Design of artificial metallonucleases with oxidative mechanism

Studies of DNA-Binding and DNA-Cutting Mechanism of an Azamacrocyclic Cerium Complex with Carboxyl Branch

An azamacrocyclic compound with a carboxyl branch, 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclo-tetradecane- N/-acetic acid (L), and its cerium complex were synthesised and characterised. The mode of combination of the cerium complex with DNA was investigated by fluorescence and UV-Vis absorption spectroscopy. The cutting function of the cerium complex towards supercoiled DNA was studied by the gel electrophoresis method. The results show that metal complex can bind to the phosphate group of DNA double helix and promote the hydrolysis of the phosphodiester bond of supercoiled DNA (Form I); under certain conditions, supercoiled form DNA (Form I) was transformed into the nicked form DNA (Form II) under the strong cutting effect of the macrocyclic cerium complex; the cutting is completed by a hydrolysis mechanism.

Energy-Resolved Collision-Induced Dissociation Studies of 2,2'-Bipyridine Complexes of the Late First-Row Divalent Transition-Metal Cations: Determination of the Third-Sequential Binding Energies

The third-sequential binding energies of the late first-row divalent transition-metal cations with 2,2'-bipyridine (Bpy) are determined using guided-ion-beam tandem mass spectrometry (GIBMS) techniques. The metal cations investigated include the late first-row divalent transition-metal cations, Fe²⁺ , Co²⁺ , Ni²⁺ , Cu²⁺ , and Zn²⁺ . The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the M²⁺ (Bpy)₃ complexes are analyzed to extract absolute 0 and 298 K bond dissociation energies (BDEs) for the loss of an intact Bpy ligand. Theoretical electronic structure calculations at the B3LYP, BHandHLYP, and M06 levels of theory are performed to determine stable geometries and sequential BDEs of the M²⁺ (Bpy)_x complexes (x=1-3). BDEs computed using the M06 functional are the largest, BHandHLYP values are intermediate, whereas B3LYP produces the smallest values. Very good agreement between the B3LYP theoretically calculated and threshold collision-induced dissociation experimentally determined BDEs is found, which suggests that the B3LYP functional is capable of accurately describing the binding in these M²⁺ (Bpy)₃ complexes. Periodic trends in the binding of the M²⁺ (Bpy)_x complexes are examined and compared to the analogous complexes with 1,10-phenanthroline (Phen), M²⁺ (Phen)_x . Comparisons are also made to the analogous Bpy complexes, M⁺ (Bpy)_x , with the late first-row monovalent transition-metal cations, Co⁺ , Ni⁺ , Cu⁺ , and Zn⁺ investigated previously.

Self-activating nuclease and anticancer activities of copper(II) complexes with aryl-modified 2,6-di(thiazol-2-yl)pyridine

Three mononuclear copper complexes [Cu(PDTP)Cl2] (PDTP = 4-phenyl-2,6-di(thiazole-2-yl)pyridine, CuPDTP), [Cu(ADTP)Cl2] (ADTP = 4-(anthracen-9-yl)-2,6-di(thiazole-2-yl)pyridine, CuADTP) and [Cu(BFDTP)Cl2] (BFDTP = 4-(benzofuran-2-yl)-2,6-di(thiazole-2-yl)pyridine, CuBFDTP) were synthesized and characterized. The X-ray single crystallography results indicated that the Cu(II) ions showed slightly distorted square pyramid coordination environments, and the ligands deviated from ideal planarity in all three compounds. Based on the DNA binding studies, it was demonstrated that these three complexes exhibited weak DNA binding strengths, which were most likely groove binding modes. CuPDTP, CuADTP and CuBFDTP induced efficient DNA cleavage in the dark without the addition of external catalysts (oxidant or reductant). In contrast, in the presence of reducing or oxidizing agents, the nuclease activities increased more than 10-fold. Mechanistic investigations revealed the participation of reactive oxygen species, which can be trapped by ROS radical scavengers and ROS sensors. In the same experimental conditions, the free ligands and CuCl2 did not display any DNA cleaving activity. This result indicates that the complexes, rather than their components, play a significant role in the nuclease reaction process and that DNA cleavage may be initiated in an oxidative pattern. The proposed mechanism was attributed to the in situ activation of molecular oxygen by the oxidation of the copper complexes. In the MTT cytotoxicity studies, the three Cu(II) complexes exhibited an antitumor activity against the HeLa, BEL-7402 and HepG2 tumor cell lines. The HeLa cells treated with Cu(II) complexes demonstrated marked changes in their nuclear morphology, which were detected by Hoechst 33258 nuclear staining and acridine orange/ethidium bromide (AO/EB) staining assays. Nuclear chromatin cleavage also was observed from alkaline single-cell gel electrophoresis (comet assay).

Improving nuclease activity of copper(II)-terpyridine complex through solubilizing and charge effects of glycine

Copper complexes are potential metallonucleases that may find application in biotechnology and molecular biology. In this study, a ternary copper-terpyridine complex [Cu(ttpy)(Gly)(NO3)](NO3)·H2O (1) (ttpy=4'-p-tolyl-2,2':6,2″-terpyridine) is synthesized and characterized by X-ray crystallography and ESI-MS as an artificial nuclease. Glycine (Gly) is introduced into the complex to enhance the water-solubility and electrostatic affinity for the nucleic acid target. The interaction between complex 1 and DNA has been studied by spectroscopy and gel electrophoresis, using a structural analog [Cu(ttpy)(NO3)2] (2) as the reference. Complex 1 demonstrates an increased DNA binding ability and oxidative cleavage activity towards supercoiled pBR322 DNA as compared with complex 2. The enhanced water-solubility and positive charge of complex 1 may facilitate its access to DNA and formation of hydrogen bonds with the sugar-phosphate backbone. The results indicate that carefully positioned auxiliary groups in a copper complex can significantly affect the substrate binding or activation ability and consequently the nuclease efficiency of the complex.

Effect of coordinated ligands on antiproliferative activity and DNA cleavage property of three mononuclear Cu(II)-terpyridine complexes

Three mononuclear copper(II) complexes, [Cu(tpy)Cl(2)] 1, [Cu(tpy)(NO(3))(2)(H(2)O)] 2 and [Cu(Ptpy)Cl(2)]·H(2)O·HCl 3 have been synthesised and characterized by various spectroscopic techniques and single crystal X-ray diffraction. Complexes 1 and 3 have five coordinate geometry in solid state, whereas complex 2 has six coordinate geometry. Mass spectral and EPR evidence suggest that in solution all the three complexes exist predominantly as a four coordinate species. Molecular modelling and DNA cleavage studies indicate that complexes 1 and 2 are DNA minor groove binders, whereas 3 is an intercalator. All the three complexes show nuclease activity in the presence of hydrogen peroxide. The three complexes have been found to be cytotoxic towards A549 lung adenocarcinoma cells.

Progress in artificial metallonucleases

The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.

The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme

DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.

Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies

Fluorescence resonance energy transfer (FRET) has been used to study the global folding of an uranyl (UO(2)(2+))-specific 39E DNAzyme in the presence of Mg(2+), Zn(2+), Pb(2+), or UO(2)(2+). At pH 5.5 and physiological ionic strength (100 mM Na(+)), two of the three stems in this DNAzyme folded into a compact structure in the presence of Mg(2+) or Zn(2+). However, no folding occurred in the presence of Pb(2+) or UO(2)(2+); this is analogous to the "lock-and-key" catalysis mode first observed in the Pb(2+)-specific 8-17 DNAzyme. However, Mg(2+) and Zn(2+) exert different effects on the 8-17 and 39E DNAzymes. Whereas Mg(2+) or Zn(2+)-dependent folding promoted 8-17 DNAzyme activity, the 39E DNAzyme folding induced by Mg(2+) or Zn(2+) inhibited UO(2)(2+)-specific activity. Group IIA series of metal ions (Mg(2+), Ca(2+), Sr(2+)) also caused global folding of the 39E DNAzyme, for which the apparent binding affinity between these metal ions and the DNAzyme decreases as the ionic radius of the metal ions increases. Because the ionic radius of Sr(2+) (1.12 Å) is comparable to that of Pb(2+) (1.20 Å), but contrary to Pb(2+), Sr(2+) induces the DNAzyme to fold under identical conditions, ionic size alone cannot account for the unique folding behaviors induced by Pb(2+) and UO(2)(2+). Under low ionic strength (30 mM Na(+)), all four metal ions (Mg(2+), Zn(2+), Pb(2+), and UO(2)(2+)), caused 39E DNAzyme folding, suggesting that metal ions can neutralize the negative charge of DNA-backbone phosphates in addition to playing specific catalytic roles. Mg(2+) at low (<2 mM) concentration promoted UO(2)(2+)-specific activity, whereas Mg(2+) at high (>2 mM) concentration inhibited the UO(2)(2+)-specific activity. Therefore, the lock-and-key mode of DNAzymes depends on ionic strength, and the 39E DNAzyme is in the lock-and-key mode only at ionic strengths of 100 mM or greater.

Structural analysis of zinc-finger (TTK) + [Cu(BPA)]2+ /[Cu(IDB)]2+ + DNA complexes: an investigation by molecular dynamics simulation

In the present study, the molecular dynamics simulation technique is employed to investigate the hydrogen abstraction possibility from sugar of DNA in two designed complexes of copper-based chemical nuclease [Cu(BPA)](2+) bis(2-pyridylmethyl) amine (BPA) or [Cu(IDB)](2+) N,N-bis(2-benzimidazolylmethyl) amine (IDB) bound to the zinc finger protein Tramtrack (TTK). The simulated results show that each of the designed complexes can form a stable conformation within 30 ns of simulation time with the substrate OOH(-) and an 18-base pair (bp) DNA segment and is located in the major groove of the DNA segment. The active terminal O atom of the OOH(-) substrate is found in close proximity to the target C2'H, C3'H, C4'H or C5'H proton of the DNA in TTK + [Cu(BPA)OOH](+) + DNA or TTK + [Cu(IDB)OOH](+) + DNA complex, which is crucial to propose the hydrogen abstraction possibility that is responsible for the DNA cleavage. The positions of copper-based chemical nucleases bound to TTK may substantially influence the hydrogen abstraction possibility. The structures and sizes of ligands in copper-based nucleases are also found to have influence on the order of difficulty of the hydrogen abstraction from the sugars of DNA.

Artificial DNA cutters for DNA manipulation and genome engineering

This tutorial review provides recent developments in artificial cutters for site-selective scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for molecular biology and biotechnology, since their site-selectivity of scission is much higher than that of naturally occurring restriction enzymes and also their scission site is freely chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an artificial restriction DNA cutter, prepared from Ce(iv)/EDTA and pseudo-complementary peptide nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and scission specificity are determined simply in terms of the Watson-Crick rule so that even the whole genome of human beings was selectively cut at one predetermined site. Consistently, homologous recombination in human cells was successfully promoted by this tool. For the purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also briefly described. The potential applications of these cutters and their future aspects are discussed.

DNA binding, prominent DNA cleavage and efficient anticancer activities of tris(diimine)iron(II) complexes

The complexes rac-[Fe(diimine)(3)](ClO(4))(2)1-4, where diimine = 2,2'-bipyridine (bpy) 1, 1,10-phenanthroline (phen) 2, 5,6-dimethyl-1,10-phenanthroline (5,6-dmp) 3 and dipyrido[3,2-d:2',3'-f]quinoxaline (dpq) 4, have been isolated, characterized and their interaction with calf thymus DNA studied by using a host of physical methods. The X-ray crystal structure of rac-[Fe(5,6-dmp)(3)](ClO(4))(2)3 has been determined and the packing diagram shows the presence of two enantiomeric forms of the complex cations in the same unit cell. The structures of 1-4 in solution have also been studied using UV-Visible, Cyclic Voltammetry and ESI-MS data and all data available suggests that they retain their solid state structures even in solution. The absorption spectral titrations of the iron(ii) complexes with CT DNA reveal that the DNA binding affinities of the complexes vary in the order, 4 (K(b): 9.0 × 10(3)) > 2 (6.8 × 10(3)) > 3 (4. 8 × 10(3)) > 1 (2.9 × 10(3) M(-1)). The DNA interaction of dpq complex (4) involves partial insertion of the extended phen ring in between the DNA base pairs, which is deeper than that of phen (2). The 5,6-dmp (3) complex is involved in groove binding in the major groove of DNA. The lower DNA binding affinity of 1 is due to electrostatic interaction of the cationic complexes with exterior phosphates of DNA. The EthBr displacement assay and DNA viscosity study support these DNA binding modes and the above trend in DNA binding affinities. The complexes of 1 and 2 show induced CD (ICD) upon interaction with CT DNA while 3 and 4 bound to DNA exhibit inversion in the positive band with the helicity band showing very small changes, which implies that 3 and 4 bind enantiopreferentially to DNA. The DNA cleavage abilities of 1-4 have been observed at 10 μM concentration of complexes in the presence of 100 μM H(2)O(2) and the DNA cleavage efficiency (> 90%) follows the order 3 > 1 > 2 > 4. The anticancer activity of 1-4 against human breast cancer cell line (MCF-7) has also been studied. The IC(50) values of the complexes at different incubation time intervals of 24 and 48 h follow the order, 3 (0.8, 0.6) < 4 (20.0, 17.0) < 2 (28.0, 22.0) < 1 (32.0, 29.0 μM). Interestingly, 3 exhibits anticancer activity more potent than 1, 2 and 4 and cisplatin for both 24 and 48 h. It induces cell death both through apoptosis and necrosis mechanisms, as revealed by morphological assessment data obtained by using AO/EB and Hoechst 33258 fluorescence staining methods.

Synergy between quantum dots and 1,10-phenanthroline-copper(II) complex towards cleaving DNA

We have found that the DNA cleaving activity of quantum dots and 1,10-phenanthroline-Cu(II) complex is significantly enhanced when they are combined.

Photoenhanced oxidative DNA cleavage with non-heme iron(II) complexes

The DNA cleavage activity of iron(II) complexes of a series of monotopic pentadentate N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine (N4Py)-derived ligands (1-5) was investigated under laser irradiation at 473, 400.8, and 355 nm in the absence of a reducing agent and compared to that under ambient lighting. A significant increase in activity was observed under laser irradiation, which is dependent on the structural characteristics of the complexes and the wavelength and power of irradiation. Under photoirradiation at 355 nm, direct double-stand DNA cleavage activity was observed with Fe(II)-1 and Fe(II)-3-5, and a 56-fold increase in the single-strand cleavage activity was observed with Fe(II)-2. Mechanistic investigations revealed that O(2)(•-), (1)O(2), and OH(•) contribute to the photoenhanced DNA cleavage activity, and that their relative contribution is dependent on the wavelength. It is proposed that the origin of the increase in activity is the photoenhanced formation of an Fe(III)OOH intermediate as the active species or precursor.

Investigation and improvement of DNA cleavage models of polyamide + Cu(II) nuclease + OOH- ligands bound to DNA

Background

Copper nucleases as a famous class of artificial metallonucleases have attracted considerable interest in relation to their diverse potentials not only as therapeutic agents but also in genomic researches. Copper nucleases present high efficient oxidative cleavage of DNA, in which DNA strand scission occurs generally after hydrogen atom abstracted from a sugar moiety. In order to achieve the selective cleavage of DNA sequences by copper nucleases, the DNA specific recognition agents of the Dervan-type hairpin and cyclic polyamides can be considered as proper carriers of copper nucleases. Investigation of the DNA cleavage selectivity of copper nucleases assisted by the hairpin and cyclic polyamides at the molecular level has not yet been elucidated.

Results

We carried out a series of molecular dynamics simulations for the nuclease [Cu(BPA)]²⁺ or [Cu(IDB)]²⁺ bound to the hairpin/cyclic polyamide and associated with DNA to investigate the selective DNA cleavage properties of Cu(II)-based artificial nucleases. The simulated results demonstrate that the DNA cleavage selectivity of the two nucleases assisted by the hairpin polyamide is improved efficiently. The [Cu(BPA)]²⁺ or [Cu(IDB)]²⁺ nuclease with a substrate OOH^- bound to the hairpin polyamide can be stably located at the minor groove of DNA, and possibly abstracts H atom from the sugar of DNA. However, the DNA cleavage properties of the two nucleases assisted by the cyclic polyamide are significantly poor due to the rigidity of linking region between the cyclic polyamide and nuclease. With introduction of the flexible linker -CH₂CH₂CH₂NH₂, the modified cyclic polyamide can assist the two copper nucleases to improve the selective DNA cleavage properties efficiently.

Conclusion

A flexible linker and a proper binding site of the polyamide-type recognition agents play an important role in improving the DNA cleavage selectivity of copper nucleases. Current investigations provide an insight into the DNA cleavage specificities of chemical nucleases assisted by an appropriate nucleic acid recognition agent.