Synthesis, DNA intercalation and europium(III)-triggered DNA photocleavage by a bis-proflavine succinamide conjugate

We describe the synthesis of a bis-proflavine derivative containing a succinamide linking chain. Levels of pUC19 plasmid DNA photocleavage by this compound are significantly enhanced in the presence of Eu³⁺ (350 nm, 22 °C, pH 7.0). UV-visible spectrophotometric studies of the ligand with calf thymus DNA show bathochromic-shifts and hypochromicity in the major absorption bands of the bis-proflavine derivative. Viscosimetric analysis of the helical extension of sonicated calf thymus DNA agrees with a monofunctional intercalation process.     

Syntheses and copper(II)-dependent DNA photocleavage by acridine and anthracene 1,10-phenanthroline conjugate systems

We report the syntheses and characterization of a series of compounds based on 1,10-phenanthroline covalently tethered, at the 2 and 9 positions, to either two benzene, naphthalene, acridine or anthracene chromophores. The acridine and anthracene derivatives are shown to efficiently cleave pUC19 plasmid DNA upon irradiation with ultraviolet light (pH = 7.0, 22 degrees C, 350 nm). Furthermore, photocleavage levels are markedly increased by the addition of Cu2+ to the DNA photolysis reactions. Interestingly, when the concentrations of the anthracene compounds are lowered from 35 microM to 0.25 microM, the reverse trend is observed. DNA photocleavage is markedly reduced in the presence of copper(II).     

Syntheses and DNA photocleavage by mono- and bis-phenothiazinium-piperazinexylene intercalators

Chromophore systems consisting of one (compound 5) or two (compound 6) phenothiazine rings covalently attached to a bis-piperazinexylene chain were synthesized and evaluated as DNA photocleaving agents. In the presence of DNA, the compounds were shown to monointercalate in their deaggregated forms and to strongly absorb red wavelengths of light. Reactions containing micromolar concentrations of compound produced robust photocleavage of plasmid DNA under near-physiological conditions of temperature and pH (22 °C and pH 7.0). Phenothiazines 5 and 6 increased the T_m of calf thymus DNA by 17 and 19 °C, indicating that significant levels of duplex stabilization were produced.     

Site-specific DNA photocleavage by rhodium intercalators analyzed by MALDI-TOF mass spectrometry

The DNA photocleavage reaction of mismatch-selective Rh complexes has been analyzed by MALDI-TOF mass spectrometry as well as gel electrophoresis analysis of radioactively tagged oligonucleotides. Analogous results are obtained with these two techniques showing site-specific cleavage neighboring the mismatch to yield primarily 5'- and 3'-phosphate termini. Additional intermediates and products are observed, however, using MALDI-TOF analysis. MALDI-TOF mass spectrometry is seen to be particularly powerful in the analysis of DNA cleavage by site-specific molecules. The method requires no radioactive labeling, only little material, and analysis can be accomplished within minutes. Moreover, this mass spectral analysis of DNA cleavage yields direct information regarding products rather than simply the base pair site of cleavage.     

DNA photocleavage by a supramolecular Ru(II)-viologen complex

A novel Ru(II) complex possessing two sequentially linked viologen units, Ru-V(1)-V(2)(6+), was synthesized and characterized. Upon excitation of the Ru(II) unit (lambda(exc) = 532 nm, fwhm approximately 10 ns), a long-lived charge-separated (CS) state is observed (tau = 1.7 micros) by transient absorption spectroscopy. Unlike Ru(bpy)(3)(2+), which cleaves DNA upon photolysis through the formation of reactive oxygen species, such as (1)O(2) and O(2)(-), the photocleavage of plasmid DNA by Ru-V(1)-V(2)(6+) is observed both in air and under N(2) atmosphere (lambda(irr) > 395 nm).     

Photoinduced DNA cleavage by fullerene-lysine conjugate

A novel water-soluble [60] fullerene-substituted lysine derivative 3 has been synthesized and characterized by elemental analysis, ¹H NMR, ¹³C NMR and FAB-MS. The synthetic procedure involved condensation of Boc-protected lysine with terephthaldehyde followed by 1,3-dipolar cycloaddition reaction with C₆₀ in the presence of sarcosine and finally deprotection of the amino group using trifluoroacetic acid. The synthesized compound 3 exhibited high DNA cleavage efficiency upon visible light irradiation in the presence of NADH.     

The heavy atom effect on photocleavage of DNA by mono-hydroxyl halogenated corroles

<正>DNA photocleavage properties of halogenated mono-hydroxyl corrole 1-5 were investigated.It was found that these corroles were able to photocleavage supercoiled pBR 322 DNA(SC) into nicked-circular DNA(NC).The activity of these corroles follows an order of 432≈15.The photosensitized singlet oxygen(Φ_△) quantum yield by these corroles also follows that same order,showing the photocleavage activity is related to the heavy atom effect of halogen atoms on corroles.     

Enantioselective DNA alkylation by a pyrrole-imidazole S-CBI conjugate

Conjugates 12S and 12R of N-methylpyrrole (Py)-N-methylimidazole (Im) seven-ringed hairpin polyamide with both enantiomers of 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) were synthesized, and their DNA alkylating activity was examined. High-resolution denaturing gel electrophoresis revealed that 12S selectively and efficiently alkylated at one match sequence, 5'-TGACCA-3', in 450-bp DNA fragments. The selectivity and efficiency of the DNA alkylation by 12S were higher than those of the corresponding cyclopropapyrroloindole (CPI) conjugate, 11. In sharp contrast, another enantiomer, 12R, showed very weak DNA alkylating activity. Product analysis of the synthetic decanucleotide confirmed that the alkylating activity of 12S was comparable with 11 and that 12S had a significantly higher reactivity than 12R. The enantioselective reactivity of 12S and 12R is assumed to be due to the location of the alkylating cyclopropane ring of the CBI unit in the minor groove of the DNA duplex. Since the CBI unit can be synthesized from commercially available 1,3-naphthalenediol, the present results open up the possibility of large-scale synthesis of alkylating Py-Im polyamides for facilitating their use in future animal studies.     

DNA binding and photocleavage properties of two mixed-ligand oxovanadium complexes

An oxovanadium complex [VO(satsc)(bipy)] (1) (satsc = salicylaldehyde thiosemicarbazone, bipy = 2,2′-bipyridine) and its dibromo derivative [VO(3,5-dibrsatsc)(bipy)] (2) (3,5-dibrsatsc = 3,5-dibromosalicylaldehyde thiosemicarbazone) have been synthesized and characterized by elemental analysis, IR, ES-MS and ¹H NMR. The interaction of these two complexes with calf-thymus DNA (CT-DNA) was studied using UV/Vis, fluorescence spectroscopic titration, viscosity measurements and thermal denaturation. The results suggest that complexes 1 and 2 interact with CT-DNA by intercalative modes. The DNA-binding affinity of complex 1 is larger than that of complex 2. In addition, their photocleavage reactions with pBR322 supercoiled plasmid DNA were investigated by gel electrophoresis experiments. Both complexes exhibit significant DNA cleavage activity, and complex 1 showed greater cleaving efficiency than complex 2.     

Synthesis of phenothiazine-corrole dyads: the enhanced DNA photocleavage properties

Three new phenothiazine-corrole dyads were prepared by the reaction of phenothiazine-10-carbonyl chloride and mono-hydroxyl triaryl corrole in the presence of DBU. As compared to corrole monomer, these phenothiazine-corrole dyads exhibit significant enhanced DNA photocleavage activity as compared to corrole monomer precursors.     

DNA binding and photocleavage specificities of a group of tricationic metalloporphyrins

The interactions of 5,10,15-tris(1-methylpyridinium-4-yl)-20-(4-hydroxyphenyl)porphyrinatozinc(II) Zn[TMPyHP]³⁺ (2) along with Cu[TMPyHP]³⁺ (3), Co[TMPyHP]⁴⁺ (4), Mn[TMPyHP]⁴⁺ (5) and the free base porphyrin H₂[TMPyHP]³⁺ (1) with duplex DNA have been studied by using a combination of absorption, fluorescence titration, surface-enhanced Raman spectroscopy (SERS), induced circular dichroism (ICD) spectroscopy, thermal DNA denaturation, viscosity measurements as well as gel electrophoresis experiment. Their binding modes and intrinsic binding constants (K_b) to calf DNA (CT DNA) were comparatively studied and were found significantly influenced by different metals coordinated with the porphyrin plane. Except 3, which has four-coordination structure at the metal, all the metal derivatives showed non-intercalative DNA-binding mode and lower K_b than the free base porphyrin 1, most probably due to the steric hindrance results from the axial ligands of the inserted metals which are five or six-coordination structures. Meanwhile, the insertion of metals into cationic porphyrin greatly removed the self-aggregation of the metal-free porphyrins, and thus fully enhanced the singlet oxygen (¹O₂) productivities in the DNA photocleavage experiments. Therefore, these metalloporphyrins have comparable DNA cleavage ability with the free base porphyrin.     

A water-soluble C60-porphyrin compound for highly efficient DNA photocleavage

A water-soluble covalently linked C(60)-porphyrin compound-C(60)Por is reported to show enhanced DNA-cleaving activity. The highly enhanced DNA-cleaving activity is expected to be ascribed to the high water-solubility and affinity of C(60)Por to DNA, as well as to the accessibility to the charge-separated states C(60)˙(-)-Por˙(+) formed under radiation.     

Efficient photocleavage of DNA by cationic porphyrin-acridine hybrids with the effective length of diamino alkyl linkage

Positively charged porphyrins bearing an acridine with various lengths of diamino alkyl linkage, 5-[4-[(6-chloro-2-methoxy-9-acridyl)aminoalkylaminocarbonyl]phenyl]-10,15,20-tris(4-N-methylpyridiniumyl)porphine triiodide, alkyl=ethyl, butyl, hexyl, or octyl, were synthesized. They exhibited more enhanced photocleavage activity of pUC18 plasmid DNA than TMPyP, meso-tetrakis(4-N-methylpyridiniumyl)porphine, which is well known to bind to DNA tightly and to cleave DNA effectively; the hybrid linked with the hexamethylene chain showed particularly high activity. An equilibrium dialysis experiment demonstrated that the binding ability of the hybrids to calf thymus (CT) DNA correlated quantitatively with the photocleavage activity. The lack of the substantial red-shift of the Soret maxima of the hybrids through the titration with CTDNA denied the intercalative binding of the porphyrin part. In their circular dichroism (CD) spectral change on binding to CTDNA, two negative peaks appeared at 275 nm and at 285-290 nm in the UV range. The latter negative peak was observed for hybrids, but not for TMPyP, and thus we assigned it to induced CD (ICD) derived from intercalation of acridine chromophore. In the visible range, the hybrids showed only a positive peak around their Soret maxima, and this feature suggested the porphyrin moiety lay in the DNA groove. In addition, the length of the linker markedly influenced the ellipticity of their visible ICD, suggesting that the proximity of the porphyrin moiety to DNA was greatly affected by the linker.     

A multifunctional tetrametallic Ru-Pt supramolecular complex exhibiting both DNA binding and photocleavage

A new tetrametallic supramolecular complex, [{(bpy)2Ru(dpp)}2Ru(dpp)PtCl2](PF6)6 (bpy = 2,2'-bipyridine, dpp = 2,3-bis(2-pyridyl)pyrazine), has been prepared and characterized. This supramolecular assembly is multifunctional, forming coordinate covalent bonds to DNA through its cis-PtCl2 moiety and photocleaving DNA through its Ru polypyridine chromophores. Electronic absorption spectroscopy shows ligand-based pi-->pi* transitions in the UV with Ru-based metal-to-ligand charge transfer transitions throughout much of the visible. The Ru-->dpp CT transitions center at 542 nm (eta = 35 000 M-1 cm-1). This complex has a HOMO localized on peripheral Ru with E(1/2)oxd = 1.58 V vs Ag/AgCl, and a LUMO based on the mu-dpp connecting Ru and Pt, E(1/2)red = -0.40 V. Gel electrophoresis analysis shows the tetrametallic coordinates to pUC18 DNA and, when excited with visible light, cleaves DNA through an oxygen-mediated pathway.     

Site-directed cleavage of DNA by an oligonucleotide conjugate with o-bromobenzoic acid in the presence of copper ions

Site-directed cleavage of single- and double-stranded DNAs by an oligonucleotide conjugate with 5-[N-(3-aminopropyl)sulfamoyl]-2-bromobenzoic acid was investigated. When forming duplex complexes with a single-stranded DNA and triplex complexes with a double-stranded DNA, this conjugate cleaves DNA near the binding site in the presence of copper ions and free o-bromobenzoic acid. The efficacy and specificity of DNA cleavage by this conjugate and other oligonucleotide conjugates bearing tetracarboxyphthalocyanine Co^II and bleomycin A5 as reactive groups were compared.     

Selective photocleavage of DNA and RNA by anthraquinone derivatives: targeting the single-strand region of hairpin structures

A tetracationic anthraquinone derivative (27AQS2) binds to hairpin DNA and RNA. Ultraviolet irradiation of the bound quinone causes cleavage in the loop region of both oligonucleotides and at guanines in the stem region of the DNA hairpin. The absence of observable strand cleavage at guanines in the RNA hairpin suggests that either aniline treatment does not cause cleavage at damaged guanines in RNA or that radical cation migration does not occur readily in RNA duplexes. The ability to target the single-stranded regions of DNA and RNA structures is an important property of this photonuclease.     

DNA sensors using a ferrocene-oligonucleotide conjugate

Using the redox-active DNA conjugate (ferrocene-modified oligonucleotide 12 mer) as a probe, the novel electrochemical gene sensor, which is sensitive, convenient, and not relying on radio isotope, has been developed. Oligonucleotide (16 mer) complementary to the target (19 mer) was immobilized onto gold electrode through the specific chemisorption of successive phosphorothioates which were introduced into 5'-end of the oligonucleotide. The sequence of the conjugate was designed to be also complementary to another site of the target. Therefore, the conjugate and the oligonucleotide anchoring on the electrode formed a sandwich-type ternary complex with a target DNA to give electric currents based on the ferrocene oxidation. By using this system, we have distinguished the mutant that has one base substitution from the fully complementary target.