Oxidative DNA strand scission induced by a trinuclear copper(II) complex

A novel trinuclear copper(II) complex, Cu3-L (L = N,N,N',N',N' ',N' '-hexakis(2-pyridyl)-1,3,5-tris(aminomethyl)benzene), exhibited efficient oxidative strand scission of plasmid DNA. The solution behavior of the complex has been studied by potentiometric titration, UV spectroscopy, and cyclic voltammetry. The data showed that there are three redox-active copper ions in the complex with three types of bound water. The complex demonstrated a moderate binding ability for DNA. Cu3-L readily cleaves plasmid DNA in the presence of ascorbate to give nicked (form II) and then linear (form III) products, while the cleavage efficiency using H2O2 is less than by ascorbate, suggesting that the cleavage mode of the trinuclear complex is somewhat different from the traditional Fenton-like catalysis. Meanwhile, Cu3-L is far more efficient than its mononuclear analogue Cu-DPA (DPA = 2,2'-dipyridylamine) at the same [Cu2+] concentration, which suggests a possible synergy between the three or at least two Cu(II) centers in Cu3-L that contributes to its relatively high nucleolytic efficiency. Furthermore, the presence of standard radical scavengers does not have clear effect on the cleavage efficiency, suggesting the reactive intermediates leading to DNA cleavage are not freely diffusible radicals.     

Recognition of guanines at a double helix-coil junction in DNA by a trinuclear copper complex

Coordination between guanine N7 and a trinuclear copper complex appears critical for selective and efficient strand scission of DNA at a helix-coil junction as indicated by the lack of reactivity of comparable DNA containing 7-deazaguanine in place of guanine; both the base pair at the junction and coil flexibility also modulate the specificity of DNA oxidation.     

Targeted strand scission of DNA substrates by a tricopper(II) coordination complex

A trinuclear copper complex, [Cu(3)(II)(L)(H(2)O)(3)(NO(3))(2)](NO(3))(4).5H(2)O (1) (L = 2,2',2' '-tris(dipicolylamino)triethylamine), with pyridyl and alkylamine coordination exhibits a remarkable ability to promote specific strand scission at junctions between single- and double-stranded DNA. Strand scission occurs on the 3' overhang at the junction of a hairpin or frayed duplex structure and is not dependent on the identity of the base at which cleavage occurs. Target recognition minimally requires a purine at the first unpaired position and a guanine at the second unpaired position on the 5' strand. Incorporation of the necessary recognition elements into an otherwise unreactive junction resulted in specific strand scission at that new target and helped to confirm the predictive nature of this complex. Selective strand scission requires both a reductant and dioxygen, suggesting activation of O(2) by the reduced form of 1. The reaction utilizing the trinuclear complex does not appear to involve a diffusible radical species as suggested by its high specificity of target oxidation and its lack of sensitivity to radical quenching agents. Comparisons between the trinuclear copper complex, mononuclear analogues of 1, and [Cu(OP)(2)](2+) (OP = 1,10-phenanthroline) indicate that recognition and reactivity described in this report are dependent on the multiple metal ions within the same complex which together support its unique activity.     

Oxidative DNA strand scission induced by peptides

Cellular oxidative stress promotes chemical reactions causing damage to DNA, proteins, and membranes. Here, we describe experiments indicating that reactive oxygen species, in addition to degrading polypeptides and polynucleotides through direct reactions, can also promote damaging biomolecular cross reactivity by converting protein residues into peroxides that cleave the DNA backbone. The studies reported show that a variety of residues induce strand scission upon oxidation, and hydrogen abstraction occurring at the DNA backbone is responsible for the damage. The observation of peptide-promoted DNA damage suggests that crossreactions within protein/DNA complexes should be considered as a significant cause of the toxicity of reactive oxygen species.     

Efficient and specific strand scission of DNA by a dinuclear copper complex: comparative reactivity of complexes with linked tris(2-pyridylmethyl)amine moieties

The compound [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4) (D(1) = dinucleating ligand with two tris(2-pyridylmethyl)amine units covalently linked in their 5-pyridyl positions by a -CH(2)CH(2)- bridge) selectively promotes cleavage of DNA on oligonucleotide strands that extend from the 3' side of frayed duplex structures at a site two residues displaced from the junction. The minimal requirements for reaction include a guanine in the n (i.e. first unpaired) position of the 3' overhang adjacent to the cleavage site and an adenine in the n position on the 5' overhang. Recognition and strand scission are independent of the nucleobase at the cleavage site. The necessary presence of both a reductant and dioxygen indicates that the intermediate responsible for cleavage is produced by the activation of dioxygen by a copper(I) form of the dinuclear complex. The lack of sensitivity to radical quenching agents and the high level of site selectivity in scission suggest a mechanism that does not involve a diffusible radical species. The multiple metal center exhibits a synergy to promote efficient cleavage as compared to the action of a mononuclear analogue [Cu(II)(TMPA)(H(2)O)](ClO(4))(2) (TMPA = tris(2-pyridylmethyl)amine) and [Cu(OP)(2)](2+) (OP = 1,10-phenanthroline) at equivalent copper ion concentrations. The dinuclear complex, [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4), is even capable of mediating efficient specific strand scission at concentrations where [Cu(OP)(2)](2+) does not detectably modify DNA. The unique coordination and reactivity properties of [Cu(II)(2)(D(1))(H(2)O)(2)](ClO(4))(4) are critical for its efficiency and site selectivity since an analogue, [Cu(II)(2)(DO)(Cl(2))](ClO(4))(2), where DO is a dinucleating ligand very similar to D(1), but with a -CH(2)OCH(2)- bridge, exhibits only nonselective cleavage of DNA. The differences in the reactivity of these two complexes with DNA and their previously established interaction with dioxygen suggest that specific strand scission is a function of the orientation of a reactive intermediate.     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

DNA oxidation in anionic reverse micelles: ruthenium-mediated damage at Guanine in single- and double-stranded DNA

One-electron guanine oxidation in DNA has been investigated in anionic reverse micelles (RMs). A photochemical method for generating Ru3+ from the ruthenium polypyridyl complex tris(2-2'-bipyridine)ruthenium(II) chloride ([Ru(bpy)3]Cl2) is combined with high-resolution polyacrylamide gel electrophoresis (PAGE) to quantify piperidine-labile guanine oxidation products. As characterized by emission spectroscopy of Ru(bpy)3(2+), the addition of DNA to RMs containing Ru(bpy)3(2+) does not perturb the environment of Ru(bpy)3(2+). The steady-state quenching efficiency of Ru(bpy)3(2+) with K3[Fe(CN)6] in buffer solution is approximately 2-fold higher than that observed in RMs. Consistent with the difference in quenching efficiency in the two media, a 1.5-fold higher yield of piperidine-labile damage products as monitored by PAGE is observed for duplex oligonucleotide in buffer vs RMs. In contrast, a 13-fold difference in the yield of PAGE-detected G oxidation products is observed when single-stranded DNA is the substrate. Circular dichroism spectra showed that single-stranded DNA undergoes a structural change in anionic RMs. This structural change is potentially due to cation-mediated adsorption of the DNA phosphates on the anionic headgroups of the RMs, leading to protection of the guanine from oxidatively generated damage.     

Targeted guanine oxidation by a dinuclear copper(II) complex at single stranded/double stranded DNA junctions

A dinuclear copper(II) complex [Cu(II)2(PD'O-)(H2O)2](ClO4)3 (5) with terminal Cu(II)-H(2)O moieties and a Cu...Cu distance of 4.13 A (X-ray structure) has been synthesized and characterized by EPR spectroscopy (ferromagnetic coupling observed) and cyclic voltammetry. Dizinc(II) and mononuclear copper(II) analogues [Zn(II)2(PD'O-)(H2O)2]3+ (7) and [Cu(II)(mPD'OH)(H2O)]2+ (6), respectively, have also been synthesized and structurally characterized. Reacting 5/MPA/O(2) (MPA = 3-mercaptopropionic acid) with DNA leads to a highly specific oxidation of guanine (G) at a junction between single- and double-stranded DNA. Mass spectrometric analysis of the major products indicates a gain of +18 and +34 amu relative to initial DNA strands. The most efficient reaction requires G at the first and second unpaired positions of each strand extending from the junction. Less reaction is observed for analogous targets in which the G cluster is farther from the junction or contains less than four Gs. Consistent with our previous systems, the multinuclear copper center is required for selective reaction; mononuclear complex 6 is not effective. Hydrogen peroxide as a substitute for MPA/O2 also does not lead to activity. Structural analysis of a [Cu(II)2(PD'O-)(G)]3+ complex (8) and dizinc analogue [Zn(II)(2)(PD'O-)(G)](ClO4)3 (9) (G = guanosine) reveals coordination of the G O6 and N7 atoms with the two copper (or zinc) centers and suggests that copper-G coordination likely plays a role in recognition of the DNA target. The Cu2-O2 intermediate responsible for guanine oxidation appears to be different from that responsible for direct-strand scission induced by other multinuclear copper complexes; the likely course of reaction is discussed.     

Enantio-differentiating catalytic oxidation by a biomimetic trinuclear copper complex containing L-histidine residues

The trinuclear complex [Cu3PHI]6+, derived from a ligand containing two chiral L-histidine residues, performs the catalytic oxidation of L- and D-Dopa with remarkable enantio-differentiation; this depends on the anchoring effect provided by the copper center which is not participating in the catalytic reaction and recognizes the chirality of the substrate.     

Creation of mammalian single- and double-stranded DNA surfaces: a real-time QCM-D study

The quartz crystal microbalance with dissipation monitoring (QCM-D) is an excellent method for studying the creation of DNA-based surfaces and films. Previous studies have used QCM-D to focus on the construction of DNA surfaces composed of short synthetic DNA oligomers or plasmid DNA. Here, we have used QCM-D to monitor the creation of genomic single- and double-stranded calf thymus DNA surfaces on a polycation adsorbed to a SiO2 support. We have successfully monitored the hybridization between the ssDNA surfaces and their complementary strands in solution and have also shown that DNA multilayer formation can be observed using denatured calf thymus DNA. We have furthermore established that the ssDNA and dsDNA surfaces show different binding characteristics to ethidium bromide, a common dsDNA intercalator, demonstrating the potential use of such surfaces to identify possible DNA ligands.     

Excited-state intramolecular proton transfer distinguishes microenvironments in single- and double-stranded DNA

Herein, the efficient interaction of an environment-sensitive fluorophore that undergoes excited-state intramolecular proton transfer (ESIPT) with DNA has been realized by conjugation of a 3-hydroxychromone (3HC) with polycationic spermine. On binding to a double-stranded DNA (dsDNA), the ratio of the two emission bands of the 3HC conjugates changes up to 16-fold, so that emission of the ESIPT product increases dramatically. This suggests an efficient screening of the 3HC fluorophore from the water molecules in the DNA complex, which is probably realized by its intercalation into dsDNA. In sharp contrast, the 3HC conjugates show only moderate changes in the dual emission on binding to a single-stranded DNA (ssDNA), indicating a much higher fluorophore exposure to water at the binding site. Thus, the 3-hydroxychromone fluorophore being conjugated to spermine discriminates the binding of this polycation to dsDNA from that to ssDNA. Consequently, ESIPT-based dyes are promising for monitoring the interaction of polycationic molecules with DNA and probing the microenvironment of their DNA binding sites.     

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.     

Dissecting the strand folding orientation and formation of G-quadruplexes in single- and double-stranded nucleic acids by ligand-induced photocleavage footprinting

The widespread of G-quadruplex-forming sequences in genomic DNA and their role in regulating gene expression has made G-quadruplex structures attractive therapeutic targets against a variety of diseases, such as cancer. Information on the structure of G-quadruplexes is crucial for understanding their physiological roles and designing effective drugs against them. Resolving the structures of G-quadruplexes, however, remains a challenge especially for those in double-stranded DNA. In this work, we developed a photocleavage footprinting technique to determine the folding orientation of each individual G-tract in intramolecular G-quadruplex formed in both single- and double-stranded nucleic acids. Based on the differential photocleavage induced by a ligand tetrakis(2-trimethylaminoethylethanol) phthalocyaninato zinc tetraiodine (Zn-TTAPc) to the guanines between the two terminal G-quartets in a G-quadruplex, this method identifies the guanines hosted in each terminal G-quartets to reveal G-tract orientation. The method is extremely intuitive, straightforward, and requires little expertise. Besides, it also detects G-quadruplex formation in long single- and double-stranded nucleic acids.     

Selective covalent binding of a positively charged water-soluble benzoheterocycle triosmium cluster to single- and double-stranded DNA

The water-soluble triosmium cluster [Os₃(CO)₉(μ-η²-(4-CHO)C₉H₅N)(μ-H)(P(OCH₂CH₂N(CH₃)₃I)₃)] (4) was tested for its reactivity with plasmid DNA. In contrast to the band retardation previously observed with a related series of positively charged clusters, an intensification and retardation of three discrete bands was observed with increasing cluster concentration. In order to further investigate the apparent modification of DNA by 4, its interaction with a 22-oligomer (sequence 5′-AGT TGT GGT GAC TTT CCC AGG C-3′) was examined. Incubation with this oligonucleotide (pH 7.4 in Tris-HCl buffer and 100 mM NaCl) followed by HPLC analysis revealed the formation of three dose dependent products assigned as covalent modifications at three sites of the oligonucleotide. Incubation of 4 with ³²P-ATP labeled oligonucleotide at the 5′-end followed by treatment with piperidine and comparison with the standard Maxam-Gilbert sequencing protocol products revealed only general background cleavage, indicating that the modification products are piperidine labile and suggesting that the modification involved formation of a Schiff base. An alternative approach was then pursued which involved annealing the 4-oligonucleotide products with their complementary strand and treatment of the resulting duplex DNAwith the exonuclease, Exo III. This assay indicated three exonuclease stops, consistent with the three products observed by HPLC whose electrophoretic mobility approximately matched guanine containing fragments when compared with the Maxam-Gilbert sequencing lanes. Reduction of the 4-oligonucleotide products with borohydride reducing agents, followed by treatment with piperidine, resulted in the formation of one product (by HPLC) with the same electrophoretic mobility as the AGTT fragment based on comparison with the Maxam-Gilbert sequencing lanes. This product most likely results from reduction of an initially formed Schiff base adduct (to the corresponding amine) with the guanine of the TGT fragment of the oligonucleotide, and corresponds to the most stable of the three Schiff base adducts detected by HPLC and by incubation with the exonuclease. The other two products are less stable and competitive reduction of the free aldehyde functionality on the cluster in equilibrium with these adducts precludes their detection after treatment with the reducing agents. The formation of the Schiff base adduct is further corroborated by the model reaction of [Os₃(CO)₁₀(μ-η²-(4-CHO)C₉H₅N)(μ-H)] (4′) with acetylated guanine in nonaqueous solvents where disappearance of the aldehyde resonance and the appearance of several new resonances in the 6-9 ppm region of the ¹H NMR of the reaction mixture is noted.     

Synthesis, crystal structure and DFT analysis of a new trinuclear complex of copper

The new trinuclear complex [Cu₂(μ-L)₂CuCl₂] has been synthesized and characterized by elemental analysis, IR, UV-Vis and X-ray spectroscopy, where L is a dianionic tetradentate Schiff base ligand with N₂O₂ donor atoms. The molecular structure of [Cu₂(μ-L)₂CuCl₂] was determined by X-ray crystallography. In the complex, the most remarkable aspect of the trinuclear complex is that it adopts a bent structure for the three copper atoms, with a Cu1Cu3Cu2 intramolecular angle of approximately 90.62(2)°. All three copper atoms are five coordinate, with a slightly distorted square pyramidal geometry. In the two terminals moieties, the basal plane of the square pyramidal is formed by two oxygen atoms and two nitrogen atoms of the Schiff base ligand, and the apical position at the Cu atom is occupied by the bridging Cl1 anion. The Cu1Cl1Cu2 angle is 110.51(5)°. The central copper atom also has a five-coordinate, slightly distorted square pyramidal geometry, with four phenolato oxygens belonging to the Schiff base ligands from Cu(salpn) units describing the square planar base and the Cl anions being apical. The optimized structure of the complex has been studied using the B3LYP/6-31G(d)/LanL2TZf level of theory. The calculation shows that all the copper atoms are five coordinate with distorted square pyramidal structures, which is consistent with experimental data.     

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.     

The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures

The pH-induced helix-coil transition of DNA and its complexes with EtBr is carried out at acidic pH in a wide interval of change of concentration ratio of EtBr/DNA. The binding isotherms of EtBr on double and single-stranded DNA at pH = 7.0 and pH = 3.0 (t = 25(o)C) are obtained by absorption and fluorimetric methods. Binding constants (K) and number of bases (n), corresponding to one binding site were determined. Non fluorescent "strong" complex with ds-DNA at pH = 7.0 and t = 25(o)C as well as "strong" and "weak" complexes with ss-DNA at pH = 3.0 and t = 25(o)C are revealed.     

Recognition of oxalate by a copper(II) polyaza macrobicyclic complex

A new polyamine macrobicyclic compound was synthesised through a [1+1] "tripod-tripod coupling" strategy and using a Schiff base condensation reaction, followed by sodium borohydride reduction. The resulting compound is a heteroditopic cage (btpN(7)) in which one of the head units is appropriate for the coordination of copper(II), whereas the other head is available for additional hydrogen-bonding and electrostatic interactions with substrates. The acid-base behaviour of the new compound, the stability constants of its complex with the Cu(2+) ion and the association constants of the copper(II) cryptate with oxalate (oxa(2-)), malonate (mal(2-)), succinate (suc(2-)), maleate (male(2-)) and fumarate (fum(2-)) were determined by potentiometry at 298.2 K in aqueous solution and at an ionic strength of 0.10 mol dm(-3) in KNO(3). These studies revealed a clear preference of the receptor [CuH(h)btpN(7)H(2)O]((2+h)+) for oxa(2-) over the other dicarboxylate substrates. This arises from co-operativity between metal-anion coordination and electrostatic and hydrogen-bonding interactions, in accordance with the ideal size of this dicarboxylate, which allow it to take full advantage of the potential binding sites of the receptor. A qualitative indicator-displacement study, in agreement with the potentiometric studies, demonstrated that the copper cryptate receptor can be used as a selective visual sensor for oxalate.     

Noncovalent interactions between a trinuclear monofunctional platinum complex and human serum albumin

Interactions between platinum complexes and human serum albumin (HSA) play crucial roles in the metabolism, distribution, and efficacy of platinum-based anticancer drugs. Polynuclear monofunctional platinum(II) complexes represent a new class of anticancer agents that display distinct molecular characters of pharmacological action from those of cisplatin. In this study, the interaction between a trinuclear monofunctional platinum(II) complex, [Pt(3)LCl(3)](ClO(4))(3) (L = N,N,N',N',N",N"-hexakis(2-pyridylmethyl)-1,3,5-tris(aminomethyl)benzene) (1), and HSA was investigated using ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, circular dichroism spectroscopy, fluorescence spectroscopy, molecular docking, and inductively coupled plasma mass spectrometry. The spectroscopic and thermodynamic data show that the interaction is a spontaneous process with the estimated enthalpy and entropy changes being 14.6 kJ mol(-1) and 145.5 J mol(-1) K(-1), respectively. The reactive sites of HSA to complex 1 mainly locate within its hydrophobic cavity in domain II. Noncovalent actions such as π-π stacking and hydrophobic bonding are the primary contributors to the interaction between HSA and complex 1, which is different from the scenario for cisplatin in similar conditions. The results suggest that the connection between complex 1 and HSA is reversible, and therefore the cytotoxic activity of the complex could be preserved during blood circulation.