Selective recognition of consecutive G sequence in double-stranded DNA by a zinc(II)-macrocyclic tetraamine complex appended with an anthraquinone

Hydrogen bonding and protonation effects in amino acids' anthraquinone derivatives - Spectroscopic and electrochemical studies

Six novel amino acid chromophores were synthesized and their spectroscopic, acid-base, and electrochemical properties are discussed in this work. In studied compounds, selected amino acid residues (l-Aspartic acid, l-Glutamic acid, l-Glutamine, l-Histidine, l-Lysine, l-Arginine) are attached to the 1-(piperazine) 9,10-anthraquinone skeleton via the amide bond between the carboxyl group of amino acid and nitrogen atom of the piperazine ring. All derivatives have been characterized using a variety of spectroscopic techniques (mass spectrometry, 1HNMR, UV-Vis, IR spectroscopy), acid-base (electrochemical and UV-Vis) titrations, and cyclic voltammetry methods. Basing on observed experimental effects, supported by quantum chemical simulations, the structure-properties links were established. They are indicative of the specific interactions within and/or in-between amino acid side groups, which are prone to form both, intra- and intermolecular hydrogen bonds as well as electrostatic interactions with the anthraquinone system.

Interaction of safranal and picrocrocin with ctDNA and their preferential mechanisms of binding to GC- and AT-rich oligonucleotides

Saffron (Crocus sativus L.) shows different biological properties, some of which relate to its special components including safranal (deglycosylated picrocrocin). In our previous study on the mechanism of saffron functions, interaction of saffron carotenoids with DNA and oligonucleotides was reported. The present study aimed to investigate the interaction of safranal with calf thymus DNA (ctDNA), oligo(GC)15, and oligo(AT)15 in comparison with picrocrocin. Circular dichroism (CD) and fluorometric results show the nonintercalative/minor groove binding of the mentioned ligands to ctDNA. The CD plots indicate that picrocrocin interacts with DNA and oligonucleotides at lower concentrations than safranal does, which is accompanied by B- to C-DNA transition. At higher concentrations, it induces more conformational changes, that is, unstacking of DNA and oligonucleotides bases, the same as saffron carotenoids. However, similar results are obtained for safranal interaction with ctDNA (56% AT) and oligo(AT)15, but after adding safranal (with a free aldehyde group) to oligo(GC)15, the CD spectra show some changes (two positive and a displaced negative peaks) that are characteristics of triple-helix DNA. Thus, the mechanism for B- to H-DNA transition, due to the interaction of safranal with GC-rich sequences, is presented here.

Binding of [Pt(1C3)(dien)](2+) to the duplex DNA oligonucleotide 5'-d(TGGCCA)-3': the effect of an appended positive charge on the orientation and location of anthraquinone intercalation

The binding of a platinum intercalator complex [Pt(1C3)(dien)](2+) (1C3 = 1-[(3-aminopropyl)amino]-anthracene-9,10-dione, dien = 3-azapentane-1,5-diamine) to DNA and to the self-complementary oligonucleotide 5'-d(TGGCCA)-3' has been investigated by UV-visible spectrophotometry and 2D NMR spectroscopy, respectively. The uncomplexed anthraquinone, 1C3, has an apparent DNA binding constant of 1.4 x 10(4), similar to that of ethidium bromide. Addition of the coordinatively saturated {Pt(dien)} moiety increases the binding constant to 3.7 x 10(5) M(-1), showing the effect of the increased positive charge introduced by this moiety. Multiple binding modes are evident from the lack of isosbestic points in the titration spectra and the non-linear nature of the half-reciprocal plot used to calculate the binding constant. [Pt(1C3)(dien)](2+) forms a 2 : 1 adduct with 5'-d(TGGCCA)-3' and is shown by 2D NMR to intercalate primarily in the TG:CA base pairs at the ends of the oligonucleotide with the side chain and {Pt(dien)} situated in the minor groove.

Interaction of an Fe derivative of TMAP (Fe(TMAP)OAc) with DNA in comparison with free-base TMAP

We investigated the interaction of meso-tetrakis (N-para-methylanilium) porphyrin (TMAP) in its free base and Fe(II) form (Fe(TMAP)OAc) as a new derivative, with high molecular weight DNA at different ionic strengths, using various spectroscopic methods and microcalorimetry. The data obtained by spectrophotometery, circular dichroism (CD), fluorescence quenching and resonance light scattering (RLS) have demonstrated that TMAP association with DNA is via outside binding with self-stacking manner, which is accompanied with the "end-on" type complex formation in low ionic strength. However, in the case of Fe(TMAP)OAc, predominant mode of interaction is groove binding and after increasing in DNA concentration, unstable stacking-type aggregates are formed. In addition, isothermal titration calorimetric measurements have indicated the exothermic process of porphyrins binding to DNA, but the exothermisity in metal derivative of porphyrin is less than the free base. It confirmed the formation of a more organized aggregate of TMAP on DNA surface. Interactions of both porphyrins with DNA show high sensitivity to ionic strength. By addition of salt, the downfield CD signal of TMAP aggregates is shifted to a higher wavelength, which indicates some changes in the aggregates position. In the case of Fe(TMAP)OAc, addition of salt leads to changes in the mode of binding from groove binding to outside binding with self-stacking, which is accompanied with major changes in CD spectra, possibly indicating the formation of "face-on" type complex.

Cleavage of an RNA analog by Zn(II) macrocyclic catalysts appended with a methyl or an acridine group

Two macrocycles (1 and 2) are prepared that incorporate pendent groups in macrocycle 3 (3=1-oxa-4,7,10-triazacyclododecane) with the goal of studying the effect of these pendent groups on metal ion complexation, solution chemistry and catalysis. Zn(1) contains a macrocyclic ligand with a pendent acridine group and Zn(2) has an appended methyl group. Water ligand pK(a) values for Zn(1) (6.7) and Zn(2) (7.3) are lower than that of Zn(3) (7.7). Zn(II) complexes of 1 and 2 are studied as catalysts for the cleavage of 2-hydroxypropyl 4-nitrophenylphosphate (HpPNP), an RNA analog. Zn(2) has a lower catalytic activity over the pH range 7-10 for cleavage of HpPNP compared to the parent macrocyclic complex, Zn(3). In contrast, Zn(1) has a threefold larger rate constant at pH 7.0 compared to Zn(2), attributed to the presence of a catalytic species which has a protonated acridine amino group. The binding constant of 1.5mM at pH 8.0 for formation of the Zn(2)-uridine adduct is similar to that for Zn(3), suggesting that N-alkylation of the macrocyclic ligand does not interfere with binding of the Zn(II) complex to uridine groups. Binding of cytidine to Zn(2) was not detectable under similar conditions up to 25mM nucleoside. Binding experiments under similar conditions could not be carried out for adenosine or guanosine due to their low solubility.

The first synthesis of chiral PNA monomer-cyclen conjugates

A synthetic route to novel chiral PNA monomer-cyclen conjugates was described for the first time, the targeted products were obtained in high yields under mild reaction conditions. The preliminary results demonstrated that the uracil-PNA monomer-cyclen conjugates can rapidly bind Zn2+ in aqueous solution, and the structure of the Zn(II) complex was confirmed facilely by HRMS spectra, 1H NMR spectra and elemental analysis.

A new zinc(II) fluorophore 2-(9-anthrylmethylamino)ethyl-appended 1,4,7,10-tetraazacyclododecane

A new 2-(9-anthrylmethylamino)ethyl-appended cyclen, L(3) (1-(2-(9-anthrylmethylamino)ethyl)-1,4,7,10-tetraazacyclododecane) (cyclen = 1,4,7,10-tetraazacyclododecane), was synthesized and characterized for a new Zn(2+) chelation-enhanced fluorophore, in comparison with previously reported 9-anthrylmethylcyclen L(1) (1-(9-anthrylmethyl)-1,4,7,10-tetraazacyclododecane) and dansylamide cyclen L(2). L(3) showed protonation constants log K(a)(i)() of 10.57 +/- 0.02, 9.10 +/- 0.02, 7.15 +/- 0.02, <2, and <2. The log K(a3) value of 7.15 was assigned to the pendant 2-(9-anthrylmethylamino)ethyl on the basis of the pH-dependent (1)H NMR and fluorescence spectroscopic measurements. The potentiometric pH titration study indicated extremely stable 1:1 Zn(2+)-L(3) complexation with a stability constant log K(s)(ZnL(3)) (where K(s)(ZnL(3)) = [ZnL(3)]/[Zn(2+)][L(3)] (M(-)(1))) of 17.6 at 25 degrees C with I = 0.1 (NaNO(3)), which is translated into the much smaller apparent dissociation constant K(d) (=[Zn(2+)](free)[L(3)](free)/[ZnL(3)]) of 2 x 10(-)(11) M with respect to 5 x 10(-)(8) M for L(1) at pH 7.4. The quantum yield (Phi = 0.14) in the fluorescent emission of L(3) increased to Phi = 0.44 upon complexation with zinc(II) ion at pH 7.4 (excitation at 368 nm). The fluorescence of 5 microM L(3) at pH 7.4 linearly increased with a 0.1-5 microM concentration of zinc(II). By comparison, the fluorescent emission of the free ligand L(1) decreased upon binding to Zn(2+) (from Phi = 0.27 to Phi = 0.19) at pH 7.4 (excitation at 368 nm). The Zn(2+) complexation with L(3) occurred more rapidly (the second-order rate constant k(2) is 4.6 x 10(2) M(-)(1) s(-)(1)) at pH 7.4 than that with L(1) (k(2) = 5.6 x 10 M(-)(1) s(-)(1)) and L(2) (k(2) = 1.4 x 10(2) M(-)(1) s(-)(1)). With an additionally inserted ethylamine in the pendant group, the macrocyclic ligand L(3) is a more effective and practical zinc(II) fluorophore than L(1).

Highly selective binding of organometallic ruthenium ethylenediamine complexes to nucleic acids: novel recognition mechanisms

We have investigated the recognition of nucleic acid derivatives by organometallic ruthenium(II) arene anticancer complexes of the type [(eta(6)-arene)Ru(II)(en)X] where en = ethylenediamine, arene = biphenyl (Bip), tetrahydroanthracene (THA), dihydroanthracene (DHA), p-cymene (Cym) or benzene (Ben), X = Cl(-) or H(2)O using (1)H, (31)P and (15)N ((15)N-en) NMR spectroscopy. For mononucleosides, [(eta(6)-Bip)Ru(en)](2+) binds only to N7 of guanosine, to N7 and N1 of inosine, and to N3 of thymidine. Binding to N3 of cytidine was weak, and almost no binding to adenosine was observed. The reactivity of the various binding sites of nucleobases toward Ru at neutral pH decreased in the order G(N7) > I(N7) > I(N1), T(N3) > C(N3) > A(N7), A(N1). Therefore, pseudo-octahedral diamino Ru(II) arene complexes are much more highly discriminatory between G and A bases than square-planar Pt(II) complexes. Such site-selectivity appears to be controlled by the en NH(2) groups, which H-bond with exocyclic oxygens but are nonbonding and repulsive toward exocyclic amino groups of the nucleobases. For reactions with mononucleotides, the same pattern of site selectivity was observed, but, in addition, significant amounts of the 5'-phosphate-bound species (40-60%) were present at equilibrium for 5'-TMP, 5'-CMP and 5'-AMP. In contrast, no binding to the phosphodiester groups of 3', 5'-cyclic-GMP (cGMP) or cAMP was detected. Reactions with nucleotides proceeded via aquation of [(eta(6)-arene)Ru(en)Cl](+), followed by rapid binding to the 5'-phosphate, and then rearrangement to give N7, N1, or N3-bound products. Small amounts of the dinuclear species, e.g., Ru-O(PO(3))GMPN7-Ru, Ru-O(PO(3))IMPN1-Ru, Ru-O(PO(3))TMPN3-Ru, Ru-N7IMPN1-Ru, and Ru-N7InoN1-Ru were also detected. In competitive binding experiments for [(eta(6)-Bip)Ru(en)Cl](+) with 5'-GMP versus 5'-AMP or 5'-CMP or 5'-TMP, the only final adduct was [(eta(6)-Bip)Ru(en)(N7-GMP)]. Ru-H(2)O species were more reactive than Ru-OH species. The presence of Cl(-) or phosphate in neutral solution significantly decreased the rates of Ru-N7 binding through competitive coordination to Ru. In kinetic studies (pH 7.0, 298 K, 100 mM NaClO(4)), the rates of reaction of cGMP with [(eta(6)-arene)Ru(II)(en)X](n+) (X = Cl(-) or H(2)O) decreased in the order: THA > Bip > DHA >> Cym > Ben, suggesting that N7-binding is promoted by favorable arene-purine hydrophobic interactions in the associative transition state. These findings have revealed that the diamine NH(2) groups, the hydrophobic arene, and the chloride leaving group have important roles in the novel mechanism of recognition of nucleic acids by Ru arene complexes, and will aid the design of more effective anticancer complexes, as well as new site-specific DNA reagents.

[Creation of new supramolecular chemistry based on multiple interaction in aqueous solution]

Novel supramolecular chemistry of multinuclear zinc(II) complexes in aqueous solution has been created by utilizing multiple interactions with polyanions. We have established reliable and convenient synthetic methods of multidentate macrocyclic polyamines and their zinc(II) complexes and thereby undertook a focused investigation of four topics: 1) efficient inhibition of photo[2 + 2] cycloaddition of thymidine dimer by dimeric zinc(II) complexes; 2) selective extraction and transport of thymidine nucleotide derivatives from the aqueous phase to the organic phase by lipophilic zinc(II) complexes and selective recognition of thymidine nucleotides by ditopic zinc(II) complexes in aqueous solution; 3) supramolecular polyhedrons formed by self-assembly of a trimeric zinc(II) complex with cyanuric acid or trithiocyanuric acid; and 4) a selective fluorescent probe for lanthanide ions such as Y3+ and La3+ based on a double-functionalized ligand with carbamoyl and dansyl groups. This knowledge should afford new methodology for supramolecular chemistry in aqueous solution.

Recent progress in artificial receptors for phosphate anions in aqueous solution

Phosphate esters exist ubiquitously in nature in the form of nucleoside phosphates (nucleotides) as components of RNA (or DNA), sugar nucleotides for glycosylation of oligosaccharides or proteins, activated form of proteins responding to extracellular signals, and chemical mediators playing central roles in intracellular signaling signals. Phosphorylation of anti-viral nucleoside analogues by intracellular kinases yields nucleoside phosphates (nucleotide) as biologically active forms as anti-viral agents. Development of artificial phosphate receptors would afford new methodologies for detection, separation, or transport of biologically important phosphates. Herein, a recent progress of artificial phosphate receptors is reviewed with special focus on macrocyclic polyamines and their metal complexes as a new prototype. In comparison to most of the previous artificial receptors (most of them are organic molecules), our system characteristically works in aqueous solution at neutral pH with extremely strong affinities with phosphate anions. Moreover, zinc(II)-macrocyclic tetraamine (cyclen) complexes were discovered to selectively bind thymine and uracil, so that nucleotides of these bases are specifically recognized by the bis(Zn2+-cyclen) complexes.

Inhibition of succinate-cytochrome C reductase by a ferromacrocyclic complex

Succinate-cytochrome c reductase (SCR) from mouse liver was inhibited strongly and reversibly by an iron (II) macrocyclic complex 3. The inhibition was observed for the enzyme toward the reduction of both 2,6-dichlorophenol indophenol (DCIP) and cytochrome c (cyt c). The inhibition was a mixed type and noncompetitive with respect to the reduction of DCIP and cyt c, respectively. Values of the inhibition constant ranged from 6.6 to 8.3 microM. The IC50 for the complex 3 was found to be 16.6 +/- 0.8 and 12.1 +/- 0.5 microM for the enzyme toward DCIP and cyt c, respectively. The reduced form of complex 3 also exhibited enzyme inhibition but to a less extent. Complex 3, at a lower level, equal to 25% of its LD50 showed about 50% inhibition of the enzyme through in vivo dose-dependent effect. These findings suggested that the structure of the equatorial benzoquinoid macrocyclic ligand of the Fe(II) complex is involved in the enzyme inhibition.