Imposing a Three-Way Junction on DNA or Recognizing One: A Metal Triple Helicate Meets Double Helix

Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads

The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of Ag^I -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.

Binding-induced formation of DNA three-way junctions and its application to protein detection and DNA strand displacement

DNA three-way junctions (DNA TWJs) are important building blocks to construct DNA architectures and dynamic assemblies. We describe here a binding-induced DNA TWJ strategy that is able to convert protein bindings to the formation of DNA TWJ. The binding-induced DNA TWJ makes use of two DNA motifs each conjugated to an affinity ligand. The binding of two affinity ligands to the target molecule triggers assembly of the DNA motifs and initiates the subsequent DNA strand displacement, resulting in a binding-induced TWJ. Real-time fluorescence monitoring of the binding-induced TWJ enables detection of the specific protein targets. A detection limit of 2.8 ng/mL was achieved for prostate-specific antigen. The binding-induced TWJ approach compares favorably with the toehold-mediated DNA strand-displacement, the associative (combinative) toehold-mediated DNA strand-displacement, and the binding-induced DNA strand-displacement. Importantly, the binding-induced TWJ broadens the scope of dynamic DNA assemblies and provides a new strategy to design protein-responsive DNA devices and assemblies.

Metal ion as both a cofactor and a probe of metal-binding sites in a uranyl-specific DNAzyme: a uranyl photocleavage study

DNAzymes are known to bind metal ions specifically to carry out catalytic functions. Despite many studies since DNAzymes were discovered nearly two decades ago, the metal-binding sites in DNAzymes are not fully understood. Herein, we adopt uranyl photocleavage to probe specific uranyl-binding sites in the 39E DNAzyme with catalytically relevant concentrations of uranyl. The results indicate that uranyl binds between T23 and C25 in the bulge loop, G11 and T12 in the stem loop of the enzyme strand, as well as between T2.4 and G3 close to the cleavage site in the substrate strand. Control experiments using two 39E DNAzyme mutants revealed a different cleavage pattern of the mutated region. Another DNAzyme, the 8–17 DNAzyme, which has a similar secondary structure but shows no activity in the presence of uranyl, indicated a different uranyl-dependent photocleavage as well. In addition, a close correlation between the concentration-dependent photocleavage and enzymatic activities is also demonstrated. Together, these experiments suggest that uranyl photocleavage has been successfully used to probe catalytically relevant uranyl-binding sites in the 39E DNAzyme. As uranyl is the cofactor of the 39E DNAzyme as well as the probe, specific uranyl binding has now been identified without disruption of the structure.

Container molecules based on imine type ligands

This chapter will give a short overview about container molecules, their synthesis and possible applications. The main focus is on those which are based on imine type ligands. These containers can be used for example for guest exchange, gas separation, as chemical sensors or for the stabilisation of white phosphorus under water. The described cages have wide openings or tightly closed ones. For one cage the reversible opening and closing is also described.

A mechanistic approach for the DNA binding of chiral enantiomeric L- and D-tryptophan-derived metal complexes of 1,2-DACH: cleavage and antitumor activity

A new chiral series of potential antitumor metal-based complexes 1-3(a and b) of L- and D-tryptophan have been synthesized and thoroughly characterized. Both enantiomers of 1-3 bind DNA noncovalently via phosphate interaction with slight preference of metal center for covalent coordination to nucleobases. The K(b) values of L-enantiomer, however, possess higher propensity for DNA binding in comparison with the D-enantiomeric analogs. The relative trend in K(b) values is as follows: 2(a) > 2(b) > 3(a) > 1(a) > 3(b) > 1(b). These observations together with the findings of circular dichoric and fluorescence studies reveal maximal potential of L-enantiomeric form of copper complex to bind DNA, thereby exerting its therapeutic effect. The complex 2a exhibits a remarkable DNA cleavage activity with pBR322DNA in the presence of different activators such as H(2) O(2) , ascorbic acid, 3-mercaptopropionic acid, and glutathione, suggesting the involvement of active oxygen species for the DNA scission. In vitro anticancer activity of complexes 1-3(a) were screened against 14 different human carcinoma cell lines of different histological origin, and the results reveal that 2a shows significant antitumor activity in comparison with both 1a and 3a and is particularly selective for MIAPACA2 (pancreatic cancer cell line).

Palladium and platinum 3,5-diacetyl-1,2,4-triazol bis(thiosemicarbazones): Chemistry, cytotoxic activity and structure–activity relationships

The preparation of platinum(II) complexes derived from 3,5-diacetyl-1,2,4-triazol bis(4-phenylthiosemicarbazone) (H(5)L(1)), 3,5-diacetyl-1,2,4-triazol bis(thiosemicarbazone) (H(7)L(2)), 3,5-diacetyl-1,2,4-triazol bis(4-methylthiosemicarbazone) (H(5)L(3)) and 3,5-diacetyl-1,2,4-triazol bis(4-ethylthiosemicarbazone) (H(5)L(3)) is described. The new complexes [Pt(mu-H(3)L(1))](2), [Pt(mu-H(5)L(2))](2), [Pt(mu-H(3)L(3))](2) and [Pt(mu-H(3)L(4))](2) have been characterized by elemental analyses, fast atom bombardment mass spectrometry (FAB(+)) and spectroscopic studies. The crystal and molecular structure of compounds [Pt(mu-H(3)L(1))](2), parent ligand H(5)L(1) and [Pt(mu-H(3)L(3))](2) have been determined by single crystal X-ray diffraction. The ligands coordinate, in a dideprotonate form to the platinum ions in a new tridentate fashion (NNS) and S-brigding bonding modes. Thus the molecular units of the platinum complexes are stacked as dimers. The testing of the cytotoxic activity of the synthesized compounds together with their palladium analogues against human A2780 and A2780cisR epithelial ovarian carcinoma cells lines suggests that the compounds may be endowed with important antitumor properties since they show IC(50) values in a micromolar range similar to those of cisplatin. The structure and antitumor activity relationships of platinum and palladium complexes are also discussed.