Double-strand hydrolysis of plasmid DNA by dicerium complexes at 37 degrees C

Synthetic artificial peptidases and nucleases using macromolecular catalytic systems

Effective artificial enzymes have been designed by adopting macromolecular systems for catalyst-substrate complexes. Artificial active sites comprising two or more organic functional groups were built on macromolecular backbones, leading to several types of organic artificial proteases. The activity of metal centers for peptide or DNA hydrolysis was greatly enhanced by attachment to polystyrene, leading to artificial metallopeptidases with substrate selectivity as well as artificial metallonucleases with high catalytic activity for double stranded DNA. A small artificial protease selective for a macromolecular target protein was synthesized. Target-specific artificial proteases can be used as protein-cleaving catalytic drugs.

Monte Carlo simulation of a 1,4,7,10-tetraazacyclododecane/lithium complex in aqueous solution

Monte Carlo simulations have been carried out for the system consisting of a 1,4,7,10-tetraazacyclododecane (cyclen)-lithium complex in 201 water molecules. The volume of the periodic cube was calculated using the experimental density of pure water at 298 K and 1 atm of 1 g.cm(-)(3), plus additional space occupied by the complex. The geometry of the complex is the alternated form, where the ion is located at the center of the cyclen. The complex-water interaction was represented by the cyclen-water and lithium-water pair potentials, both of which were developed on the basis of ab initio calculations. The results show two layers of solvation shells consisting of 2 and 6.9 water molecules. Two water molecules in the first solvation shell (O(1) and O(2)) bind directly to the ion in which the ion-oxygen distance is 2.38 A, the dipole vector points to the ion, and rotation takes place around the ion-oxygen axis. In the next layer, 4 water molecules coordinate simultaneously to the first 2 water molecules in the first shell and the NH functional groups of cyclen. The remaining 2.9 water molecules in the second layer are also coordinated to be in the first half-hydration shell of O(1) and O(2).

Sequence-selective DNA cleavage by a chimeric metallopeptide

A chimeric metallopeptide derived from the sequences of two structurally superimposable motifs was designed as an artificial nuclease. Both DNA recognition and nuclease activity have been incorporated into a small peptide sequence. P3W, a 33-mer peptide comprising helices alpha2 and alpha3 from the engrailed homeodomain and the consensus EF-hand Ca-binding loop binds one equivalent of lanthanides or calcium and folds upon metal binding. The conditional formation constants (in the presence of 50 mM Tris) of P3W for Eu(III) (K(a) = (2.1 +/- 0.1) x 10(5) M(-1)) and Ce(IV) (K(a) = (2.6 +/- 0.1) x 10(5) M(-1)) are typical of isolated EF-hand peptides. Circular dichroism studies show that 1:1 CeP3W is 26% alpha-helical and EuP3W is up to 40% alpha-helical in the presence of excess metal. The predicted helicity of the folded peptide based on helix length and end effects is about 50%, showing the metallopeptides are significantly folded. EuP3W has considerably more secondary structure than our previously reported chimeras (Welch, J. T.; Sirish, M.; Lindstrom, K. M.; Franklin, S. J. Inorg. Chem. 2001, 40, 1982-1984). Eu(III)P3W and Ce(IV)P3W nick supercoiled DNA at pH 6.9, although EuP3W is more active at pH 8. CeP3W cleaves linearized, duplex DNA as well as supercoiled plasmid. The cleavage of a 5'-(32)P-labeled 121-mer DNA fragment was followed by polyacrylamide gel electrophoresis. The cleavage products are 3'-OPO(3) termini exclusively, suggesting a regioselective or multistep mechanism. In contrast, uncomplexed Ce(IV) and Eu(III) ions produce both 3'-OPO(3) and 3'-OH, and no evidence of 4'-oxidative cleavage termini with either metal. The complementary 3'-(32)P-labeled oligonucleotide experiment also showed both 5'-OPO(3) and 5'-OH termini were produced by the free ions, whereas CeP3W produces only 5'-OPO(3) termini. In addition to apparent regioselectivity, the metallopeptides cut DNA with modest sequence discrimination, which suggests that the HTH motif binds DNA as a folded domain and thus cleaves selected sequences. The de novo artificial nuclease LnP3W represents the first small, underivatized peptide that is both active as a nuclease and sequence selective.

Hydrolysis of phosphodiesters by diiron complexes: design of nonequivalent iron sites in purple acid phosphatase models

New mu-oxo-diferric complexes have been designed for hydrolysis of phosphodiesters. To mimic the diiron active site of purple acid phosphatase, a combinatorial method has been used to select complexes containing two distinct iron coordination spheres. The introduction of a bidentate ligand, a substituted phenanthroline (L) into complex 1, [Fe2O(bipy)4(OH2)2](NO3)4, generates in solution the complex [Fe2O(bipy)3(L)(OH2)2](NO3)4 as shown by ESI/MS and 1H NMR studies. The latter complex was found to be 20-fold more active than complex 1. On the basis of kinetic studies, we demonstrated that the complex [Fe2O(bipy)3(L)(OH)(OH2)](NO3)3 was the active species and the reaction proceeded through the formation of a ternary complex in which one iron binds a hydroxide and the second, the substrate. At nonsaturating concentrations of the substrate, the increased activity with increased methyl substituents in L was due to an increased affinity of the complex for the substrate. The activity of [Fe2O(bipy)3(33'44'Me2-Phen)(OH2)2](NO3)4 [33'44'Me2Phen = 3,3',4,4'-dimethyl-1,10-phenanthroline] was found to be comparable to that reported for Co(III) or Ce(IV) complexes.

Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex

A new strategy for site-selective DNA hydrolysis, which takes advantage of the difference in reactivity between the phosphodiester linkages at the target site and the others, is presented. As the molecular scissors, homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex is used without being bound to any sequence-recognizing moiety. When a gap structure is formed at the target site by using two short oligonucleotides and the composite is treated with the Ce(IV)/EDTA complex at pH 7.0 and 37 degrees C, the gap site in the substrate DNA is preferentially hydrolyzed over the double-stranded portion of the DNA. Site-selective DNA scission is also achieved by forming a bulge structure at the target site with the use of the appropriate oligonucleotide. These site-selective scissions are based on the following two factors: (i) the phosphodiester linkages in a single-stranded DNA are far more susceptible to the hydrolysis by the Ce(IV) complex than are the linkages in double-stranded DNA, and (ii) the phosphodiester linkages in the bulge sites are still more reactive than those in single-stranded DNA. In both cases, the addition of spermine significantly accelerates the scission.

Hydrolytically active Eu(III) and Ce(IV) EF-hand peptides

A chimeric peptide (P4) has been designed to incorporate an EF-hand metal-binding loop into the context of the helix-turn-helix DNA binding motif of the engrailed homeodomain. This construct binds lanthanides, and in the presence of these metals, promotes the cleavage of supercoiled DNA and model phosphate esters (bisnitrophenyl phosphate). P4 binds lanthanides with moderate affinities (Eu(III), log K(a)=4.85; and Ce(IV), log K(a)=5.23). The structure of P4 is enhanced by metal binding, but the increase in secondary structure observed by CD is small, and suggests the metallopeptide is also quite flexible. Despite this flexibility, the efficient cleavage of DNA at low concentrations is dependent on the metallopeptide, and not on peptide or metal alone. This enhanced reactivity suggests the designed DNA-binding EF-hand peptides deliver the metal to the DNA for catalysis, even without rigid secondary structure.

Triisopropyltriazacyclononane copper(II): an efficient phosphodiester hydrolysis catalyst and DNA cleavage agent

A 6000-fold rate enhancement has been observed for the hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) in the presence of 0.2 mM Cu(i-Pr(3)[9]aneN(3))(2+) at pH 9.2 and 50 degrees C. In a direct comparison, the rate of hydrolysis of BNPP is accelerated at least 60-fold over the previously reported catalyst Cu([9]aneN(3))(2+). As observed for Cu([9]aneN(3))(2+), hydrolysis is selective for diesters over monoesters. Hydrolysis of BNPP by Cu(i-Pr(3)[9]aneN(3))(2+) is catalytic, exhibiting both rate enhancement and turnover. The reaction is inhibited by both p-nitrophenyl phosphate and inorganic phosphate. The reaction is first-order in substrate and half-order in metal complex, with a k(1.5) of 0.060 +/- 0.004 M(-1/2) s(-1) at 50 degrees C. The temperature dependence of the rate constant results in a calculated activation enthalpy (Delta H(++) of 51 +/- 2 kJ mol(-1) and activation entropy (Delta S(++)) of -110 +/- 6 J mol(-1) K(-1). The kinetic pK(a) of 7.8 +/- 0.2 is close to the thermodynamic pK(a) of 7.9 +/- 0.2, consistent with deprotonation of a coordinated water molecule in the active form of the catalyst. The active catalyst [Cu(i-Pr(3)[9]aneN(3))(OH)(OH(2))](+) is in equilibrium with an inactive dimer, and the formation constant for this dimer is between 216 and 1394 M(-1) at pH 9.2 and 50 degrees C. Temperature dependence of the dimer formation constant K(f) indicates an endothermic enthalpy of formation for the dimer of 27 +/- 3 kJ mol(-1). The time course of anaerobic DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is presented over a wide range of concentrations at pH 7.8 at 50 degrees C. The concentration dependence of DNA cleavage by Cu([9]aneN(3))(2+) and Cu(i-Pr(3)[9]aneN(3))(2+) reveals a maximum cleavage efficiency at sub-micromolar concentrations of cleavage agent. DNA cleavage by Cu(i-Pr(3)[9]aneN(3))(2+) is twice as efficient at pH 7.8 as at pH 7.2.

DNA hydrolysis and oxidative cleavage by metal-binding peptides tethered to rhodium intercalators

With the goal of developing artificial nucleases for DNA hydrolysis, metal-coordinating peptides have been tethered to a DNA-intercalating rhodium complex to deliver metal ions to the sugar-phosphate backbone. The intercalator, [Rh(phi)(2)bpy']Cl(3) [phi = 9,10-phenanthrenequinone diimine; bpy' = 4-(butyric acid)-4'-methyl-2,2'-bipyridine], provides DNA binding affinity, and a metal-binding peptide contributes reactivity. This strategy for DNA hydrolysis is a general one, and zinc(II)-promoted cleavage has been demonstrated for two widely different tethered metallopeptides. An intercalator coupled with a de novo-designed alpha helix containing two histidine residues has been demonstrated to cleave both supercoiled plasmid and linear DNA substrates. Mutation of this peptide confirms that the two histidine residues are essential for Zn(2+) binding and cleavage. Zinc(II)-promoted cleavage of supercoiled plasmid has also been demonstrated with an intercalator-peptide conjugate containing acidic residues and modeled after the active site of the BamHI endonuclease. Other redox-active metals, such as copper, have been delivered to DNA with our intercalator-peptide conjugates to effect oxidative chemistry. Copper cleavage experiments and photocleavage experiments with [Rh(phi)(2)bpy'](3+) complement the hydrolysis studies and provide structural information about the interactions between the tethered metallopeptides and DNA. Variation of the rhodium intercalator was also explored, but with a mismatch-specific intercalator, no site-specific hydrolysis was found. These experiments, in which the peptide, the metal cation, and the intercalator components of the conjugate are each varied, illustrate some of the issues involved in creating an artificial nuclease with DNA intercalators and metallopeptides.

Hydrolysis of linear DNA duplex catalyzed by Co(III) complex of cyclen attached to polystyrene

To design artificial restriction enzymes, synthetic catalytic centers that effectively hydrolyze linear double-stranded polydeoxyribonucleotides are needed. The Co(III) complex of cyclen (CoCyc) attached to polystyrene derivatives hydrolyzes linearized pUC18 DNA with half-lives as short as 30 min at 25 degrees C. The catalytic activity of CoCyc is enhanced by >150 times on attachment to the resin.

Chemical nucleases

Substantial progress is being made in the synthesis of functional mimics of metallonuclease enzymes, although a comparison with enzyme-promoted rates of reaction shows considerable room for future improvement. Improved ligand design allows facile substrate binding to metal ion catalysts, while maintaining the stability of the metal complex. The execution of double-strand cleavage of DNA under hydrolytic conditions has been reported and new levels of activity achieved. Finally, considerable progress has been made in identifying the molecular determinants for site-selective cleavage of RNA (in particular) and the design of ligands to achieve targeted recognition and cleavage.

Hydrolysis of plasmid DNA catalyzed by Co(III) complex of cyclen attached to polystyrene

Reactivity of the Co(III) complex of cyclen (CoCyc) in the hydrolytic cleavage of supercoiled pUC18 DNA leading to the formation of the corresponding open circular form was enhanced by >200 times upon attachment of CoCyc to cross-linked polystyrenes. Thus, half-lives as short as 40 min were achieved by the resin-based CoCyc in cleavage of the supercoiled DNA at 4 degrees C.