Steric effects on the catalytic activities of zinc(II) complexes containing [12]aneN3 ligating units in the cleavage of the RNA and DNA model phosphates

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

Dipeptide interactions with Zn(II)-cyclen artificial model for molecular recognition

The Zn(II)-cyclen-dipeptide ternary systems (where cyclen is abbreviated as L and dipeptide is glycylglycine (HL(1)) or glycyl-(S)-alanine (HL(2))) were investigated by potentiometry applying both "out-of-cell" and direct titrations and by (1) H NMR spectroscopy. Especially, the (1)H NMR study was found to be very efficient to estimate speciation in the systems. The results obtained under full equilibria indicated two main species, [Zn(L)(HL(1,2))](2+) and [Zn(L)(L(1,2))](+), in both the systems. In the [Zn(L)(HL(1,2))](2+) complex, presence of carbonyl-carboxylate chelate was confirmed, and in the [Zn(L)(L(1,2))](+) species, the peptide coordination is re-organized to carbonyl-amine chelate or only terminal amino group is coordinated. Equilibrium constants describing [Zn(L)](2+)-dipeptide interaction are relatively low, log K = 3.4 for Gly-Gly and 4.1 for Gly-(S)-Ala, respectively. Nevertheless, the values are slightly higher than stability constants for interaction of Zn(II) with the dipeptides (i.e. [Zn(L(1,2))](+) species) where a chelate formation is expected. It indicates that interaction between Zn(II) ion in [Zn(L)](2+) and the dipeptides should be supported by some additional interactions. Potentiometry carried out under non-equilibrum condition showed different species where these additional stabilizing forces play more important role.

Mononuclear Cu(ii) and Zn(ii) complexes with a simple diamine ligand: synthesis, structure, phosphodiester binding and DNA cleavage studies

Mononuclear Cu(ii) and Zn(ii) complexes with simple 1,2-diaminocylohexane were synthesized. They interact with phosphodiesters and CT-DNA. Cu(ii) complex with ascorbate efficiently cleaves supercoiled DNA up to Form III at 25 µM under oxidative pathway.

Mono- and dinuclear metal complexes containing the 1,5,9-triazacyclododecane ([12]aneN3) unit and their interaction with DNA

It takes two to tango: Only the dinuclear but not the mononuclear metal complexes of triazacyclododecane ([12]aneN₃) were able to induce the Z-DNA of poly d(GC).