Design of photoactivated DNA oxidizing agents: synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines

A new series of photoactivated DNA oxidizing agents in which an acridine moiety is covalently linked to viologen by an alkylidene spacer was synthesized, and their photophysical properties and interactions with DNA, including DNA cleaving properties, were investigated. The fluorescence quantum yields of the viologen-linked acridines were found to be lower than that of the model compound 9-methylacridine (MA). The changes in free energy for the electron transfer reactions were found to be favorable, and the fluorescence quenching observed in these systems is explained by an electron transfer mechanism. Intramolecular electron transfer rate constants were calculated from the observed fluorescence quantum yields and singlet lifetime of MA and are in the range from 1.06x10(10) s(-1) for 1 a (n=1) to 6x10(8) s(-1) for 1 c (n=11), that is, the rate decreases with increasing spacer length. Nanosecond laser flash photolysis of these systems in aqueous solutions showed no transient absorption, but in the presence of guanosine or calf thymus DNA, transient absorption due to the reduced viologen radical cation was observed. Studies on DNA binding demonstrated that the viologen-linked acridines bind effectively to DNA in both intercalative and electrostatic modes. Results of PM2 DNA cleavage studies indicate that, on photoexcitation, these molecules induce DNA damage that is sensitive to formamidopyrimidine DNA glycosylase. These viologen-linked acridines are quite stable in aqueous solutions and oxidize DNA efficiently and hence can be useful as photoactivated DNA-cleaving agents which function purely by the co-sensitization mechanism.     

DNA cleavage induced by photoexcited antimalarial drugs: a photophysical and photobiological study

The interactions and the photosensitizing activity of three antimalarial drugs quinine (Q), mefloquine (MQ) and quinacrine (QC) toward DNA was studied. Evidences obtained by absorption and emission spectroscopy and by linear dichroism measurements indicate that these derivatives bind the macromolecule with a high affinity (binding constants Ka approximately 10(5) M(-1)). The absorption characteristics of the drugs changed markedly by addition of DNA and their fluorescence was quenched with rate constants higher than that of diffusion. The geometry of binding involves predominantly the intercalation into the double helix. The DNA photocleavage properties of antimalarials was investigated using plasmid DNA as a model, at different [drug]/ [DNA] ratios. The results indicate that mainly MQ and Q are able to induce significant photodamage to DNA. In particular the marked effect of the former drug is evidenced after treatment of photosensitized DNA by two base excision repair enzymes, formamydo-pyrimidine glycosilase (Fpg) and Endonuclease III (Endo III). From a mechanistic point of view, experiments carried out in different experimental conditions indicate that these drugs photoinduce DNA damage through singlet oxygen and/or radical cation production. These findings are further supported by the determination of two photoproducts of 2'-deoxyguanosine, which are diagnostic for Type I and Type II pathways, namely 2,2-diamino(2-deoxy-beta-D-erythro-pentofuranosyl)-4-amino-5(2H)-oxazolone and (R,S)4-hydroxy-8-oxo-4,8-dihydro-2'-deoxyguanosine (4-OH-8-oxo-dGuo). Laser flash photolysis experiments carried out in the presence of DNA indicates that the excitation produces mainly the triplet state for Q and the triplet and radical cation for QC. Moreover the singlet and triplet states and radical cations of the drugs are quenched by 2'-deoxyguanosine monophosphate. The absorbances of these transients decrease with increasing DNA concentration.     

Excess electron interactions with solvated DNA nucleotides: strand breaks possible at room temperature

When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C(3')-O(3') bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.     

Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

Background

Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase.

Results

We have cloned and purified SSB from Bacillus anthracis (SSB_BA). In the absence of DNA, at concentrations ??100 ??g/ml, SSB_BA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSB_BA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)₇₀ binding suggested that SSB_BA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure.

Conclusions

Unlike other prokaryotic SSB proteins, SSB_BA from Bacillus anthracis appeared to be monomeric at concentrations ??100 ??g/ml as determined by SE-HPLC. SSB_BA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSB_BA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSB_BA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.     

Synthesis of nicotinonitrile derivatives and study of their photophysical properties

Abstract  

A convenient route was developed for the synthesis of novel nicotinonitrile derivatives by a three-component Dimroth reaction of chalcones, malononitrile, and secondary heterocyclic amines or sodium alcoholate. Nicotinonitrile derivatives are obtained in fair to good yields. The structures of all new compounds were established by spectroscopic characteristics and their photophysical properties were studied.     

Intermolecular vs. intramolecular photoinduced electron transfer from nucleotides in DNA to acridinium ion derivatives in relation with DNA cleavage

Photoirradiation of various 10-methylacridinium ions (AcrR⁺, R = H, ⁱPr, and Ph) intercalated in DNA results in ultrafast intramolecular electron transfer, followed by rapid back electron transfer between AcrR⁺ and nucleotides in DNA. The electron-transfer dynamics in DNA were monitored by femtosecond time-resolved transient absorption spectroscopy. Both acridinyl radical and nucleotide radical cations, formed in the photoinduced electron transfer in DNA, were successfully detected in an aqueous solution. These transient absorption spectra were assigned by the comparison with those of DNA nucleotide radical cations, which were obtained by the intermolecular electron-transfer oxidation of nucleotides with the electron-transfer state of 9-mesityl-10-methylacridinium ion (Acr–Mes⁺) produced upon photoexcitation of Acr⁺–Mes. Photoinduced cleavage of DNA with various acridinium ions (AcrR⁺, R = H, ⁱPr, Ph, and Mes) has also been examined by agarose gel electrophoresis, which indicates that the rapid intramolecular back electron transfer between acridinyl radical and nucleotide radical cation in DNA suppresses the DNA cleavage as compared with the intermolecular electron-transfer oxidation of nucleotides with Acr–Mes⁺.     

A study of binding interactions between terpyridine derivatives and cucurbit[10]uril

The binding interactions of a series of 2,2′:6′,2″-terpyridine (TPY) derivatives and their metal complexes with cucurbit[10]uril (CB[10]) were investigated by ¹H NMR, UV/Vis, emission spectroscopy, and ESI mass spectrometry. ¹H NMR titrations revealed CB[10] could encapsulate methylated TPY (MTPY), and the binding ratio between guest MTPY and host was 1:1 and 2:1 via ESI-MS characterization. For the transition metal complexes composed of Fe(II) or Ru(II) or Rh(III) and TPY derivatives, the octahedral TPY?metal?TPY core can be included in the cavity of CB[10]. Three binding modes (1:1, 1:2 and 1:3) have been detected for the binding of the metal?MPTY complexes with CB[10] by ESI-MS.     

Isolated and solvated thioxanthone: a photophysical study

Quantum chemical methods have been employed to study the photophysics of thioxanthone in vacuum and various solvents. Structurally, the solvation leads to a lengthening of the carbonyl bond, whereas the benzene skeleton is mostly unaffected. This is mirrored by the larger blue shift of the (n(O)π*) states as compared to the red shift which the (ππ*) states undergo. For a proper understanding of the radiative and radiationless processes occurring, the excitation energy profile along a linearly interpolated path has been determined in various cases. The interesting interplay of excited states thus revealed, has been investigated to qualitatively suggest the relaxation pathways available (or dominant) in the cases under study. Rates for these processes have also been computed wherever possible.     

Encapsulation of TCNQ and the acridinium ion within a bisporphyrin cavity: synthesis, structure, and photophysical and HOMO-LUMO-gap-mediated electron-transfer properties

The encapsulation of tetracyanoquinodimethane (TCNQ) and fluorescent probe acridinium ions (AcH(+)) by diethylpyrrole-bridged bisporphyrin (H(4)DEP) was used to investigate the structural and spectroscopic changes within the bisporphyrin cavity upon substrate binding. X-ray diffraction studies of the bisporphyrin host (H(4)DEP) and the encapsulated host-guest complexes (H(4)DEP?TCNQ and [H(4)DEP?AcH]ClO(4)) are reported. Negative and positive shifts of the reduction and oxidation potentials, respectively, indicated that it was difficult to reduce/oxidize the encapsulated complexes. The emission intensities of bisporphyrin, upon excitation at 560?nm, were quenched by about 65?% and 95?% in H(4)DEP?TCNQ and [H(4)DEP?AcH]ClO(4), respectively, owing to photoinduced electron transfer from the excited state of the bisporphyrin to TCNQ/AcH(+); this result was also supported by DFT calculations. Moreover, the fluorescence intensity of encapsulated AcH(+) (excited at 340?nm) was also remarkably quenched compared to the free ions, owing to photoinduced singlet-to-singlet energy transfer from AcH(+) to bisporphyrin. Thus, AcH(+) acted as both an acceptor and a donor, depending on which part of the chromophore was excited in the host-guest complex. The electrochemically evaluated HOMO-LUMO gap was 0.71 and 1.42?eV in H(4)DEP?TCNQ and [H(4)DEP?AcH]ClO(4), respectively, whilst the gap was 2.12?eV in H(4)DEP. The extremely low HOMO-LUMO gap in H(4)DEP?TCNQ led to facile electron transfer from the host to the guest, which was manifested in the lowering of the CN stretching frequency (in the solid state) in the IR spectra, a strong radical signal in the EPR spectra at 77?K, and also the presence of low-energy bands in the UV/Vis spectra (in the solution phase). Such an efficient transfer was only possible when the donor and acceptor moieties were in close proximity to one another.     

Optical and photophysical properties of indolocarbazole derivatives

We present a study of the optical and photophysical properties of five ladder indolo[3,2-b]carbazoles, namely, M1, M2, M3, M4, and M5. The ground-state optimized structures were obtained by B3LYP/6-31G* density functional theory (DFT) calculations, whereas the optimization (relaxation) of the first singlet excited electronic state (S1) was performed using the restricted configuration interaction (singles) (RCIS/6-31G*) approach. The excitation to the S1 state does not cause important changes in the geometrical parameters of the compounds, as corroborated by the small Stokes shifts. The excitation and emission energies have been obtained by employing the time-dependent density functional theory (TDDFT). For all the compounds, excitation to the S1 state is weakly allowed, whereas the S2 <-- S0 electronic transition of each oligomer possesses a much larger oscillator strength. The absorption and fluorescence spectra of the compounds have been recorded in chloroform. A reasonable agreement is obtained between TDDFT vertical transition energies and the (0,0) absorption and fluorescence bands. On one hand, the pattern of the aliphatic side chains does not affect the absorption and fluorescence maxima of the compounds. On the other hand, the replacement of aliphatic chains by phenyl or thiophene rings induces hypsochromic shifts in the absorption and fluorescence spectra. Finally, the fluorescence quantum yield and lifetime of the compounds in chloroform have been obtained. From these data, the radiative and nonradiative rate constants of the deactivation of the S1 state have been determined.     

Study of DNA interactions with cyclic chalcone derivatives by spectroscopic techniques

A series of chalcone derivatives (1-4) were studied. The interaction between these ligands and calf thymus DNA was studied with UV-vis spectrophotometry, fluorescence and circular dichroism spectroscopy. The binding constants K were estimated at 0.5-4.6×10(5) M(-1). All these measurements indicated that the compounds behave as effective DNA-intercalating agents. Electrophoretic separation proved that ligands inhibited topoisomerase I at a concentration of 60 μM.     

Selective DNA strand scission with binuclear copper complexes: implications for an active Cu2-O2 species

A homologous series of binuclear copper(II) complexes [Cu(II)(2)(Nn)(Y)(2)](2+) (1-3) (n = 3-5 and Y = (ClO(4))(-) or (NO(3))(-)) were studied to investigate the intermediate(s) responsible for selective DNA strand scission in the presence of MPA/O(2) (MPA = 3-mercaptopropanoic acid). While the N3 complex does not react, the N4 and N5 analogues show comparable activity with strand scission occurring at a single-strand/double-strand junction. Identical reactivity is also observed in the alternate presence of H(2)O(2). Spectroscopic and reactivity studies with [Cu(II)(2)(N4)(Y)(2)](2+) (2) and H(2)O(2) are consistent with DNA oxidation mediated by formation of a side-on peroxodicopper(II) (Cu(2)-O(2)) complex.     

Theoretical design study on photophysical property of the organoboron quinolate derivatives

The photophysical properties of organoboron quinolate derivatives can be modified readily by manipulating the coordination environment around the central boron atom. This class of compounds applied in organic light-emitting diodes (OLEDs) materials has been studied by quantum chemistry. To reveal the relationship between the structures and properties of these electroluminescent materials, the ground- and excited-state geometries were optimized at the B3LYP/6-31G(d) and CIS/6-31G(d) levels, respectively. The ionization potentials and electron affinities were computed. The mobilities of hole and electron in these compounds were studied computationally based on the Marcus electron transfer theory. The maximum absorption and emission wavelengths of these compounds were calculated using the time-dependent density functional theory method. The solvent effect on the absorption and emission wavelengths of these compounds was also considered by a polarizable continuum model. These results show that boron compounds which containing both the hydroxyquinoline/hydroxybenzoquinoline as ligand and O/S in position X follow the rule, that is, the emission shifts to longer wavelength as covalent nature of the boron–ligand bonding is increased. Meanwhile, the negative HOMO and IPs decrease but the negative LUMO and EAs increase by substitution of O with S in position X. It was deduced that both the hole- and electron-injection abilities are improved by substituting S in place of O in position X. After chemical modification in position R ₂ with electron-donating properties of NH₂ or 1,4-diethynyl-2,5-dihexyloxybenzene, introduced 1,4-diethynyl-2,5-dihexyloxybenzene improves both the hole- and electron-transfer rate, which leads to better equilibrium property. It can be concluded that the better equilibrium property depends on the conjugated length of side chain in position R ₂. Moreover, exchanging the substituents R ₁ and R ₂ in BNO1a and BNO1’a can slightly change the hole-transfer rate by 0.04 eV. According to these calculations, series BNO and BNS can be applied as electron transport and hole transport materials at the same time. Specially, series BNO2 and BNS have better performance than Mes₂B[p-4,4’-biphenyl-NPh(1-naphthyl)] (BNPB) in both the hole- and electron-injection ability.     

Oxovanadium phenanthroimidazole derivatives: synthesis,DNA binding and antitumor activities

Four unsymmetrical oxovanadium phenanthroimidazole complexes, [VO(hntdtsc)(NPIP)] (1), [VO(hntdtsc)(CPIP)] (2), [VO(hntdtsc)(MEPIP)] (3) and [VO(hntdtsc)(HPIP)] (4) (hntdtsc = 2-hydroxy-1-naphthaldehyde thiosemicarbazone, NPIP = 2-(4-nitrophenyl)-imidazo[4,5-f]1,10-phenanthroline, CPIP = 2-(4-chlorphenyl)-imidazo[4,5-f]1,10-phenanthroline), MEPIP = 2-(4-methylphenyl)-imidazo[4,5-f]1,10-phenanthroline), HPIP = 2-(4-hydroxylphenyl)-imidazo[4,5-f] 1,10-phenanthroline), have been synthesized and characterized. Their DNA binding and antitumor activities were determined by biochemical methods. All four oxovanadium complexes can bind with CT-DNA by an intercalation model and can also cleave supercoiled plasmid DNA in the presence of H₂O₂. The antitumor properties and mechanism of the complexes have been analyzed by MTT assay, cell cycle analysis, apoptosis assay and Western blot analysis. The results showed that the free ligands and their corresponding complexes all possess antiproliferative activities with very low IC₅₀ values against Hela, BIU-87 and SPC-A-1 cell lines. Complex 1, which has a strongly electron-withdrawing nitro group, exhibited the best antiproliferative activities. Complex 1 caused G₀/G₁ phase arrest of the cell cycle and induced apoptosis in Hela cells. Additionally, complex 1 attenuated the phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2).This indicates that inhibition of the ERK1/2 signaling pathway may contribute to the antitumor effects of these complexes.     

Cobaltocenium acetylsalicylate: synthesis and circular dichroism study of interactions with DNA

Russian Chemical Bulletin - Cobaltocenium acetylsalicylate was synthesized and characterized for the first time. The concentration dependences observed in its interaction with the double helix of...     

Double strand DNA cleavage with a binuclear iron complex

Covalently linking two single strand DNA cleaving agents resulted in a new biomimetic binuclear iron complex capable of effecting oxidative double strand DNA cleavage.     

Photoaddition of thienocoumarin derivatives to DNA: stoichiometry and kinetics of binding

Photoreaction of the 6,9-dimethyl-4-methoxymethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound I) and 4-acetoxymethyl-6,9-dimethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound II) to DNA was studied. The quantitative evaluation of the photobound molecules was performed by means of inductively coupled plasma atomic emission spectrometry (ICP-AES), exploiting the presence of the sulphur atom inside the tricyclic chromophore. The concurrent estimation of the phosphorus atom, present exclusively in the macromolecule, allowed possible intercalation sites to be identified and their involvement in the photoaddition reaction to be determined. The development of a kinetic model made it possible to discriminate and evaluate the single kinetic events that constitute the overall photoaddition process of I and II to DNA.