Nucleic Acid and Phosphoester Hydrolytic Cleavage Catalysed by Aza-Crown Ether Metal Complexes as Synthetic Nucleases

Synthesis, characterization and computational investigation of the phosphatase activity of a dinuclear Zinc(II) complex containing a new heptadentate asymmetric ligand

We report the synthesis of a new asymmetric heptadentate ligand based on the 1,3-diaminopropan-2-ol backbone. The ligand 3-[[3-(bis-pyridin-2-ylmethyl-amino)-2-hydroxy-propyl]-(2-carbamoyl-ethyl)-amino]-propionamide (HL1) contains two amide and two pyridine groups attached to the 1,3-diaminopropan-2-ol core. Reaction between HL1 and Zn(ClO₄)₂.6H₂O resulted in the formation of the dinuclear [Zn₂(L1)(μ-OAc)](ClO₄)₂ complex, characterized by single crystal X-ray diffraction, ¹H, ¹³C and ¹⁵N NMR, ESI-(+)-MS, CHN elemental analysis as well as infrared spectroscopy. The phosphatase activity of the complex was studied in the pH range 6-11 employing pyridinium bis(2,4-dinitrophenyl)phosphate (py(BDNPP)) as substrate. The complex exhibited activity dependent on the pH, presenting an asymmetric bell shape profile with the highest activity at pH 9; at high pH ligand exchange is rate-limiting. The hydrolysis of BDNPP^- at pH 9 displayed behavior characteristic of Michaelis-Menten kinetics, with k_cat = 5.06 × 10^-3 min^-1 and K_m = 5.7 ± 1.0 mM. DFT calculations map out plausible reaction pathways and identify a terminal, Zn(II)-bound hydroxide as likely nucleophile.

Nuclease Activity of Diaza-Crown Ether Complexes of Cerium(III) with Different Functional Groups as Side Arms

Cerium(III) complexes of two ligands of a diaza-crown ether with different functional groups as side arms were synthesised and characterised. The catalytic ability of the cerium(III) complexes for pUC19 DNA cleavage was investigated and compared using agarose gel electrophoresis. The results indicate that the catalytic activity of the complex CeL2 [L2 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diacetamide] with two carbamoylmethyl groups is significantly higher than the complex CeL1 [L1 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diethanol] with two hydroxyethyl groups under the same conditions. The optimum catalytic concentrations of CeL1 and CeL2 were 7.69 × 10−5 and 3.08 × 10−5 mol L−1 respectively and excessively high concentrations of the complexes can reduce their catalytic efficiency due to the formation of inactive μ-hydroxo dimers. The optimum catalytic acidities of CeL1 and CeL2 were pH 7.0 and 7.5 respectively and excessively high pH of the reaction system can reduce the catalytic efficiency of the complexes due to the formation of cerium(III) hydroxide. DNA cleavage promoted by the two complexes takes place via the same hydrolytic pathway and so the activity difference of the two complexes is attributed to the stability of the complexes, rather than the catalytic mechanism.

Transition Metal Complexes of a Diaza-Crown Ether with two Carbamoylmethyl Substituents: Synthesis and Assessment as a Functional Nuclease

We report the synthesis, catalytic function and catalytic mechanism of two transition metal complexes (CuL, ZnL) of a diaza-crown ether with two acetylamino side arms [L = 2,2′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl)diacetamide] in the hydrolysis of DNA. Their nuclease functions on pUC19 DNA cleavage were investigated. The results indicated that the active species might be formed by the deprotonation of the water-coordinated molecules in the complex and the optimum pH is 8.0 for both CuL and ZnL. The catalytic activity of CuL is higher than that of ZnL in DNA hydrolytic cleavage due to the difference in the Lewis acidity of the central metal ions, which is contrary to the result with the Cu and Zn complexes of the parent ligand L0 (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane) as artificial nuclease. Comparison studies of DNA cleavage in the presence and absence of several oxygen scavengers showed that these complexes can promote DNA cleavage by a hydrolytic pathway. Our proposed mechanism suggests that the negative charge on the phosphorus oxygen atom of the substrate molecule is dispersed and the intermediate is formed and stabilised by hydrogen bonding between the DNA molecule and the acetylamino group of the complex.

Comparison of catalytic activities of new La (III) and Ce (III) complexes with different diaza-crown ether ligands for DNA hydrolytic cleavage

A new diaza-crown ether with double hydroxypropyl branches (L = 1,1'-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl)dipropan-2-ol) and its two lanthanide complexes (LaL and CeL) were synthesised and characterised. Their nuclease activities on pUC19 DNA cleavage were investigated using agarose gel electrophoresis, and pseudo-first-order rate constants kobs of 0.067 h–1 for LaL, 0.041 h–1 for CeL, 0.013 h–1 for LaL0, and 0.027 h–1 CeL0 were obtained (L0 = 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane). The results indicated that the CeL complex was more efficient than the LaL complex for DNA cleavage at low concentrations, but the LaL complex was more efficient than the CeL complex at high concentrations. Moreover, kinetic studies demonstrated that introducing hydroxypropyl side arms in the ring of the diaza-crown ether can improve the catalytic ability of the complexes in DNA cleavage, which may be due to the hydroxypropyl side arms enhancing the bonding interaction between the complex and the DNA molecule by hydrogen bonding. A hydrolytic mechanism for DNA cleavage was demonstrated by applying several oxygen scavengers to the DNA catalytic cleavage. A proposed mechanism for the DNA cleavage shows that the hydroxypropyl side groups can recognise and bind the phosphodiester bond of DNA by hydrogen bonding and electrostatic interaction.

Copper and zinc complexes of a diaza-crown ether as artificial nucleases for the efficient hydrolytic cleavage of DNA

Copper and zinc complexes of a diaza-crown ether, serving as artificial nucleases, exhibited high nuclease activities towards the hydrolytic cleavage of DNA.