lower than that of guanine bases. The results of the electrochemical experiment show the reversible electron transfer (ET) between Ga(tpfc)(SO3Na)2 and guanine bases of ct-DNA is thermodynamically favorable. The dynamical analysis of the transient absorption spectra reveals that an ultrafast forward ET from the guanine bases to Ga(tpfc)(SO3Na)2 occurs within the pulse duration (156 fs), leading to the formation of an intermediate state. The following back ET to the ground state of Ga(tpfc)(SO3Na)2 may be accomplished in 520 fs.

The effects of linear assembly of two carbazole groups on acid-base and DNA-binding properties of a ruthenium(II) complex

A novel Ru(II) complex of [Ru(bpy)2(Hbcpip)](ClO4)2 {where bpy=2,2-bipyridine, Hbcpip=2-(4-(9H-3,9'-bicarbazol-9-yl)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline} is synthesized and characterized. Calf-thymus DNA-binding properties of the complex were studied by UV-vis absorption and luminescence titrations, steady-state emission quenching by [Fe(CN)6](4-), DNA competitive binding with ethidium bromide, thermal denaturation and DNA viscosity measurements. The results indicate that the complex partially intercalated into the DNA with a binding constant of (5.5±1.4)×10(5) M(-1) in buffered 50 mM NaCl. The acid-base properties of the complex were also studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constant values were derived.

Application of a europium complex, Eu(AA)3phen (AA=acrylic acid, phen=1,10-phenanthroline) as a spectroscopic probe and cleaving reagent of DNA

A complex Eu(AA)3phen was synthesized and characterized by elemental analysis, IR spectroscopy and (1)H NMR. Interaction between Eu(AA)3phen and DNA was studied by UV/visible absorption spectroscopy, fluorescence spectrophotometer, circular-dichroism (CD) spectra and gel-electrophoresis measurements. Absorption spectral indicated that Eu(AA)3phen binding to DNA was an electrostatic mode, which was authenticated by the effect of ionic strength, thermal denaturation and fluorescence quenching experiments. The intrinsic binding constant Kb of Eu(AA)3phen was calculated to be 1.6×10(4) L mol(-1).

Preparation of a DNA-bound [Ru(bpy)₂(mbpibH2)]²+ film and its two-mode luminescence tuning by copper(II) ions and EDTA

An imidazophenanthroline-containing ruthenium(II) complex [Ru(bpy)(2)(mbpibH2)](2+) (bpy=2,2'-bipyridine, mbpibH2=1,3-bis([1,10]phenanthroline[5,6-d]imidazol-2-yl)benzene) can bind DNA through groove-binding and/or non-classical intercalation modes, revealed by spectrophotometric methods, viscosity measurements and variable ionic strength experiments. On the basis of binding interactions between cationic [Ru(bpy)(2)(mbpibH2)](2+) and anionic DNA at a molar ratio of 1:1, a yellow transparent cast film has been assembled on an indium-tin oxide (ITO) surface using a solution-based self-standing method. The prepared DNA-[Ru(bpy)(2)(mbpibH2)](2+) film shows a bi-exponential luminescence decay with τ(1)=62.1 ns (8.0%) and τ(2)=594.5 ns (92.0%), whose lifetimes become much shorter than those of DNA-bound [Ru(bpy)(2)(mbpibH2)](2+) in buffer solutions. The Ru(II) complex with a free bi-dentate coordination site in the DNA cast film shows tunable luminescence, quenched dynamically by Cu(2+) and restored by using EDTA to eliminate two modes of Cu(2+)-binding. The results from this study provide a significant foundation for better understanding the fabrication and modulation of a DNA-based solid luminescence device using the Ru(II) complexes as DNA-concentrating and signal-sensing agents.

Theoretical studies on DNA-photocleavage efficiencies and mechanisms of Ru(II) polypyridyl complexes

Theoretical studies on the DNA-photocleavage efficiencies and mechanisms of Ru(II) complexes [Ru(bpy)(2)(L)](2+) (bpy = 2,2'-bipyridine; L: dppz = dipyrido[3,2-a:2',3'-c]phenazine; mitatp = 5-methoxy-isatino[1,2-b]-1,4,8,9-tetraazatriphenylene; nitatp = 5-nitro-isatino [1,2-b]-1,4,8,9-tetraazatriphenylene) 1-3 were carried out using density functional theory (DFT). First, the accuracies of redox potentials computed for [Ru(bpy)(3)](2+) in the ground state and the excited state by different computational methods were tested, and then the redox potentials of complexes 1-3 in their excited states were computed accurately. Secondly, the trend in the DNA-photocleavage efficiencies (ϕ) of complexes 1-3 [i.e., ϕ(2) > ϕ(3) > ϕ(1)] was reasonably well explained by their excited-state reduction potentials and their electron-transfer activation energies. Finally, the photoinduced oxidation-reduction mechanism utilized by these complexes was explored, and the DNA-photocleavage process was explained rationally.

DFT/TDDFT STUDY ON DNA-BINDING AND SPECTRAL PROPERTIES OF "LIGHT SWITCH" COMPLEX [Ru(phen)2 (taptp)]2+ IN AQUEOUS SOLUTION

The theoretical studies on the electronic structure, DNA-binding, and absorption-spectral properties of "light switch" complex [ Ru ( phen )2( taptp )]2+ (phen = 1,10-phenanthroline; taptp = 4,5,9,18-tetraazaphenanthreno-[9,10-b]triphenylene) in aqueous solution have been carried out using density functional theory (DFT) and time-dependent DFT (TDDFT) methods. The results show the following: (i) The solvent effect makes all the frontier molecular orbital energies of complex to increase to a certain extent; however, the energies (ε LUMO + x) of some frontier unoccupied molecular orbitals (MOs) in aqueous solution are still negative and rather lower than those of the energies (ε HOMO - x) of some frontier-occupied MOs of DNA-base pairs, and thus the complex in aqueous solution is still an excellent electron-acceptor in its DNA-binding. (ii) The solvent effect further shows that simply increasing the conjugative planar area of intercalative ligand may be ineffective on the improvement of DNA-binding of the resulting complex because of going along with the increase in the LUMO (and LUMO + x) energy. It is the reason why the DNA-binding affinity of "light switch" complex [ Ru ( phen )2( taptp )]2+ is not better than that of the well-known complex [ Ru ( phen )2( dppz )]2+ yet. (iii) The three main experimental bands (~450 nm, ~360 nm, and ~290 nm) of the studied complex in aqueous solution were further well calculated, simulated, and explained by the TDDFT computations.

DNA- and RNA-binding and enhanced DNA-photocleavage properties of a ferrocenyl-containing ruthenium(II) complex

The interaction of [Ru(bpy)(2)(fip)](PF(6))(2) {bpy=2,2'-bipyridine, fip=2-ferrocenyl-1H-imidazo[4,5-f][1,10]-phenanthroline} with calf thymus DNA and yeast tRNA was investigated comparatively by UV-visible absorption and luminescence spectrophotometric titrations, steady-state emission quenching by [Fe(CN)(6)](4-), ethidium bromide competition experiment, DNA thermal denaturation, viscosity measurements and salt effect studies. The results suggest that the complex binds to the DNA more strongly than to the RNA. The density functional theory calculations were also carried out in order to better understand the nucleic acid binding properties. Agarose gel electrophoresis showed that the complex exhibited enhanced DNA-photocleavage capacity on pUC 18 plasmid DNA under irradiation at 360 nm as compared with a ferrocenyl-free analogous complex.

Synthesis, and Acid–Base and DNA-Binding Properties of a Thiophen-Appended Ruthenium Complex

2-(5-Phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (Hptip) and its RuII complex [Ru(bpy)2(Hptip)](PF6)2 (where bpy = 2,2′-bipyridine) have been synthesized and characterized by elemental analysis, 1H NMR spectroscopy, and mass spectrometry. The acid–base properties of the complex were studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constants were derived. The DNA-binding properties of [Ru(bpy)2(Hptip)](PF6)2 were also investigated by means of UV-vis and emission spectroscopy, salt effects, steady-state emission quenching by [Fe(CN)6]4–, DNA competitive binding with ethidium bromide, DNA melting experiments, and viscosity measurements. Density functional theoretical calculations were also carried out in order to understand the DNA binding properties.

Density Functional Theory/Time-dependent DFT Studies on the Structures, Trend in DNA-binding Affinities, and Spectral Properties of Complexes [Ru(bpy)2(p-R-pip)]2+ (R = −OH, −CH3, −H, −NO2)

Studies on the electronic structures and trend in DNA-binding affinities of a series of Ru(II) complexes [Ru(bpy)2(p-R-pip)]2+ (bpy = 2,2-bipyridine; pip = 2-phenylimidazo[4,5-f] [1,10]-phenanthroline; R = -OH, -CH3, -H, -NO2) 1-4 have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The electronic absorption spectra of these complexes were also investigated using time-dependent DFT (TDDFT) at the B3LYP//LanL2DZ/6-31G level. The computational results show that the substituents on the parent ligand (pip) have a significant effect on the electronic structures of the complexes, in particular, on the energies of the lowest unoccupied molecular orbital (LUMO) and near some unoccupied molecular orbitals (LUMO+x, x = 1-4). With the increase in electron-withdrawing ability of the substituent in this series, the LUMO+x (x = 0-4) energies of the complexes are substantially reduced in order, for example, epsilon(LUMO)(1) approximately epsilon(LUMO)(2) > epsilon(LUMO)(3) > epsilon(LUMO)(4), whereas the pi-component populations of the LUMO+x (x = 0-4) are not substantially different. Combining the consideration of the bigger steric hindrance of complex 2, the trend in DNA-binding affinities (K(b)) of the complexes, that is, K(b)(2) < K(b)(1) < K(b)(3) < K(b)(4) can be reasonably explained. In addition, the experimental singlet metal-to-ligand charge transfer ((1)MLCT) spectra of these complexes can be well simulated and discussed by the TDDFT calculations.