Formation of a Thymine‐HgII‐Thymine Metal‐Mediated DNA Base Pair: Proposal and Theoretical Calculation of the Reaction Pathway

A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg^II ion, which results in the formation of a (T)N3‐Hg^II‐N3(T) metal‐mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg^II? N3(T) bond is triggered by deprotonation of the imino N3 atom in thymine with a hydroxo ligand on the Hg^II ion. The formation of the second Hg^II? N3(T) bond proceeds through water‐assisted tautomerization of the remaining, metal‐nonbonded thymine base or through thymine deprotonation with a hydroxo ligand of the Hg^II ion already coordinated to the thymine base. The thermodynamic parameters ΔG_R=?9.5 kcal mol^?1, ΔH_R=?4.7 kcal mol^?1, and ΔS_R=16.0 cal mol^?1 K^?1 calculated with the ONIOM (B3LYP:BP86) method for the reaction agreed well with the isothermal titration calorimetric (ITC) measurements by Torigoe et al. [H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010 , 16, 13218–13225]. The peculiar positive reaction entropy measured previously was due to both dehydration of the metal and the change in chemical bonding. The mercury reactant in the theoretical model contained one hydroxo ligand in accord with the experimental pK_a value of 3.6 known for an aqua ligand of a Hg^II center. The chemical modification of T:T mismatched to the T‐Hg^II‐T metal‐mediated base pair was modeled for the middle base pair within a trinucleotide B‐DNA duplex, which ensured complete dehydration of the Hg^II ion during the reaction.     

1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase

A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔT_m=7.3 °C) Hg^II-mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two Hg^II ions coordinated to O2 and O4 of the thymine base.     

N‐Methyl‐2, 2'‐Dipicolylamine Complexes as Potential Models for Metal‐Mediated Base Pairs

Metal‐mediated base pairs can be used to insert metal ions into nucleic acids at precisely defined positions. As structural data on the resulting metal‐modified DNA are scarce, appropriate model complexes need to be synthesized and structurally characterized. Accordingly, the molecular structures of nine transition metal complexes of N‐methyl‐2, 2'‐dipicolylamine (dipic) are reported. In combination with an azole‐containing artificial nucleoside, this tridentate ligand had recently been used to generate metal‐mediated base pairs (Chem. Commun. 2011 , 47, 11041–11043). The Pd^II and Pt^II complexes reported here confirm that the formation of planar complexes (as required for a metal‐mediated base pair) comprising N‐methyl‐2, 2'‐dipicolylamine is possible. Two Hg^II complexes with differing stoichiometry indicate that a planar structure might also be formed with this metal ion, even though it is not favored. In the complex [Ag₂(dipic)₂](ClO₄)₂, the two Ag^I ions are located close to one another with an Ag ··· Ag distance of 2.9152(3) Å, suggesting the presence of a strong argentophilic interaction.     

A Novel DNA Helical Wire Containing HgII‐Mediated T:T and T:G Pairs

Numerous applications of metal‐mediated base pairs (metallo‐base‐pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively studied. Many of these metallo‐base‐pairs are formed in DNA and RNA duplexes containing Watson–Crick base pairs. Recently, a crystal structure of a metal–DNA nanowire with an uninterrupted one‐dimensional silver array was reported. We now report the crystal structure of a novel DNA helical wire containing Hg^II‐mediated T:T and T:G base pairs and water‐mediated C:C base pairs. The Hg‐DNA wire does not contain any Watson–Crick base pairs. Crystals of the Hg‐DNA wire, which is the first DNA wire structure driven by Hg^II ions, were obtained by mixing the short oligonucleotide d(TTTGC) and Hg^II ions. This study demonstrates the potential of metallo‐DNA to form various structural components that can be used for functional nanodevices.     

Regulated Incorporation of Two Different Metal Ions into Programmed Sites in a Duplex by DNA Polymerase Catalyzed Primer Extension

Metal‐mediated base pairs formed by the coordination of metal ions to natural or artificial bases impart unique chemical and physical properties to nucleic acids and have attracted considerable interest in the field of nanodevices. Ag^I ions were found to mediate DNA polymerase catalyzed primer extension through the formation of a C–Ag^I–T base pair, as well as the previously reported C–Ag^I–A base pair. The comparative susceptibility of dNTPs to Ag^I‐mediated enzymatic incorporation into the site opposite cytosine in the template was shown to be dATP>dTTP?dCTP. Furthermore, two kinds of metal ions, Ag^I and Hg^II, selectively mediate the incorporation of thymidine 5′‐triphosphate into sites opposite cytosine and thymine in the template, respectively. In other words, the regulated incorporation of different metal ions into programmed sites in the duplex by DNA polymerase was successfully achieved.     

CaII Binding Regulates and Dominates the Reactivity of a Transition‐Metal‐Ion‐Dependent Diesterase from Mycobacterium tuberculosis

The diesterase Rv0805 from Mycobacterium tuberculosis is a dinuclear metallohydrolase that plays an important role in signal transduction by controlling the intracellular levels of cyclic nucleotides. As Rv0805 is essential for mycobacterial growth it is a promising new target for the development of chemotherapeutics to treat tuberculosis. The in vivo metal‐ion composition of Rv0805 is subject to debate. Here, we demonstrate that the active site accommodates two divalent transition metal ions with binding affinities ranging from approximately 50 nm for Mn^II to about 600 nm for Zn^II. In contrast, the enzyme GpdQ from Enterobacter aerogenes, despite having a coordination sphere identical to that of Rv0805, binds only one metal ion in the absence of substrate, thus demonstrating the significance of the outer sphere to modulate metal‐ion binding and enzymatic reactivity. Ca^II also binds tightly to Rv0805 (K_d≈40 nm ), but kinetic, calorimetric, and spectroscopic data indicate that two Ca^II ions bind at a site different from the dinuclear transition‐metal‐ion binding site. Ca^II acts as an activator of the enzymatic activity but is able to promote the hydrolysis of substrates even in the absence of transition‐metal ions, thus providing an effective strategy for the regulation of the enzymatic activity.     

Synthesis and Characterization of Novel Template Complexes

Novel neutral polynuclear Ni^II chelates of L ‐cysteine (L ‐cyst) or D ‐penicillamine (D ‐pen) with dicyandiamide (dcda) were synthesized and characterized using elemental analysis, UV, CD, reflectance, and IR spectroscopy and/or thermogravimetric and X‐ray analysis. The obtained dinuclear compounds add important information about the chemistry of nickel(II) ions, which form types of bonds that cannot be obtained with other metal ions such as Co^II. These dinuclear nickel compounds contain four‐membered rings with two sulfur and two nickel atoms. Electronic transitions were elucidated from reflectance, CD and absorbance spectroscopy and confirm a distorted square planar arrangement of the nickel ions. Because the same structure with Co^II ions could not be obtained directly, dimethylglyoxime was added to a suspension of the template complex with D ‐pen in water to separate the nickel ions. The separation of the ligand was confirmed by elemental analysis, IR, and ¹H NMR spectroscopy. It reacted with Co^II to give a different mononuclear crystalline complex that was studied by X‐ray single crystal diffraction. The crystals are orthorhombically with space group C222₁, a = 0.11769(4) pm, b = 0.13632(4) pm, c = 0.25239(8) pm, V = 0.0040490(2) pm³, and Z = 8.     

Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson–Crick‐like T–HgII–T Base Pairs

The metallo DNA duplex containing mercury‐mediated T–T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B‐form DNA duplex containing two consecutive T–Hg^II–T base pairs. The Hg^II ion occupies the center between two T residues. The N3‐Hg^II bond distance is 2.0 Å. The relatively short Hg^II‐Hg^II distance (3.3 Å) observed in consecutive T–Hg^II–T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B‐form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg^II. The structure of the metallo DNA duplex itself and the Hg^II‐induced structural switching from the nonhelical form to the B‐form provide the basis for structure‐based design of metal‐conjugated nucleic acid nanomaterials.     

A New 3D Manganese(II) Coordination Polymer with 4,4‐Dicarboxy‐2,2′‐bipyridine and 1,10‐Phenanthroline: Synthesis,Structural, and Magnetic Properties

A new 3D Mn^II metal‐organic framework compound {Mn(phen)(dcbp)}_n (H₂dcbp = 4,4‐dicarboxy‐2,2′‐bipyridine, phen = 1,10‐phenanthroline) was isolated under hydrothermal conditions and structurally characterized. In the compound, the dcbp ligand is deprotonated to give a neutral species (metal:ligand with 1:1 stoichiometry). Along the c axis, the neighboring Mn^II ions are linked by two carboxylate bridges in µ₂‐coordinating mode to generate a 1D zigzag chain, and these chains are interlinked by dicarboxylate groups of long dcbp ligands to generate a 3D (4,4)‐connected structure with the (4².8⁴) net topology. IR and UV/Vis spectroscopy and variable temperature magnetic susceptibility measurements were made, which indicated weak antiferromagnetic interactions between the Mn^II ions of the compound.     

Structural Adaptability of Zinc Binding Sites: Different Structures in Partially,Fully, and Heavy‐Metal Loaded States

The present study demonstrates that both the nature (Zn^II, Cd^II or Hg^II) and supply of metal ions determine whether zinc fingers fold into the well‐known, fully loaded structures or alternatively populate a variety of structural states under substoichiometric conditions. Metal‐bridged species are observed by perturbed angular correlation (PAC), EXAFS, UV spectroscopy, and stopped‐flow kinetics. Transitions between structural states as adaptive reactions to changed metal‐ion supply might represent intelligent system changes in zinc homeostasis, trafficking and signalling, and reflect features of heavy‐metal toxicity at the molecular level. Because the zinc fingers exist in structural states that are different from the metal‐free and fully loaded species, the prevailing view on metal‐mediated molecular regulation in terms of “on and off control” might be oversimplified.     

A Highly Stabilizing Silver(I)‐Mediated Base Pair in Parallel‐Stranded DNA

The first parallel‐stranded DNA duplex with Hoogsteen base pairing that readily incorporates an Ag⁺ ion into an internal mispair to form a metal‐mediated base pair has been created. Towards this end, the highly stabilizing 6 FP ‐Ag⁺‐ 6 FP base pair comprising the artificial nucleobase 6‐furylpurine ( 6 FP ) was devised. A combination of temperature‐dependent UV spectroscopy, CD spectroscopy, and DFT calculations was used to confirm the formation of this base pair. The nucleobase 6 FP is capable of forming metal‐mediated base pairs both by the Watson–Crick edge (i.e. in regular antiparallel‐stranded DNA) and by the Hoogsteen edge (i.e. in parallel‐stranded DNA), depending on the oligonucleotide sequence and the experimental conditions. The 6 FP ‐Ag⁺‐ 6 FP base pair within parallel‐stranded DNA is the most strongly stabilizing Ag⁺‐mediated base pair reported to date for any type of nucleic acid, with an increase in melting temperature of almost 15 °C upon the binding of one Ag⁺ ion.     

Synthesis,Structure, and Magnetic Properties of a Dinuclear Antiferromagnetically Coupled Cobalt Complex

A new dinuclear cobalt(II) compound,[(TPA*)Co^II(DHBQ^2–)Co^II(TPA*)]²⁺ ( 1 ²⁺) {TPA* =tris[(3, 5‐dimethyl‐pyrazol‐l‐yl)methyl] amine, DHBQ = deprotonated 2, 5‐dihydroxy‐1, 4‐benzoquinone}, was prepared and structurally and magnetically characterized. X‐ray crystallography revealed the centrosymmetric dinuclear divalent cobalt ions bridged by DHBQ^2– unit. The cobalt ions in the title compound have a distorted octahedral arrangement by coordination with four nitrogens of a TPA* and two oxygens of a bridging DHBQ unit. Due to the interdimer offset face‐to‐face π–π stacking in the crystallographic ac plane, the complex shows extended 2D supramolecular structure. Magnetic experiments showed the cobalt‐based dinuclear compound exhibits antiferromagnetic interactions with g = 2.35 and J/k_B = –2.76 K, respectively.     

Metal-mediated DNA base pairing of easily prepared 2-oxo-imidazole-4-carboxylate nucleotides

Metal-mediated DNA base pairs, which consist of two ligand-type artificial nucleobases and a bridging metal ion, have attracted increasing attention in recent years as a different base pairing mode from natural base pairing. Metal-mediated base pairing has been extensively studied, not only for metal-dependent thermal stabilisation of duplexes, but also for metal assembly by DNA templates and construction of functional DNAs that can be controlled by metals. Here, we report the metal-mediated base paring properties of a novel 2-oxo-imidazole-4-carboxylate (Im^OC) nucleobase and a previously reported 2-oxo-imidazole-4-carboxamide (Im^OA) nucleobase, both of which can be easily derived from a commercially available uridine analogue. The Im^OC nucleobases were found to form stable Im^OC–Cu^II–Im^OC and Im^OC–Hg^II–Im^OC base pairs in the presence of the corresponding metal ions, leading to an increase in the duplex melting temperature by +20 °C and +11 °C, respectively. The Im^OC bases did not react with other divalent metal ions and showed superior metal selectivity compared to similar nucleobase design reported so far. The Im^OC–Cu^II–Im^OC base pair was much more stable than mismatch pairs with other natural nucleobases, confirming the base pair specificity in the presence of Cu^II. Furthermore, we demonstrated the quantitative assembly of three Cu^II ions inside a DNA duplex with three consecutive Im^OC–Im^OC pairs, showing great potential of DNA-template based Cu^II nanoarray construction. The study of easily-prepared Im^OC base pairs will provide a new design strategy for metal-responsive DNA materials.

A novel 2-oxo-imidazole-4-carboxylate (Im^OC) nucleobase, which can be easily derived from a commercially available uridine analogue, was found to form stable Cu^II- and Hg^II-mediated base pairs in DNA duplexes.     

Unidimensional Self‐assembling of {HgII[NNN(PhBr)2]2} through Metal‐η4‐arene π‐Interactions: Synthesis and X‐Ray Characterization of a Bis Diaryl Symmetric‐substituted Triazenide Complex Polymer of Mercury(II)

A solution of deprotonated 1,3‐bis(4‐bromophenyl)triazene reacts with Hg(CH₃COO)₂ in methanol / tetrahydrofurane to give yellow crystalline needles of {Hg^II[NNN(PhBr)₂]₂}_n, a triazenide complex polymer of Hg^II with metal‐η²,η²‐arene π‐interactions, performed by coordinated single triazenide chains. The crystal structure of the new polymeric complex of Hg^II belongs to the monoclinic space group P2₁/n. The lattice of [Hg^II(BrPhNNNPhBr)₂]_n can be viewed as a one‐dimensional assembling of planar tectons [Hg^II(BrPhNNNPhBr)₂] linked through metalocene alike Hg^II‐η²,η²‐arene π‐interactions along the crystallographic b axis.     

Selective Coordination of Gallium(III), Zinc(II), and Copper(II) by an Asymmetric Dinucleating Ligand: A Model for Metallophosphatases

Complexation studies of the dinucleating ligand H₃L (H₃L=2‐{[bis(pyridin‐2‐ylmethyl)amino]methyl}‐6‐{[bis(6‐pivaloylamidopyridin‐2‐ylmethyl)amino]methyl}‐4‐methylphenol), with metal‐binding sites A and B, which both provide four donors to a metal ion; a tertiary amine; two pyridines (substituted with amide hydrogen‐bond donors in site B), and a bridging phenolate, with Zn^II, Cu^II, and Ga^III are reported. The titration of H₃L with the three metal ions in solution was monitored by NMR spectroscopy or EPR and UV/Vis/near‐IR spectroscopy, as well as by ESI‐MS to analyze the selectivity of the two metal‐ion sites A and B of this model ligand for metallophosphatases; the spectroscopic assignments are supported by X‐ray crystallography results. The first Zn^II ion coordinates to site A with unsubstituted pyridine donors and, upon addition of a second equivalent of Zn^II, this coordinates to the sterically less accessible site B. From a similar titration with Ga^III, it emerges that only a mononuclear complex is obtained, with the Ga^III center coordinated to site A. When one equivalent of Ga^III is reacted with the mononuclear Zn^II complex, Zn^II is forced by Ga^III to exchange the site; this results in a dinuclear complex with Ga^III in site A and Zn^II in site B. With Cu^II, two isomers are observed: one with and the other without a bridging phenolate; these differ significantly in their spectroscopic and magnetic properties.     

Probing the Coordination Environment of the Human Copper Chaperone HAH1: Characterization of HgII‐Bridged Homodimeric Species in Solution

Although metal ion homeostasis in cells is often mediated through metallochaperones, there are opportunities for toxic metals to be sequestered through the existing transport apparatus. Proper trafficking of Cu^I in human cells is partially achieved through complexation by HAH1, the human metallochaperone responsible for copper delivery to the Wilson and Menkes ATPase located in the trans‐Golgi apparatus. In addition to binding copper, HAH1 strongly complexes Hg^II, with the X‐ray structure of this complex previously described. It is important to clarify the solution behavior of these systems and, therefore, the binding of Hg^II to HAH1 was probed over the pH range 7.5 to 9.4 using ¹⁹⁹Hg NMR, ^199mHg PAC and UV–visible spectroscopies. The metal‐dependent protein association over this pH range was examined using analytical gel‐filtration. It can be concluded that at pH 7.5, Hg^II is bound to a monomeric HAH1 as a two coordinate, linear complex (HgS₂), like the Hg^II–Atx1 X‐ray structure (PDB ID: 1CC8). At pH 9.4, Hg^II promotes HAH1 association, leading to formation of HgS₃ and HgS₄ complexes, which are in exchange on the μs–ns time scale. Thus, structures that may represent central intermediates in the process of metal ion transfer, as well as their exchange kinetics have been characterized.     

Poly[[[tri(urea‐κO)manganese(II)]‐μ‐thiocyanato‐κ2N:S‐mercury(II)]‐tri‐μ‐tetrathiocyanato]

The title complex, [MnHg(SCN)₄(CH₄N₂O)₃]_n, consists of slightly distorted octahedral MnN₃O₃ and tetrahedral HgS₄ units. The Mn^II atom is coordinated by the O atoms of three urea mol­ecules and by the N atoms of three SCN^? ions; Hg^II is coordinated by four S atoms from SCN^? ions. Each pair of Mn^II and Hg^II atoms is connected by an –SCN– bridge, forming infinite two‐dimensional –Mn—NCS—Hg– networks.     

A Dinuclear Ruthenium(II) Schiff Base Complex with Dissimilar Coordination: Synthesis,Characterization, and Biological Activity

A dinuclear Schiff base Ru^II complex derived from 5‐chlorosalicylaldehyde and 2‐aminopyridine was synthesized. The structure of the compound was analyzed by mass spectrometry as well as IR, UV/Vis, and ¹H NMR spectroscopy, along with chemical analysis,as well as magnetic, cyclovoltammetric and conductivity measurements. Two Ru^II atoms are octahedrally coordinated by azomethine and pyridine nitrogen atoms from two tridentate monobasic Schiff bases and bridging phenol oxygen atoms. The formula of the complex is [Ru₂L₂Cl₂(Et₂NH)(H₂O)] [L = N‐(2‐pyridyl)‐5‐chlorosalicylideneimine and Et₂NH = isodiethylamine]. The Ru^II atoms in the dinuclear neutral complex species have different coordination environments, RuN₃O₂Cl and RuN₂O₃Cl. Interaction with CT DNA showed moderate hydrophobic binding. The compound demonstrates strong activity against methicillin‐resistant Staphylococcus aureus, methicillin‐sensitive Staphylococcus aureus, and especially Enterococcus faecalis. Microbiological tests showed significant inhibition of growth and ability to kill pathogens, similar or even improved compared to reference antibiotics vancomycin.     

Synthesis,Crystal Structure,Thermal Stability,Magnetic Property,and Biological Activity of a New Copper(II) Complex Based on 1,2,4‐Benzenetricarboxylic Acid and 2,2′‐Bipyridine

Based on an asymmetric 1,2,4‐benzenetricarboxylic acid (H₃btc) and 2,2′‐bipyridine (bpy), a new Cu^II complex, Cu₂(H₂btc)₄(bpy)₂ · 8H₂O ( 1 ), was synthesized and structurally characterized by single‐crystal X‐ray diffraction, hirshfeld surface (HS) analysis, IR spectroscopy, powder X‐ray analysis, thermal gravimetry analysis (TGA), magnetic susceptibility, EPR measurement, and UV/Vis spectrometry. Complex 1 shows a dinuclear copper structure. The Cu^II of each dinuclear moiety are in a slightly distorted square‐pyramidal environments. Magnetic susceptibility of 1 shows a ferromagnetic coupling between both metal atoms. The interaction of 1 with bovine serum albumin (BSA) is investigated using UV/Vis, fluorescence spectroscopic methods. The Cu^II complex shows strong binding propensity in albumin binding study.