A Dinuclear Mercury(II)‐Mediated Base Pair in DNA

The first dinuclear metal‐mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N⁶‐ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N−M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of Hg^II and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T‐Hg^II₂‐ϵA base pair. This metal‐mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature‐dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.     

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.     

Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences

Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear Hg^II-mediated base pairs featured a coordinated covalent bond between Hg^II and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear Hg^II-mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one Hg^II ion coordinated to a thio and the other one to an oxo substituent.     

5‐Mercuricytosine: An Organometallic Janus Nucleobase

The base‐pairing properties of 5‐mercuricytosine have been explored at the monomer level by NMR titrations and at the oligonucleotide level by melting temperature measurements. The NMR studies revealed a relatively high affinity for guanine, hypoxanthine, and uridine, that is, bases that are deprotonated upon coordination of Hg^II. Within an oligonucleotide duplex, 5‐mercuricytosine formed Hg^II‐mediated base pairs with thymine and guanine. In the former case, the duplex formed was as stable as the respective duplex comprising solely Watson–Crick base pairs. Based on detailed thermodynamic analysis of the melting curves, the stabilization by the Hg^II‐mediated base pairs may be attributed to a comparatively low entropic penalty of hybridization.     

Light-Induced Formation of Thymine-Containing Mercury(II)-Mediated Base Pairs

By applying caged thymidine residues, DNA duplexes were created in which Hg^II-mediated base pair formation can be triggered by irradiation with light. When a bidentate ligand was used as the complementary nucleobase, an unprecedented stepwise formation of different metal-mediated base pairs was achieved.     

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.     

Covalently Palladated Oligonucleotides Through Oxidative Addition of Pd0

An 11-mer oligonucleotide incorporating a central (2-iodobenzoylamino)methyl residue has been synthesized and palladated by oxidative addition of Pd₂(dba)₃. UV melting profiles of the duplexes formed by the palladated oligonucleotide with its natural complements were biphasic and the higher melting temperatures (T_m) exhibited considerable hysteresis. CD spectra, in turn, resembled those of canonical B-type double helices. Two-step denaturation, with the “low-T_m” melting involving only canonical base pairs and the “high-T_m” melting involving also dissociation of a Pd^II-mediated base pair, appears the most likely explanation for the observed UV melting profiles. As the latter step in all cases takes place at a higher temperature than denaturation of natural duplexes of the same length, the putative Pd^II-mediated base pairs are stabilizing.     

Crystal Structure of the Mixed‐Valent Basic Mercury Nitrate HgI2(NO3)2·HgII(OH)(NO3)·HgII(NO3)2·4HgIIO [= Hg8O4(OH)(NO3)5]

Light‐yellow single crystals of the mixed‐valent mercury‐rich basic nitrate Hg₈O₄(OH)(NO₃)₅ were obtained as a by‐product at 85 °C from a melt consisting of stoichiometric amounts of (Hg^I₂)(NO₃)₂·2H₂O and Hg^II(OH)(NO₃). The title compound, represented by the more detailed formula Hg^I₂(NO₃)₂·Hg^II(OH)(NO₃)·Hg^II(NO₃)₂·4Hg^IIO, exhibits a new structure type (monoclinic, C2/c, Z = 4, a = 6.7708(7), b = 11.6692(11), c = 24.492(2) Å, β = 96.851(2)°, 2920 structure factors, 178 parameters, R1[F² > 2σ(F²)] = 0.0316) and is made up of almost linear [O‐Hg^II‐O] and [O‐Hg^I‐Hg^I‐O] building blocks with typical Hg^II‐O distances around 2.06Å and a Hg^I‐O distance of 2.13Å. The Hg₂²⁺ dumbbell exhibits a characteristic Hg‐Hg distance of 2.5079(7) Å. The different types of mercury‐oxygen units form a complex three‐dimensional network exhibiting large cavities which are occupied by the nitrate groups. The NO₃^? anions show only weak interactions between the nitrate oxygen atoms and the mercury atoms which are at distances > 2.6Å from one another. One of the three crystallographically independent nitrate groups is disordered.     

Poly[bis(N‐methylformamide)tetra‐μ‐thiocyanato‐manganese(II)mercury(II)]

The title complex, [MnHg(NCS)₄(C₂H₅NO)₂]_n, consists of slightly distorted MnN₄O₂ octa­hedra and HgS₄ tetra­hedra. Each Mn^II cation is bound to four N atoms of the NCS groups and two O atoms of the N‐methyl­formamide (NMF) ligands in a cis configuration. Each Hg^II cation is coordinated to four S atoms of NCS groups. Each pair of Mn^II and Hg^II cations is connected by an –NCS– bridge, forming an infinite three‐dimensional –Mn—NCS—Hg– network.     

3‐(Pyridin‐4‐yl)acetylacetone: CdII and HgII compete for nitrogen coordination

3‐(Pyridin‐4‐yl)acetylacetone (HacacPy) acts as a pyridine‐type ligand towards Cd^II and Hg^II halides. With CdBr₂, the one‐dimensional polymer [Cd(μ‐Br)₂(HacacPy)Cd(μ‐Br)₂(HacacPy)₂]_∞ is obtained in which five‐ and six‐coordinated Cd^II cations alternate in the chain direction. Reaction of HacacPy with HgBr₂ results in [Hg(μ‐Br)Br(HacacPy)]_∞, a polymer in which each Hg^II centre is tetracoordinated. In both compounds, each metal(II) cation is N‐coordinated by at least one HacacPy ligand. Equimolar reaction between these Cd^II and Hg^II derivatives, either conducted in ethanol as solvent or via grinding in the solid state, leads to ligand redistribution and the formation of the well‐ordered bimetallic polymer catena‐poly[[bromidomercury(II)]‐μ‐bromido‐[aquabis[4‐hydroxy‐3‐(pyridin‐4‐yl)pent‐3‐en‐2‐one]cadmium(II)]‐di‐μ‐bromido], [CdHgBr₄(C₁₀H₁₁NO₂)₂(H₂O)]_n or [{HgBr}(μ‐Br){(HacacPy)₂Cd(H₂O)}(μ‐Br)₂]_∞. Hg^II and Cd^II cations alternate in the [100] direction. The HacacPy ligands do not bind to the Hg^II cations, which are tetracoordinated by three bridging and one terminal bromide ligand. The Cd^II centres adopt an only slightly distorted octahedral coordination. Three bromide ligands link them in a (2 + 1) pattern to neighbouring Hg^II atoms; two HacacPy ligands in a cis configuration, acting as N‐atom donors, and a terminal aqua ligand complete the coordination sphere. Classical O—H…Br hydrogen bonds stabilize the polymeric chain. O—H…O hydrogen bonds between aqua H atoms and the uncoordinated carbonyl group of an HacacPy ligand in a neighbouring strand in the c direction link the chains into layers in the (010) plane.     

The Challenge of Deciphering Linkage Isomers in Mixtures of Oligomeric Complexes Derived from 9‐Methyladenine and trans‐(NH3)2PtII Units

Metal coordination to N9‐substituted adenines, such as the model nucleobase 9‐methyladenine (9MeA), under neutral or weakly acidic pH conditions in water preferably occurs at N1 and/or N7. This leads, not only to mononuclear linkage isomers with N1 or N7 binding, but also to species that involve both N1 and N7 metal binding in the form of dinuclear or oligomeric species. Application of a trans‐(NH₃)₂Pt^II unit and restriction of metal coordination to the N1 and N7 sites and the size of the oligomer to four metal entities generates over 50 possible isomers, which display different feasible connectivities. Slowly interconverting rotamers are not included in this number. Based on ¹H NMR spectroscopic analysis, a qualitative assessment of the spectroscopic features of N1,N7‐bridged species was attempted. By studying the solution behavior of selected isolated and structurally characterized compounds, such as trans‐[PtCl(9MeA‐N7)(NH₃)₂]ClO₄ ? 2H₂O or trans,trans‐[{PtCl(NH₃)₂}₂(9MeA‐N1,N7)][ClO₄]₂ ? H₂O, and also by application of a 9MeA complex with an (NH₃)₃Pt^II entity at N7, [Pt(9MeA‐N7)(NH₃)₃][NO₃]₂, which blocks further cross‐link formation at the N7 site, basic NMR spectroscopic signatures of N1,N7‐bridged Pt^II complexes were identified. Among others, the trinuclear complex trans‐[Pt(NH₃)₂{μ‐(N1‐9MeA‐N7)Pt(NH₃)₃}₂][ClO₄]₆ ? 2H₂O was crystallized and its rotational isomerism in aqueous solution was studied by NMR spectroscopy and DFT calculations. Interestingly, simultaneous Pt^II coordination to N1 and N7 acidifies the exocyclic amino group of the two 9MeA ligands sufficiently to permit replacement of one proton each by a bridging heterometal ion, Hg^II or Cu^II, under mild conditions in water.     

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.     

基于T-T碱基错配的荧光传感器特异性检测汞离子

在本文中,我们研制了一种基于T-T碱基错配特异性键合汞离子的荧光传感器用于汞离子的检测。该传感器由两条分别标记了荧光基团（F）和淬灭基团（Q）的DNA探针组成,并且含有两对用于结合汞离子的T-T错配碱基。当汞离子存在时,两条探针之间形成T-Hg2+-T结构,作用力增强,从而拉近了荧光基团与淬灭基团之间的距离,发生能量转移,使荧光信号在一定程度上被淬灭。在优化的条件下,我们使用该传感器对汞离子进行检测,动力学响应范围为50nM到1000nM,线性相关方程为y= 5281.13 - 1650.56 lg[Hg2+] ( R2 = 0.985),检测下限为79nM。此外,我们还考察了该传感器的选择性,当用其它干扰离子（浓度都为1.0µM）代替待测离子进行实验时,没有发生明显的荧光淬灭,说明该传感器具有较高的选择性。该传感器的构建为汞离子的检测提供了一条快速、简便的新途径。     

Diketopyrrolopyrrole J‐Aggregates Formed by Self‐Organization with DNA

Bis(2‐thienyl)diketopyrrolopyrrole with two Zn^II‐cyclens (ZnCyc‐DPP) was designed and synthesized to evaluate the selective binding of Zn^II‐cyclen with thymine base in single‐strand DNA as a tool for the construction of a highly ordered multichromophore system on DNAs. Through UV/Vis titrations, gel filtration chromatography, and circular dichroism spectroscopy, ZnCyc‐DPP formed J‐type DPP aggregates with oligo‐dT_n DNAs. The DPP aggregates absorbed on a gold electrode exhibited good photocurrent responses. The present results show that binding Zn^II‐cyclen–chromophore conjugates and thymine bases together is a powerful tool for preparing DNA‐templated multichromophoric systems with specific functions.     

Assembling of transitional metal Cu<Superscript>II</Superscript> and Mn<Superscript>II</Superscript> with 4-pyridin-2-yl-pyrimidine-2-sulfonate adjusted by anions

Reactions of sodium 4-pyridin-2-yl-pyrimidine-2-sulfonate (NaL) with Cu^II and Mn^II ions in water produced a zig-zag chain polymer, [CuL(NCS)] _n (1), and a dinuclear complex, [Mn₂L₂Cl₂(H₂O)₂] (2), respectively. It is observed that counteranions and hydrogen bonds play basic roles in the resulting structure in which 3D networks were formed through intermolecular hydrogen bonding.     

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.     

An Extremely Stable Interprotein Tetrahedral Hg(Cys)4 Core Forms in the Zinc Hook Domain of Rad50 Protein at Physiological pH

In nature, thiolate-based systems are the primary targets of divalent mercury (Hg^II) toxicity. The formation of Hg(Cys)_x cores in catalytic and structural protein centers mediates mercury's toxic effects and ultimately leads to cellular damage. Multiple studies have revealed distinct Hg^II-thiolate coordination preferences, among which linear Hg^II complexes are the most commonly observed in solution at physiological pH. Trigonal or tetrahedral geometries are formed at basic pH or in tight intraprotein Cys-rich metal sites. So far, no interprotein tetrahedral Hg^II complex formed at neutral pH has been reported. Rad50 protein is a part of the multiprotein MRN complex, a major player in DNA damage-repair processes. Its central region consists of a conserved CXXC motif that enables dimerization of two Rad50 molecules by coordinating Zn^II. Dimerized motifs form a unique interprotein zinc hook domain (Hk) that is critical for the biological activity of the MRN. Using a series of length-differentiated peptide models of the Pyrococcus furiosus zinc hook domain, we investigated its interaction with Hg^II. Using UV-Vis, CD, PAC, and ¹⁹⁹Hg NMR spectroscopies as well as anisotropy decay, we discovered that all Rad50 fragments preferentially form homodimeric Hg(Hk)₂ species with a distorted tetrahedral HgS₄ coordination environment at physiological pH; this is the first example of an interprotein mercury site displaying tetrahedral geometry in solution. At higher Hg^II content, monomeric HgHk complexes with linear geometry are formed. The Hg(Cys)₄ core of Rad50 is extremely stable and does not compete with cyanides, NAC, or DTT. Applying ITC, we found that the stability constant of the Rad50 Hg(Hk)₂ complex is approximately three orders of magnitude higher than those of the strongest Hg^II complexes known to date.     

Bis(μ‐2‐sulfonatobenzoato)bis[(1,10‐phenanthroline)­lead(II)] dihydrate

In the title centrosymmetric dimer, [Pb₂(sbc)₂(phen)₂]·2H₂O [sbc is the 2‐sulfonatobenzoate dianion (C₇H₄O₅S) and phen is 1,10‐phenanthroline (C₁₂H₈N₂)], each Pb^II ion is six‐coordinated by four O atoms, viz. carboxyl­ate and sulfonate O atoms from two sbc anions, and two N atoms from a 1,10‐phenanthroline ligand. One 1,10‐phenanthroline ligand and the carboxyl­ate group of one sbc ligand are chelated to each Pb^II cation, and the sulfonate group of the other sbc unit is monodentate. One O atom of the chelated carboxyl­ate group also bridges to the other Pb^II cation, so that each pair of Pb^II ions is bridged by two sbc anions and has the same coordination environment, forming a dinuclear ring. Each pair of Pb^II ions is thus connected by two different kinds of bridges, namely a carboxyl­ate short bridge and a carboxyl­ate–sulfonate long bridge. There is also a special position of site symmetry at the centre of the two Pb^II cations.     

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.     

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.