An Anionic Diplatinum DNA Photocleavage Agent: Chemical Mechanism and Footprinting of .lambda. Repressor

Novel 2-aminothiazonaphthalimides as visible light activatable photonucleases: effects of intercalation, heterocyclic-fused area and side chains

A new family of 2-aminothiazonaphthalimides with different side chains as novel intercalative and visible light activatable photonucleases, was designed, synthesized and quantitatively evaluated. The order of their photocleaving abilities was parallel to that of their intercalative properties. The compound with linear heterocyclic-fused chromophore could intercalate into and photocleave DNA more efficiently than the one with angular heterocyclic-fused chromophore. B(2), the most efficient compound, caused obvious DNA damage at 1 microM. Mechanism experiment showed that superoxide anion was involved.

DNA binding and photocleavage in vitro by new dirhodium(II) dppz complexes: correlation to cytotoxicity and photocytotoxicity

Two new dirhodium(II) complexes possessing the intercalating dppz ligand (dppz = dipyrido[3,2-a:2',3'-c]phenazine), cis-[Rh(2)(mu-O(2)CCH(3))(2)(dppz)(eta(1)-O(2)CCH(3))(CH(3)OH)](+) (1) and cis-[Rh(2)(mu-O(2)CCH(3))(2)(dppz)(2)](2+) (2), were synthesized and characterized as potential agents for photochemotherapy. Various techniques show that 1 binds to DNA through intercalation, although some aggregation of the complex on the DNA surface is also present. In contrast, 2 does not intercalate between the DNA bases; however, strong hypochromic behavior is observed in the presence of DNA, which can be attributed to intermolecular pi-stacking of 2 enhanced by the polyanion. The apparent DNA binding constants determined using optical titrations are compared to those from dialysis experiments. Both complexes photocleave pUC18 plasmid in vitro under irradiation with visible light (lambda(irr) >or= 395 nm, 15 min), resulting in the nicked, circular form. Greater photocleavage is observed for 1 relative to 2, which may be due to the ability of 1 to intercalate between the DNA bases. The cytotoxicity toward human skin cells (Hs-27) measured as the concentration at which 50% cell death is recorded, LC(50), was found to be 135 +/- 8 microM for 2 in the dark (30 min), which is significantly lower than those of 1 (LC(50) = 27 +/- 2 microM) and Rh(2)(O(2)CCH(3))(4) (LC(50) = 15 +/- 2 microM). Irradiation of cell cultures containing 1 and Rh(2)(O(2)CCH(3))(4) with visible light (400-700 nm, 30 min) has little effect on their cytotoxicity, with LC(50) values of 21 +/- 3 and 13 +/- 2 microM, respectively. Interestingly, a 3.4-fold increase in the toxicity of 2 is observed when the cell cultures are irradiated (400-700 nm, 30 min), resulting in LC(50) = 39 +/- 1 microM. The greater toxicity of 1 compared to 2 in the dark may be related to the ability of the former compound to intercalate between the DNA bases. The lower cytotoxicity of 2, together with its significantly greater photocytotoxicity, makes this complex a potential agent for photodynamic therapy (PDT). These results suggest that intercalation or strong DNA binding may not be a desirable property of a potential PDT agent.

Electrochemical determination of triple helices: electrocatalytic oxidation of guanine in an intramolecular triplex

Electrocatalytic oxidation of the oligonucleotide 5'- GAA GAG GTT TTT CCT CTT CTT TTT CTT CTC C (TS) by Ru(bpy)(3)(2+) was studied by cyclic voltammetry. This oligonucleotide forms either an intramolecular triplex, hairpin, or single strand, depending on the pH (Plum, G. E.; Breslauer, K. J. J. Mol. Biol. 1995, 248, 679-695). In the triplex form, the guanine doublet in TS is buried inside the folded structure, and as such is less susceptible to oxidation by electrogenerated Ru(bpy)(3)(3+). Digital simulations of the catalytic voltammograms gave a rate constant of 3.5 +/- 0.2 x 10(2) M(-1) s(-1) for oxidation of the triplex form, while oxidation of the duplex and single-stranded forms occurred with much faster rate constants of (3.5-9.1) x 10(4) M(-1) s(-1). Experiments using a truncated form of TS that lacked the third strand of the triplex were consistent with these measurements. The Ru(bpy)(3)(3+) complex was also generated by photolyzing Ru(bpy)(3)(2+) in the presence of Fe(CN)(6)(3-). This reaction produced strand scission following piperidine treatment, which was visualized using high-resolution gel electrophoresis. These experiments showed decreased reactivity for the triplex form, and also gave an unusual reversal of a common selectivity for the 5'-G of GG doublets generally seen in B-form DNA. This reversal was ascribed to strain caused by the location of the GG doublet adjacent to the hairpin loop.

Metal-ligand charge-transfer-promoted photoelectronic Bergman cyclization of copper metalloenediynes: photochemical DNA cleavage via C-4' H-atom abstraction

Metal-to-ligand charge-transfer (MLCT) photolyses (lambda > or = 395 nm) of copper complexes of cis-1,8-bis(pyridin-3-oxy)oct-4-ene-2,6-diyne (bpod, 1), [Cu(bpod)(2)]PF(6) (2), and [Cu(bpod)(2)](NO(3))(2) (3) yield Bergman cyclization of the bound ligands. In contrast, the uncomplexed ligand 1 and Zn(bpod)(2)(CH(3)COO)(2) compound (4) are photochemically inert under the same conditions. In the case of 4, sensitized photochemical generation of the lowest energy (3)pi-pi state, which is localized on the enediyne unit, leads to production of the trans-bpod ligand bound to the Zn(II) cation by photoisomerization. Electrochemical studies show that 1, both the uncomplexed and complexed, exhibits two irreversible waves between E(p) values of -1.75 and -1.93 V (vs SCE), corresponding to reductions of the alkyne units. Irreversible, ligand-based one-electron oxidation waves are also observed at +1.94 and +2.15 V (vs SCE) for 1 and 3. Copper-centered oxidation of 2 and reduction of 3 occur at E(1/2) = +0.15 and +0.38 V, respectively. Combined with the observed Cu(I)-to-pyridine(pi) MLCT and pyridine(pi)-to-Cu(II) ligand-to-metal charge transfer (LMCT) absorption centered near approximately 315 nm, the results suggest a mechanism for photo-Bergman cyclization that is derived from energy transfer to the enediyne unit upon charge-transfer excitation. The intermediates produced upon photolysis degrade both pUC19 bacterial plasmid DNA, as well as a 25-base-pair, double-stranded oligonucleotide. Detailed analyses of the cleavage reactions reveal 5'-phosphate and 3'-phosphoglycolate termini that are derived from H-atom abstraction from the 4'-position of the deoxyribose ring rather than redox-induced base oxidation.

Digital simulation of catalytic cyclic voltammograms for oxidation of DNA by a heterobimetallic dimer: effects of DNA binding and mass transport

The electrocatalytic oxidation of DNA by a heterodimer, [(bpy)2Ru(tpphz)Os(bpy)2]4+ (tpphz: tetrapyrido[3,2-alpha: 2',3'-c:3'',2''-h:2''',3'''-j]phenazine) (1), was studied using cyclic voltammetry with digital simulation. This dimer was chosen because the Ru(III/II) couple (E1/2 = 1.09 V vs Ag/AgCl) is capable of catalyzing guanine oxidation while the Os(III/II) couple (E1/2 = 0.63 V) provides a convenient reporter on the binding and mass transport of the complex, which can then be determined in the same voltammetric sweep as the electrocatalysis. Proper description of the electrochemical response required careful measurement of the binding constant of 1 to herring testes (HT) DNA, which was (2.0 +/- 0.1) x 10(4) M(-1) by both absorption titration and normal pulse voltammetry. Thermal denaturation experiments were consistent with a nonintercalative binding mode and gave a deltaTm of only (2.4 +/- 0.5) degrees C. The minor groove binder distamycin did not displace 1 from HT DNA, suggesting that the complex binds in the major groove. As expected, acquisition of the cyclic voltammogram of 1 in the presence of DNA produced catalytic current for the Ru(III/II) couple, while a suppression of current was observed for the Os(III/II) couple. Although the catalytic current for the Ru(III/II) couple initially appeared as a current enhancement, higher concentrations suppressed the catalytic wave as a result of the slower mass transport of the DNA-bound complex. The binding studies were used to create a model for digital simulation that reproduced the behavior of 1 with DNA and gave rate constants that were independent of DNA concentration. The apparent second-order rate constant at 25 mV/s for oxidation of guanine in HT DNA (av 1000 bp, 25% guanine) by 1 was 3 +/- 1 x 10(4) M(-1) s(-1); similar values were obtained for a 200-bp fragment (7 +/- 3 x 10(4) M(-1) s(-1)) and a 435-bp fragment (8 +/- 2 x 10(4) M(-1) s(-1)). As observed in previous studies of these reactions, biphasic kinetics in the catalytic reaction led to a dependence of the rate constant determined by simulation on the sweep rate. Increasing the sweep rate led to a systematic increase in the simulated rate constant, consistent with a fast phase of the homogeneous catalytic reaction.

New triruthenium clusters as photoinduced DNA-binding and cleaving agents

1-Hydroxybenzotriazole and 1-hydroxypyridine-2-thione were incorporated as ligands with the cluster Ru3(CO)10 (NCMe)2 to give [(mu-H)Ru3(CO)10(mu2-2,3-eta2-NNN(O)C6 H4)] and [(mu-H)Ru3(CO)9(mu2-eta1 : eta2-C5H4N(O)S)], respectively. Irradiation of these two new triruthenium metal clusters individually with 350 nm UV light in a phosphate buffer (pH 6.0) containing form I DNA resulted in single-strand cleavage. Cluster [(mu-H)Ru3(CO)10(mu2-2,3--eta2-NNN (O)C6H4)] was also found to bind to calf thymus DNA upon UV irradiation.

Formation of modified cleavage termini from the reaction of chromium(V) with DNA

Reaction of a 25 bp oligonucleotide with the high valent chromium complex, bis(2-ethyl-2-hydroxybutyrato)oxochromate(V) (Cr(V)-EHBA) produced both Frank- and alkali-labile strand breaks that were sequence-neutral. Frank strand break formation was found to be O2-dependent while formation of alkali-labile strand breaks were O2-independent. Reaction of Cr(V)-EHBA with the 5'-32P-labeled oligomer under oxygenated conditions formed the modified 3'-terminus, 3'-phosphoglycolate, as well as the 3'-phosphate terminus. Formation of the 3'-phosphoglycolate termini, and the O2 dependence of the reactions were consistent with a mechanism involving abstraction of the C4' hydrogen atom from the deoxyribose moiety of DNA. Identical reactions using the 3'-32P-labeled oligomer yielded only 5'-phosphate termini as assigned by co-migration with Maxam-Gilbert markers. Analogous cleavage profiles and modified termini were observed for the reaction of Cr(V)-EHBA and DNA in the presence of hydrogen peroxide. With the addition of hydrogen peroxide, the DNA cleavage reactions were O2-independent and the level of DNA cleavage was enhanced over that observed with Cr(V)-EHBA alone. These findings suggest an oxidation mechanism whereby a reductive intermediate of the carcinogen chromate, Cr(V), can cause DNA damage that mimics oxygen radical DNA damaging pathways.

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

BACKGROUND

The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.

RESULTS

Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.

CONCLUSIONS

The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

Effects of secondary structure on DNA and RNA cleavage by diplatinum(II)

The photochemistry of Pt2(pop)44- with nucleic acids has been studied using radiolabeled oligomers of DNA and RNA and high-resolution electrophoresis (pop is P2O5H22-). Photolysis of Pt2(pop)44- with duplex DNA produces an even cleavage ladder and relatively little enhancement of cleavage upon treatment with piperidine. In contrast, the cleavage pattern is far less regular with single-stranded DNA, and there is a large enhancement in cleavage upon treatment with piperidine. Accordingly, photolysis of Pt2(pop)44- with the DNA hairpin 5'-d[ATCCTATTTATAGGAT] produces a much larger piperidine enhancement at the loop and end nucleotides than in the stem. There is an additional piperidine enhancement that occurs selectively at guanine residues either in RNA or in DNA at low Mg2+ concentrations that is attributed to outer-sphere electron transfer on the basis of the known excited-state redox potentials of Pt2(pop)44- and the expected oxidative chemistry of guanine. The extent of guanine oxidation is higher compared to the extent of sugar oxidation at low Mg2+ concentrations, which can be attributed to a shallower distance dependence for electron transfer compared to that for atom transfer. The effects of Mg2+ and piperidine or aniline treatment were examined on stem-loop structures of DNA and RNA and gave partial images of the expected secondary structures.

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

A tetracationic anthraquinone derivative (27AQS2) binds to hairpin DNA and irradiation of the bound quinone leads to selective strand cleavage. NMR spectroscopy reveals that 27AQS2 binds at the loop and to the stem-loop junction of hairpin DNA. UV irradiation of the bound quinone causes cleavage of the DNA in the loop region and at guanines in the stem region. Inclusion of ethidium bromide in the reaction mixture leads to a greatly increased selectivity for loop cleavage. Spectroscopic and chemical evidence suggests a three component mechanism for reaction. The ability to target single-stranded regions of DNA structures is an important property of this photonuclease.

Role of the central metal ion and ligand charge in the DNA binding and modification by metallosalen complexes

Several metal complexes of three different functionalized salen derivatives have been synthesized. The salens differ in terms of the electrostatic character and the location of the charges. The interactions of such complexes with DNA were first investigated in detail by UV-vis absorption titrimetry. It appears that the DNA binding by most of these compounds is primarily due to a combination of electrostatic and other modes of interactions. The melting temperatures of DNA in the presence of various metal complexes were higher than that of the pure DNA. The presence of additional charge on the central metal ion core in the complex, however, alters the nature of binding. Bis-cationic salen complexes containing central Ni(II) or Mn(III) were found to induce DNA strand scission, especially in the presence of co-oxidant as revealed by plasmid DNA cleavage assay and also on the basis of the autoradiogram obtained from their respective high-resolution sequencing gels. Modest base selectivity was observed in the DNA cleavage reactions. Comparisons of the linearized and supercoiled forms of DNA in the metal complex-mediated cleavage reactions reveal that the supercoiled forms are more susceptible to DNA scission. Under suitable conditions, the DNA cleavage reactions can be induced either by preformed metal complexes or by in situ complexation of the ligand in the presence of the appropriate metal ion. Also revealed was the fact that the analogous complexes containing Cu(II) or Cr(III) did not effect any DNA strand scission under comparable conditions. Salens with pendant negative charges on either side of the precursor salicylaldehyde or ethylenediamine fragments did not bind with DNA. Similarly, metallosalen complexes with net anionic character also failed to induce any DNA modification activities.

Structural modification changes the DNA binding mode of cation-substituted anthraquinone photonucleases: association by intercalation or minor groove binding determines the DNA cleavage efficiency

The mode of binding anthraquinone derivatives, bearing positively charged ammonium side chains, to duplex DNA was investigated by optical and NMR spectroscopy. Absorption, circular dichroism, emission, and one- and two-dimensional homonuclear NMR spectroscopy show that mono- and dication-substituted quinones, AQS and 27AQS, bind primarily by intercalation. In contrast, these experiments indicate that the tetracationic anthraquinone 27AQS2 is bound nonintercalatively to duplex DNA. In particular, analysis of the NMR spectrum of 27AQS2 bound to a specially designed synthetic self-complementary dodecanucleotide (5'-CGCGAATTCGCG-3') shows it to be associated primarily with the minor groove of the central AATT sequence. The change in the DNA binding mode greatly affects the photophysical and photochemical properties of these photonucleases with DNA.

Anthraquinone photonucleases: a surprising role for chloride in the sequence-neutral cleavage of DNA and the footprinting of minor groove-bound ligands

Irradiation of water-soluble anthraquinone (AQ) reagents in the presence of chloride ions results in the spontaneous, sequence-neutral cleavage of DNA. Mechanistic studies indicate that cleavage is initiated by chlorine atoms, produced by charge transfer interaction between chloride anion and AQ triplet states. High-resolution gel electrophoresis suggests that cleavage arises from abstraction of a hydrogen atom from C-4' of deoxyribose units. The targeting of this hydrogen, which is located in the minor groove of duplex DNA, can be effectively blocked by netropsin and, to a lesser degree, berenil, leading to photofootprinting of these minor groove-binding drugs.

Post-SELEX combinatorial optimization of aptamers

In vitro selection techniques provide a means of isolating nucleic acid ligands for binding to particular protein targets. Although most aptamers have quite high affinities for their target proteins, it has been shown that post-SELEX modification can result in further enhancement of binding affinity, as well as other desired properties. This has led to the current development of a more systematic approach to aptamer optimization using a combinatorial screening methodology.

Oxidation of DNA Hairpins by Oxoruthenium(IV): Effects of Sterics and Secondary Structure

The effects of steric hindrance on the oxidation of DNA by polypyridyl oxoruthenium(IV) complexes have been investigated. The complexes oxidize DNA by activation either of the 1' ribose C-H bond or by oxo transfer to the guanine nucleobase. A method is presented for determining the relative rates of activation of individual sites from the dependence of the extent of cleavage on the oxidant concentration. This analysis shows that hybridization of the labeled strand to its complement attenuates the rate of oxidation of guanine more effectively than the rate of sugar oxidation. Accordingly, higher ratios of guanine/sugar oxidation are observed in single strands. Among the individual guanine residues, however, the relative reactivities are not altered by hybridization; a similar result is obtained for sugar oxidation. This result implies that sequence-dependent chemical reactivity is partly responsible for the different extents of cleavage observed within the sequence. The ability of hybridization to protect guanine from oxidation is also apparent in hairpin studies, where the stem guanines are much less reactive than the loop guanines, and altered sugar conformations in the loop lead to modulated reactivity. Finally, a set of sterically differentiated complexes shows greater steric effects for oxidation of guanine compared to oxidation of sugar, as expected from the relative rates of the single strand and duplexes.