DNA binding by a new metallointercalator that contains a proflavine group bearing a hanging chelating unit

The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.     

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding

Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand–G-quadruplex structure determination.     

Determinants for Tight and Selective Binding of a Medicinal Dicarbene Gold(I) Complex to a Telomeric DNA G‐Quadruplex: a Joint ESI MS and XRD Investigation

The dicarbene gold(I) complex [Au(9‐methylcaffein‐8‐ylidene)₂]BF₄ is an exceptional organometallic compound of profound interest as a prospective anticancer agent. This gold(I) complex was previously reported to be highly cytotoxic toward various cancer cell lines in vitro and behaves as a selective G‐quadruplex stabilizer. Interactions of the gold complex with various telomeric DNA models have been analyzed by a combined ESI MS and X‐ray diffraction (XRD) approach. ESI MS measurements confirmed formation of stable adducts between the intact gold(I) complex and Tel 23 DNA sequence. The crystal structure of the adduct formed between [Au(9‐methylcaffein‐8‐ylidene)₂]⁺ and Tel 23 DNA G‐quadruplex was solved. Tel 23 maintains a characteristic propeller conformation while binding three gold(I) dicarbene moieties at two distinct sites. Stacking interactions appear to drive noncovalent binding of the gold(I) complex. The structural basis for tight gold(I) complex/G‐quadruplex recognition and its selectivity are described.     

Exploring New Molecular Architectures for Anion Recognition: Synthesis and ATP Binding Properties of New Cyclam‐Based Ditopic Polyammonium Receptors.

Synthesis and characterization of three new polyamine receptors, composed of a cyclam unit (cyclam=1,4,8,11‐tetraazacyclotetradecane) linked by a 2,6‐dimethylpyridinyl spacer to the linear polyamines 1,4,8,11‐tetraazaundecane ( L1py ), 1,4,7‐triazaheptane ( L2py ), and to a quaternary ammonium group ( L3 py⁺ ), are reported. All receptors form highly charged polyammonium cations at neutral pH, suitable for anion recognition studies. ATP recognition was analyzed by using potentiometric, calorimetric, ¹H and ³¹P NMR measurements in aqueous solution. All receptors form 1:1 adducts with ATP in aqueous solution, stabilized by charge–charge and hydrogen‐bonding interactions between their ammonium groups and the anionic triphosphate chain of ATP. The binding ability of the three receptors for ATP increases in the order of L3 py⁺ < L2py < L1py . These adducts are stabilized by largely favourable entropic contributions, probably due to the large desolvation of the host and guest species upon complexation. The sequence observed for the binding affinity is explained in terms of the different ability of the three receptors to wrap around the phosphate chain of ATP.     

Selective binding and fluorescence sensing of diphosphate in H2O via Zn(2+)-induced allosteric regulation of the receptor structure

A terpyridine-based receptor featuring two [9]aneN(3) units is able to selectively bind and sense diphosphate over mono- and triphosphate in aqueous solution at pH 7, thanks to the conformational change of its structure induced by Zn(2+) coordination to the polypyridyl moiety.     

Iodine Activation of Coordinated White Phosphorus: Formation and Transformation of 1,3-Dihydride-2-iodidecyclotetraphosphane

Double stabilization: Previously unknown polyphosphorus compounds are obtained by activation of white phosphorus (P(4) ) coordinated between two CpRu(PPh(3) )(2) moieties with iodine, and subsequent hydrolysis. The polyphosphorus compounds (P(4) H(2) I, P(4) H(2) , P(3) H(5) ; see scheme, Cp=cyclopentadienyl) are all stabilized by coordination to two ruthenium centers.     

Basicity and coordination properties of a new phenanthroline-based bis-macrocyclic receptor

The synthesis and characterisation of the new macrocyclic ligand 6-methyl-2,6,10-triaza-[11]-12,25-phenathrolinophane (L1), which contains a triamine aliphatic chain linking the 2,9 positions of 1,10-phenanthroline and of its derivative L2, composed by two L1 moieties connected by an ethylenic bridge, are reported. Their basicity and coordination properties toward Cu(II), Zn(II), Cd(II), Pb(II) and Hg(II) have been studied by means of potentiometric and spectroscopic (UV-Vis, fluorescence emission) measurements in aqueous solutions. L1 forms 1:1 metal complexes in aqueous solutions, while L2 can give both mono- and dinuclear complexes. In the mononuclear L2 complexes the metal is sandwiched between the two cyclic moieties. The metal complexes with L1 and L2 do not display fluorescence emission, due to the presence of amine groups not involved in metal coordination. These amine groups can quench the excited fluorophore through an electron transfer process. The ability of the Zn(II) complexes with L1 and L2 to cleave the phosphate ester bond in the presence has been investigated by using bis(p-nitrophenyl)phosphate (BNPP) as substrate. The dinuclear complex with L2 shows a remarkable hydrolytic activity, due to the simultaneous presence within this complex of two metals and two hydrophobic units. In fact, the two Zn(II) act cooperatively in substrate binding, probably through a bridging interaction of the phosphate ester; the interaction is further reinforced by pi-stacking pairing and hydrophobic interactions between the phenanthroline unit(s) and the p-nitrophenyl groups of BNPP.     

Protonation and Zn(II) coordination by dipyridine-containing macrocycles with different molecular architecture. A case of pH-controlled metal jumping outside-inside the macrocyclic cavity

The synthesis of the macrocyclic ligand 4,4'-(2,5,8,11,14-pentaaza[15])-2,2'-bipyridylophane (L3), which contains a pentaamine chain linking the 4,4'-positions of a 2,2'-dipyridine moiety, is reported. Protonation and Zn(II) complexation by L3 and by macrocycle L2, containing the same pentaamine chain connecting the 6,6'-positions of 2,2'-dipyridine, were studied by means of potentiometric, UV-vis, and fluorescent emission measurements. While in L2 all the nitrogen donor atoms are convergent inside the macrocyclic cavity, in L3 the heteroaromatic nitrogen atoms are located outside. Both ligands form mono- and dinuclear Zn(II) complexes in aqueous solution. In the mononuclear Zn(II) complexes with L2, the metal is coordinated inside the macrocyclic cavity, bound to the heteroaromatic nitrogen donors and three amine groups of the aliphatic chain. As shown by the crystal structure of the [ZnL2](2+) complex, the two benzylic nitrogens are not coordinated and facile protonation of the complex takes place at slightly acidic pH values. Considering the mononuclear [ZnL3](2+) complex, the metal is encapsulated inside the cavity, not coordinated by the dipyridine unit. Protonation of the complex occurs on the aliphatic polyamine chain and gives rise to translocation of the metal outside the cavity, bound to the heteroaromatic nitrogens.     

Synthesis and coordination properties of highly preorganised polyamine macrocycles

Synthesis and characterisation of the new macrocyclic ligands L1‐L4 are reported. The ligands present one or two pentaamine moieties, each containing two piperazine rings, linked by benzene or anthracene spacers. Interaction of L1 with H⁺, Cu(II), Zn(II), Hg(II), and Pd(II) and of L3 with H⁺, and Cu(II) has been studied by potentiometric titrations in 0.15 mol dm^?3 NaCl aqueous solution at 298.1 ±0.1 K. The thermodynamic data suggest that in the metal complexes only three nitrogen donor atoms bind each metal ion. As a consequence of the low coordination number, these complexes are promising receptors for different molecules.     

X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG)

The first crystal structures of Berberine and Sanguinarine intercalated with a d(CGTACG)(2) DNA sequence were obtained by X-ray diffraction analysis at 2.3 ? resolution. Both drugs join the end of two "two-molecules" DNA units, stacked in a non-classic intercalation site formed by six bases. Sanguinarine interacts with d(CGTACG)(2) DNA in its iminium form.