The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex

The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.     

Substrate specificity of an active dinuclear Zn(II) catalyst for cleavage of RNA analogues and a dinucleoside

The cleavage of the diribonucleoside UpU (uridylyl-3'-5'-uridine) to form uridine and uridine (2',3')-cyclic phosphate catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (Zn(2)(1)(H(2)O)) has been studied at pH 7-10 and 25 degrees C. The kinetic data are consistent with the accumulation of a complex between catalyst and substrate and were analyzed to give values of k(c) (s(-)(1)), K(d) (M), and k(c)/K(d) (M(-)(1) s(-)(1)) for the Zn(2)(1)(H(2)O)-catalyzed reaction. The pH rate profile of values for log k(c)/K(d) for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU shows the same downward break centered at pH 7.8 as was observed in studies of catalysis of cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) and uridine-3'-4-nitrophenyl phosphate (UpPNP). At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between Zn(2)(1)(H(2)O) and the bound transition states is 9.3, 7.2, and 9.6 kcal/mol for the catalyzed reactions of UpU, UpPNP, and HpPNP, respectively. The larger transition-state stabilization for Zn(2)(1)(H(2)O)-catalyzed cleavage of UpU (9.3 kcal/mol) compared with UpPNP (7.2 kcal/mol) provides evidence that the transition state for the former reaction is stabilized by interactions between the catalyst and the C-5'-oxyanion of the basic alkoxy leaving group.     

Substrate specificity for catalysis of phosphodiester cleavage by a dinuclear Zn(II) complex

The 2.4 kcal mol(-1) greater stabilization of the transition state for cleavage of the minimal substrate HpPNP compared to the nucleoside substrate UpPNP by the efficient dinuclear metal ion catalyst Zn2(L2O) provides evidence that access to the cationic core of Zn2(L2O) is sterically blocked for the bulkier nucleoside substrates, a flaw that will need to be dealt with in later generations of metal ion catalysts of RNA cleavage.     

A simple DNase model system comprising a dinuclear Zn(II) complex in methanol accelerates the cleavage of a series of methyl aryl phosphate diesters by 10(11)-10(13)

The di-Zn(II) complex of 1,3-bis[ N1, N1'-(1,5,9-triazacyclododecyl)]propane with an associated methoxide ( 3:Zn(II) 2: (-)OCH 3) was prepared and its catalysis of the methanolysis of a series of fourteen methyl aryl phosphate diesters ( 6) was studied at s (s)pH 9.8 in methanol at 25.0 +/- 0.1 degrees C. Plots of k obs vs [ 3:Zn(II) 2: (-)OCH 3] free for all members of 6 show saturation behavior from which K(M) and kcat (max) were determined. The second order rate constants for the catalyzed reactions (kcat (max)/K(M)) for each substrate are larger than the corresponding methoxide catalyzed reaction (k 2 (-OMe)) by 1.4 x 10(8) to 3 x 10 (9)-fold. The values of k cat (max) for all members of 6 are between 4 x 10(11) and 3 x 10(13) times larger than the solution reaction at s (s)pH 9.8, with the largest accelerations being given for substrates where the departing aryloxy unit contains ortho-NO 2 or C(O)OCH 3 groups. Based on the linear Br?nsted plots of k cat (max) vs s (s)pKa of the phenol, beta lg values of -0.57 and -0.34 are determined respectively for the catalyzed methanolysis of "regular" substrates that do not contain the ortho-NO 2 or C(O)OCH 3 groups, and those substrates that do. The data are consistent with a two step mechanism for the catalyzed reaction with rate limiting formation of a catalyst-coordinated phosphorane intermediate, followed by fast loss of the aryloxy leaving group. A detailed energetics calculation indicates that the catalyst binds the transition state comprising [CH 3O (-): 6], giving a hypothetical [ 3:Zn(II) 2:CH 3O (-): 6] complex, by -21.4 to -24.5 kcal/mol, with the strongest binding being for those substrates having the ortho-NO 2 or C(O)OCH 3 groups.     

Comparing a mononuclear Zn(II) complex with hydrogen bond donors with a dinuclear Zn(II) complex for catalysing phosphate ester cleavage

Introducing ligand based hydrogen bond donors to increase the activity of a mononuclear Zn(II) complex for catalysing phosphate ester cleavage can be a more effective strategy than making the dinuclear analogue.     

A reductionist biomimetic model system that demonstrates highly effective Zn(II)-catalyzed cleavage of an RNA model

The cyclization of the RNA model 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP, 1) promoted by Zn2+ alone and the 1,5,9-triazacyclododecane complex of Zn2+ (Zn2+:[12]aneN3) is studied in ethanol in the presence of 0.5 equiv of -OEt/Zn2+ to investigate the effect of a low polarity/dielectric medium on a metal-catalyzed reaction of biological relevance. Ethanol exerts a medium effect that promotes strong binding of HPNPP to Zn2+, followed by a dimerization to form a catalytically active complex (HPNPP:Zn2+)2 in which the phosphate undergoes cyclization with a rate constant of kcat = 2.9 s(-1) at s(s)pH 7.1. In the presence of the triaza ligand:Zn2+ complex, the change from water to methanol and then to ethanol brings about a mechanism where two molecules of the complex, suggested as EtOH:Zn2+:[12]aneN3 and its basic form, EtO-:Zn2+:[12]aneN3, bind to HPNPP and catalyze its decomposition with a rate constant of kcat of 0.13 s(-1) at s(s)pH 7.1. Overall, the acceleration exhibited in these two situations is 4 x 10(14)-fold and 1.7 x 10(12)-fold relative to the background ethoxide-promoted reactions at the respective s(s)pH values. The implications of these findings are discussed within the context of the idea that enzymatic catalysis is enhanced by a reduced effective dielectric constant within the active site.     

Rapid three-step cleavage of RNA and DNA model systems promoted by a dinuclear Cu(II) complex in methanol. energetic origins of the catalytic efficacy

A dinuclear Cu(II) complex of 1,3-bis-N(1)-(1,5,9-triazacyclododecyl)propane with an associated methoxide (2-Cu(II)(2):(-OCH(3))) was prepared, and its kinetics of reaction with an RNA model (2-hydroxypropyl-p-nitrophenyl phosphate (1, HPNPP)) and two DNA models (methyl p-nitrophenyl phosphate (3) and iso-butyl p-chlorophenyl phosphate (4)) were studied in methanol solution at (s)(s)pH 7.2 +/- 0.2. X-ray diffraction structures of 2-Cu(II)(2):(-OH)(H(2)O)(CF(3)SO(3)-)(3):0.5CH(3)CH(2)OCH(2)CH(3) and 2-Cu(II)(2):(-OH)((C(6)H(5)CH(2)O)(2)PO(2)-)(CF(3)SO(3)-)2 show the mode of coordination of the bridging -OH and H(2)O between the two Cu(II) ions in the first complex and bridging -OH and phosphate groups in the second. The kinetic studies with 1 and 3 reveal some common preliminary steps prior to the chemical one of the catalyzed formation of p-nitrophenol. With 3, and also with the far less reactive substrate (4), two relatively fast events are cleanly observed via stopped-flow kinetics. The first of these is interpreted as a binding step which is linearly dependent on [catalyst] while the second is a unimolecular step independent of [catalyst] proposed to be a rearrangement that forms a doubly Cu(II)-coordinated phosphate. The catalysis of the cleavage of 1 and 3 is very strong, the first-order rate constants for formation of p-nitrophenol from the complex being approximately 0.7 s(-1) and 2.4 x 10(-3) s(-1), respectively. With substrate 3, 2-Cu(II)(2):(-OCH(3)) exhibits Michaelis-Mentin kinetics with a k(cat)/K(M) value of 30 M(-1) s(-1) which is 3.8 x 10(7)-fold greater than the methoxide promoted reaction of 3 (7.9 x 10(-7) M(-1) s(-1)). A free energy calculation indicates that the binding of 2-Cu(II)(2):(-OCH(3)) to the transition states for 1 and 3 cleavage stabilizes them by -21 and -24 kcal/mol, respectively, relative to that of the methoxide promoted reactions. The results are compared with a literature example where the cleavage of 1 in water is promoted by a dinuclear Zn(II) catalyst, and the energetic origins of the exalted catalysis of the 2-Cu(II)(2) and 2-Zn(II)(2) methanol systems are discussed.     

Cooperativity between metal ions in the cleavage of phosphate diesters and RNA by dinuclear Zn(II) catalysts

A series of ligands containing linked 1,4,7-triazacyclononane macrocycles are studied for the preparation of dinuclear Zn(II) complexes including 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (L2OH), 1,5-bis(1,4,7-triazacyclonon-1-yl)pentane (L3), 2,9-bis(1-methyl-1,4,7-triazacyclonon-1-yl)-1,10-phenanthroline (L4), and alpha,alpha'-bis(1,4,7-triazacyclonon-1-yl)-m-xylene (L5). The titration of these ligands with Zn(NO(3))(2) was monitored by (1)H NMR. Each ligand was found to bind two Zn(II) ions with a very high affinity at near neutral pH under conditions of millimolar ligand and 2 equiv of Zn(NO(3))(2). In contrast, a stable mononuclear complex was formed in solutions containing 5.0 mM L2OH and 1 equiv of Zn(NO(3))(2). (1)H and (13)C NMR spectral data are consistent with formation of a highly symmetric mononuclear complex Zn(L2OH) in which a Zn(II) ion is sandwiched between two triazacyclononane units. The second-order rate constant k(Zn) for the cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP) at pH 7.6 and 25 degrees C catalyzed by Zn(2)(L2O) is 120-fold larger than that for the reaction catalyzed by the closely related mononuclear complex Zn(L1) (L1 = 1,4,7-triazacyclononane). By comparison, the observation that the values of k(Zn) determined under similar reaction conditions for cleavage of HPNP catalyzed by the other Zn(II) dinuclear complexes are only 3-5-fold larger than values of k(Zn) for catalysis by Zn(L1) provides strong evidence that the two Zn(II) cations in Zn(2)(L2O) act cooperatively in the stabilization of the transition state for cleavage of HPNP. The extent of cleavage of an oligoribonucleotide by Zn(L1), Zn(2)(L5), and Zn(2)(L2O) at pH 7.5 and 37 degrees C after 24 h incubation is 4,10, and 90%. The rationale for the observed differences in catalytic activity of these dinuclear Zn(II) complexes is discussed in terms of the mechanism of RNA cleavage and the structure and speciation of these complexes in solution.     

DNA cleavage by the photocontrolled cooperation of Zn(II) centers in an azobenzene-linked dizinc complex

We synthesized a new photoactive dinuclear zinc(II) complex by linking two zinc centers with a ligand containing an azobenzene chromophore and investigated the DNA cleavage activities of its trans and cis forms. The trans structure of the dinuclear zinc complex was determined by X-ray crystallography, where each zinc center is situated in an octahedral coordination environment comprised of three nitrogen atoms from the ligand and three oxygen atoms from two nitrate ions. The dinuclear zinc complex containing the azobenzene chromophore was photoisomerizable between the trans and cis forms. The binding affinities of the trans and cis complexes with calf thymus (CT)-DNA were similar. Although the DNA cleavage activity of the trans complex was negligible, the cis complex was able to cleave DNA. We attribute the efficient activity of the cis complex to the cooperation of the two closely located zinc centers and the inactivity of the trans complex to the two metal centers positioned far away from each other. The DNA cleavage activity of the cis complex exhibited a pH-dependent bell-shaped profile, which has been observed in the hydrolytic cleavage of DNA by zinc complexes. The DNA cleavage activity was not inhibited by a major groove binder, methyl green, but decreased significantly by a minor groove binder, 4',6-diamidino-2-phenylindole, indicating that the dinuclear zinc complex binds to the minor groove of DNA. The present work shows the importance of the cooperation of two zinc ions for hydrolytic DNA cleavage, which can be photoregulated by linking the two metal centers with a photoisomerizable spacer, such as an azobenzene chromophore.     

Synthesis,crystal structure,and DNA cleavage activity of a dinuclear nickel(II) complex with a macrocyclic ligand

A new Ni(II) complex, namely [Ni₂(OAc)L]·ClO₄·H₂O, was synthesized by [2 + 2] cyclo-condensation between 2,6-diformyl-4-methylphenol and N,N-bis(3-aminopropyl)-4-methoxybenzylamine (amba) in the presence of nickel(II) and characterized by spectroscopy, elemental analysis, and X-ray single crystal diffraction. The interactions of the complex with DNA have been measured by spectroscopy and viscosity measurements. Absorption spectroscopic investigation reveals intercalative binding of the Ni(II) complex with DNA, with a binding constant of 2.6 × 10⁴ M⁻¹. Fluorescence spectroscopy shows that the Ni(II) complex can displace ethidium bromide and bind to DNA, with a quenching constant of 7.57 × 10³ M⁻¹. The appearance of increased CD bands near 245 and 275 nm gives evidence for effective complex DNA binding. The agarose gel electrophoresis studies show that the complex displays effective DNA cleavage activity in the absence of any external agents.     

The dinuclear Zn(II) complex catalyzed cyclization of a series of 2-hydroxypropyl aryl phosphate RNA models: progressive change in mechanism from rate-limiting P-O bond cleavage to substrate binding

A methoxide-bridged dinuclear Zn(II) complex of 1,3-[N,N'-bis(1,5,9-triazacyclododecane)]propane (1-Zn(II)2:(-OCH3)) was prepared, and its catalysis of the cyclization of a series of 2-hydroxypropyl aryl phosphates (4a-g) was investigated in methanol at pH 9.8, T = 25degreesC by stopped-flow spectrophotometry. An X-ray diffraction structure of the hydroxide analogue of 1-Zn(II)2:(-OCH3), namely 1-Zn(II)2:(-OH), reveals that each of the Zn(II) ions is coordinated by the three N's of the triazacyclododecane units and a bridging hydroxide. The cyclizations of substrates 4a-g reveal a progressive change in the observed kinetics from Michaelis-Menten saturation kinetics for the poorer substrates (4-OCH3 (4g); 4-H (4f); 3-OCH3 (4e); 4-Cl (4d); 3-NO2, (4c)) to second-order kinetics (linear in 1-Zn(II)2:(-OCH3)) for the better substrates (4-NO2,3-CH3 (4b); 4-NO2, (4a)). The data are analyzed in terms of a multistep process whereby a first formed complex rearranges to a reactive complex with a doubly activated phosphate coordinated to both metal ions. The kinetic behavior of the series is analyzed in terms of change in rate-limiting step for the catalyzed reaction whereby the rate-limiting step for the poorer substrates (4g-c) is the chemical step of cyclization of the substrate, while for the better substrates (4b,a) the rate-limiting step is binding. The catalysis of the cyclization of these substrates is extremely efficient. The kcat/KM values for the catalyzed reactions range from 2.75 x 10(5) to 2.3 x 10(4) M-1 s-1, providing an acceleration of 1 x 10(8) to 4 x 10(9) relative to the methoxide reaction (k2OCH3, which ranges from 2.6 x 10(-3) to 5.9 x 10(-6) M-1 s-1 for 4a-g). At a pH of 9.8 where the catalyst is maximally active, the acceleration for the substrates ranges from (1 - 4) x 10(12) relative to the background reaction at the same pH. Detailed energetics calculations show that the transition state for the catalyzed reaction comprising 1-Zn(II)2, methoxide, and 4 is stabilized by about -21 to -23 kcal/mol relative to the transition state for the methoxide reaction. The pronounced catalytic activity is attributed to a synergism between a positively charged catalyst that has high affinity for the substrate and for the transition state for cyclization, and a medium effect involving a reduced polarity/dielectric constant that complements a reaction where an oppositely charged reactant and catalyst experience charge dispersal in the transition state.     

DNA-binding and cleavage studies of a dinuclear copper(II) complex with a 26-membered hexaazamacrocycle

The complex, [Cu₂LCl₂]Cl₂ · 3H₂O, where L = the macrocyclic ligand bis-p-xylylBISDIEN Schiff base, has been prepared and characterized by elemental analysis, i.r. and mass spectra. The binding of the complex with calf thymus DNA has been investigated using absorption spectroscopy, cyclic voltammetry, fluorescence spectroscopy and viscosity measurements. The results suggest that the complex can bind to CT DNA by intercalation via the aromatic ring on the macrocycle into the base pairs of DNA. The complex exhibits efficient nuclease activity.     

Physical and kinetic analysis of the cooperative role of metal ions in catalysis of phosphodiester cleavage by a dinuclear Zn(II) complex

A dinuclear metal ion complex Zn(2)()(L2O) and its mononuclear analogue Zn(L1OH) were synthesized and studied as catalysts of the cleavage of the phosphate diester 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP). X-ray crystal structure data, potentiometric titrations, and (1)H NMR spectra obtained over a wide range of pH values provide strong evidence that the alcohol linker in the complex Zn(2)()(L2O) is ionized below pH 6.0, while the alcohol group in the complex Zn(L1OH) remains protonated even at high pH. The ionizations observed at high pH correspond to the formation of the monohydroxo complexes, Zn(2)(L2O)(OH) and Zn(L1OH)(OH), with pK(a)'s of 8.0 and 9.2, respectively. The pH-rate profiles of second-order rate constants for metal-ion complex-catalyzed cleavage of HPNP are reported. These show downward curvature centered at the pK(a)'s for the respective zinc-bound waters, and limiting second-order rate constants at high pH of k(c) = 0.71 M(-)(1) s(-)(1) for Zn(2)()(L2O) and 0.061 M(-)(1) s(-)(1) for Zn(L1OH). The larger catalytic activity of Zn(2)()(L2O) compared with Zn(L1OH) is due to the cooperative role of the metal ions in facilitating the formation of the ionized zinc-bound water at close to neutral pH and in providing additional stabilization of the rate-limiting transition state for phosphodiester cleavage. Zn(2)()(L2O) complex (1 M) at pH 7.6 stabilizes the transition state for the uncatalyzed reaction by 9.3 kcal/mol. Assuming that the dissociation constant determined for a diethyl phosphate inhibitor is similar to that for substrate, then ca. 2.4 kcal/mol of these stabilizing interactions are expressed in the ground-state Michaelis complex, while the bulk of these interactions are only expressed as the reaction approaches the transition state for phosphodiester cleavage.     

DFT study of the asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex

We report the mechanism of asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex using density functional theory. The experimentally proposed catalytic cycle is validated, in which the first step is the deprotonation of nitromethane by the ethyl anion of the catalyst, subsequently a C? C bond formation step, and then the protonation of the resulting alkoxide. Three mechanistic scenarios (differing in binding modes) have been considered for the C? C bond formation step. The origin of the enantioselectivity is discussed. Our calculations supported that the S configurations are the major products, which is in agreement with the experimental observations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Interaction of rac-[Cu(diimine)3]2+ and rac-[Zn(diimine)3]2+ complexes with CT DNA: effect of fluxional Cu(II) geometry on DNA binding, ligand-promoted exciton coupling and prominent DNA cleavage

The complexes [Cu(phen)(3)](ClO(4))(2) 1, [Cu(5,6-dmp)(3)](ClO(4))(2) 2, [Cu(dpq)(3)](ClO(4))(2) 3, [Zn(phen)(3)](ClO(4))(2) 4, [Zn(5,6-dmp)(3)](ClO(4))(2) 5 and [Zn(dpq)(3)](ClO(4))(2) 6, where phen = 1,10-phenanthroline, 5,6-dmp = 5,6-dimethyl-1,10-phenanthroline and dpq = dipyrido[3,2-d:2',3'-f]quinoxaline, have been isolated, characterized and their interaction with calf thymus DNA studied by using a host of physical methods. The X-ray crystal structures of rac-[Cu(5,6-dmp)(3)](ClO(4))(2) and rac-[Zn(5,6-dmp)(3)](ClO(4))(2) have been determined. While 2 possesses a regular elongated octahedral coordination geometry (REO), 5 possesses a distorted octahedral geometry. Absorption spectral titrations of the Cu(II) complexes with CT DNA reveal that the red-shift (12 nm) and DNA binding affinity of 3 (K(b), 7.5 x 10(4) M(-1)) are higher than those of 1 (red-shift, 6 nm; K(b), 9.6 x 10(3) M(-1)) indicating that the partial insertion of the extended phen ring of dpq ligand in between the DNA base pairs is deeper than that of phen ring. Also, 2 with a fluxional Cu(II) geometry interacts with DNA (K(b), 3.8 x 10(4) M(-1)) more strongly than 1 suggesting that the hydrophobic forces of interaction of 5,6 methyl groups on the phen ring is more pronounced than the partial intercalation of phen ring in the latter with a static geometry. The DNA binding affinity of 1 is lower than that of its Zn(ii) analogue 4, and, interestingly, the DNA binding affinity 2 of with a fluxional geometry is higher than that of its Zn(II) analogue 5 with a spherical geometry. It is remarkable that upon binding to DNA 3 shows an increase in viscosity higher than that the intercalator EthBr does, which is consistent with the above DNA binding affinities. The CD spectra show only one induced CD band on the characteristic positive band of CT DNA upon interaction with the phen (1,4) and dpq (3,6) complexes. In contrast, the 5,6-dmp complexes 2 and 5 bound to CT DNA show exciton-coupled biphasic CD signals with 2 showing CD signals more intense than 5. The Delta-enantiomer of rac-[Cu(5,6-dmp)(3)](2+) 2 binds specifically to the right-handed B-form of CT DNA at lower ionic strength (0.05 M NaCl) while the Lambda-enantiomer binds specifically to the left-handed Z-form of CT DNA generated by treating the B-form with 5 M NaCl. The complex 2 is stabilized in the higher oxidation state of Cu(II) more than its phen analogue 1 upon binding to DNA suggesting the involvement of electrostatic forces in DNA interaction of the former. In contrast, 3 bound to DNA is stabilized as Cu(I) rather than the Cu(II) oxidation state due to partial intercalative interaction of the dpq ligand. The efficiencies of the complexes to oxidatively cleave pUC19 DNA vary in the order, 3> 1 > 2 with 3 effecting 100% cleavage even at 10 microM complex concentration. However, interestingly, this order is reversed when the DNA cleavage is performed using H(2)O(2) as an activator and the highest cleavage efficiency of 2 is ascribed to its electrostatic interaction with the exterior phosphates of DNA.     

Synthesis, crystal structure, and DNA interaction and cleavage studies of a novel dinuclear Cu(II) complex with 3-indolylacetic acid

A novel dinuclear Cu(II) complex [Cu₂(C₁₀H₈NO₂)₄(CH₃OH)₂] · 2CH₃OH (I), where C₁₀H₈NO₂ is anion of 3-indolylacetic acid, was synthesized and characterized by elemental analysis, IR spectroscopy, ¹H NMR and single crystal X-ray diffraction. X-ray crystallography shows that Cu²⁺ ion is six-coordinated, embedded in a distorted octahedral center. Each Cu²⁺ ion is coordinated with four carboxylic oxygen atoms from four ligands, one oxygen atom from methanol and the other Cu²⁺ ion. Each ligand links two Cu²⁺ ions through carboxylic oxygen atoms, forming a dinuclear Cu(II) complex. The complex forms a two-dimensional layer structure through N-H??Oⁱ intermolecular hydrogen bonds. The interaction of complex I with calf-thymus DNA (CT-DNA) has been explored by electronic absorption spectroscopy, EB (ethidium bromide) displacement experiments, salt effect, and viscosity measurements. All the results indicate that the complex binds to DNA in a partial intercalative mode. Moreover, agarose gel electrophoresis assay demonstrates that the complex possesses the ability to cleave pBR322 plasmid DNA.     

Inducement and stabilization of G-quadruplex DNA by a thiophene-containing dinuclear ruthenium(II) complex

G-quadruplex structures are attractive targets for the development of anticancer drugs, as their formation in human telomere could impair telomerase activity, thus inducing apoptosis in cancer cells. In this work, a thiophene-containing dinuclear ruthenium(II) complex, [Ru₂(bpy)₄(H₂bipt)]⁴⁺ {bpy = 2,2′-bipyridine, H₂bipt = 2,5-bis[1,10]phenanthrolin[4,5-f]-(imidazol-2-yl)thiophene}, was prepared and the interaction between the complex and human telomeric DNA oligomers 5′-G₃(T₂AG₃)₃-3′ (HTG21) has been investigated by UV-Vis, fluorescence and circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assay, polymerase chain reaction (PCR) stop assay, fluorescent intercalator displacement (FID) titrations, Job plot and color reaction studies. The results indicate that the complex can well induce and stabilize the formation of antiparallel G-quadruplex of telomeric DNA in the presence or absence of metal cations, and the ΔT_m value of the G-quadruplex DNA treated with the complex was obtained to be 12.8 °C even at levels of 50-fold molar of duplex DNA (calf-thymus DNA), suggesting that the complex exhibits higher G-quadruplex DNA selectivity over duplex DNA. The complex shows high interaction ability with G-quadruplex DNA at (1.17 ± 0.12) × 10⁷ M^?1 binding affinity using a 2:1 [complex]/[quadruplex] binding mode ratio. A novel visual method has been developed here for making a distinction between G-quadruplex DNA and duplex DNA by our ruthenium complex binding hemin to form the hemin-G-quadruplex DNAzyme.     

Hydrolytic cleavage of DNA by a ruthenium(II) polypyridyl complex

The complex [Ru(bpy)2(BPG)]Cl2 (1) containing hydrogen-bond donor (N-H atoms) and acceptor (O atoms) groups mediates hydrolytic cleavage of plasmid pBR322 DNA in an enzyme-like manner. The kinetic aspects of DNA cleavage under pseudo- and true-Michaelis-Menten conditions are detailed.     

Enzyme-like acceleration for the hydrolysis of a DNA model promoted by a dinuclear Zn(II) catalyst in dilute aqueous ethanol

The rates and products of cleavage of methyl (2-chloro-4-nitrophenyl) phosphate (2) promoted by a dinuclear Zn(II) complex (3) of 1,3-bis-N,N'(1,5,9-triazacyclododecyl)propane along with 1 equiv of ethoxide were investigated in ethanol solution containing small amounts of water (8 mM or=1.6 x 10(17) times relative to the background hydroxide reaction, suggesting that complex 3 promotes the hydrolysis at least 1000 times more effectively than ethanolysis.     

Supramolecular assembly and DNA cleavage activity of a nickel(II) complex

A new mononuclear nickel(II) complex, [NiL₂] (HL = ((2-(5-fluoro-2-hydroxybenzyl)(2-(imidazole-2-yl)ethyl))imine), has been synthesized and characterized by IR, UV–vis and X-ray diffraction technique. The X-ray crystal structure of the complex shows that the coordination environment around Ni(II) ion is an approximate octahedron. Each molecule connects with four adjacent neighbors through strong hydrogen bonding interactions (N–H···O, d(N–O) = 2.687 Å and ∠N–H···O = 158.3(1)°), forming a supramolecular network. The interaction of the complex with DNA was monitored using agarose gel electrophoresis. The results show that the complex has DNA cleavage activity. The cyclic voltammogram shows one pair of anodic and cathodic peaks with E_1/2 = ?1.06 V, assigned to the Ni(II)/Ni(I) couple.