Soft metal-mediated base pairing with novel synthetic nucleosides possessing an O,S-donor ligand

Metal-mediated base pairing with artificial ligand-bearing nucleosides allows site-selective metal incorporation inside DNA duplexes. In particular, this strategy has provided a general way of discrete, heterogeneous metal arrays in a programmable manner. To increase the kind of metallo-building blocks, we have newly synthesized two artificial nucleosides which have an O, S-donor ligand as the nucleobase moiety, mercaptopyridone ( M) and hydroxypyridinethione ( S). These nucleosides were found to efficiently form metal-mediated base pairs with soft transition metal ions such as Pd (2+) and Pt (2+).     

Sharp Switching of DNAzyme Activity through the Formation of a CuII-Mediated Carboxyimidazole Base Pair

DNAzymes are widely used as functional units for creating DNA-based sensors and devices. Switching of DNAzyme activity by external stimuli is of increasing interest. Herein we report a Cu^II-responsive DNAzyme rationally designed by incorporating one of the most stabilizing artificial metallo-base pairs, a Cu^II-mediated carboxyimidazole base pair (Im^C-Cu^II-Im^C), into a known RNA-cleaving DNAzyme. Cleavage of the substrate was suppressed without Cu^II, but the reaction proceeded efficiently in the presence of Cu^II ions. This is due to the induction of a catalytically active structure by Im^C-Cu^II-Im^C pairing. The on/off ratio was as high as 12-fold, which far exceeds that of the previously reported DNAzyme with a Cu^II-mediated hydroxypyridone base pair. The DNAzyme activity can be regulated specifically in response to Cu^II ions during the reaction through the addition, removal, or reduction of Cu^II. This approach should advance the development of stimuli-responsive DNA systems with a well-defined sharp switching function.     

1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three AgI Ions in a Duplex

Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned Ag^I ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three Ag^I ions. Nine equivalents of Ag^I led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three Ag^I ions are expected to be applicable to new DNA nanotechnologies.     

Bifacial Base‐Pairing Behaviors of 5‐Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination

A novel bifacial ligand‐bearing nucleobase, 5‐hydroxyuracil ( U^OH ), which forms both a hydrogen‐bonded base pair ( U^OH –A) and a metal‐mediated base pair ( U^OH –M– U^OH ) has been developed. The U^OH –M– U^OH base pairs were quantitatively formed in the presence of lanthanide ions such as Gd^III when U^OH – U^OH pairs were consecutively incorporated into DNA duplexes. This result established metal‐assisted duplex stabilization as well as DNA‐templated assembly of lanthanide ions. Notably, a duplex possessing U^OH –A base pairs was destabilized by addition of Gd^III ions. This observation suggests that the hybridization behaviors of the U^OH ‐containing DNA strands are altered by metal complexation. Thus, the U^OH nucleobase with a bifacial base‐pairing property holds great promise as a component for metal‐responsive DNA materials.     

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.     

A Family of “Click” Nucleosides for Metal‐Mediated Base Pairing: Unravelling the Principles of Highly Stabilizing Metal‐Mediated Base Pairs

A family of artificial nucleosides has been developed by applying the Cu^I‐catalyzed Huisgen 1,3‐dipolar cycloaddition. Starting from 2‐deoxy‐β‐D ‐glycosyl azide as a common precursor, three bidentate nucleosides have been synthesized. The 1,2,3‐triazole involved in all three nucleobases is complemented by 1,2,4‐triazole ( TriTri ), pyrazole ( TriPyr ), or pyridine ( TriPy ). Molecular structures of two metal complexes indicate that metal‐mediated base pairs of TriPyr may not be fully planar. An investigation of DNA oligonucleotide duplexes comprising the new “click” nucleosides showed that they can bind Ag^I to form metal‐mediated base pairs. In particular the mispair formed from TriPy and the previously established imidazole nucleoside is significantly stabilized in the presence of Ag^I. A comparison of different oligonucleotide sequences allowed the determination of general factors involved in the stabilization of nucleic acids duplexes with metal‐mediated base pairs.     

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.     

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.     

Cyclohexyl "base pairs" stabilize duplexes and intensify pyrene fluorescence by shielding it from natural base pairs

In this study, we investigated the stability and structure of artificial base pairs that contain cyclohexyl rings. The introduction of a single pair of isopropylcyclohexanes into the middle of DNA slightly destabilized the duplex. Interestingly, as the number of the "base pairs" increased, the duplex was remarkably stabilized. A duplex with six base pairs was even more stable than one containing six A-T pairs. Thermodynamic analysis revealed that changes in entropy and not enthalpy contributed to duplex stability, demonstrating that hydrophobic interactions between isopropyl groups facilitated the base pairing, and thus stabilized the duplex. NOESY of a duplex containing an isopropylcyclohexane-methylcyclohexane pair unambiguously demonstrated its "pairing" in the duplex because distinct NOEs between the protons of cyclohexyl moieties and imino protons of both of the neighboring natural base pairs were observed. CD spectra of duplexes tethering cyclohexyl moieties also showed a positive-negative couplet that is characteristic of the B-form DNA duplex. Taken together, these results showed that cyclohexyl moieties formed base pairs in the DNA duplex without severely disturbing the helical structure of natural DNA. Next, we introduced cyclohexyl base pairs between pyrene and nucleobases as an "insulator" that suppresses electron transfer between them. We found a massive increase in the quantum yield of pyrene due to the efficient shielding of pyrene from nucleobases. The cyclohexyl base pairs reported here have the potential to prepare highly fluorescent labeling agents by multiplying fluorophores and insulators alternately into DNA duplexes.     

Structural,Electronic, and Optical Properties of Metallo Base Pairs in Duplex DNA: A Theoretical Insight

Using density functional theory calculations, we investigated the structural, energetic, electronic, and optical properties of recently synthesized duplex DNA containing metal‐mediated base pairs. The studied duplex DNA consists of three imidazole (Im) units linked through metal (Im‐M‐Im, M=metal) and four flanking A:T base pairs (two on each side). We examined the role of artificial base pairing in the presence of two distinctive metal ions, diamagnetic Ag⁺ and magnetic Cu²⁺ ions, on the stability of duplex DNA. We found that metal‐mediated base pairs form stable duplex DNA by direct metal ion coordination to the Im bases. Our results suggest a higher binding stability of base pairing mediated by Cu²⁺ ions than by Ag⁺ ions, which is attributed to a larger extent of orbital hybridization. We furthermore found that DNA modified with Im‐Ag⁺‐Im shows the low‐energy optical absorption characteristic of π–π*orbital transition of WC A:T base pairs. On the other hand, we found that the low‐energy optical absorption peaks for DNA modified with Im‐Cu²⁺‐Im originate from spin–spin interactions. Additionally, this complex exhibits weak ferromagnetic coupling between Cu²⁺ ions and strong spin polarization, which could be used for memory devices. Moreover, analyzing the role of counter ions (Na⁺) and the presence of explicit water molecules on the structural stability and electronic properties of the DNA duplex modified with Im‐Ag⁺‐Im, we found that the impact of these two factors is negligible. Our results are fruitful for understanding the experimental data and suggest a potential route for constructing effective metal‐mediated base pairs in duplex DNA for optoelectronic applications.     

Solution studies on trace metal ion interactions with adenine as primary ligand and 5-halouracils as secondary ligands

The interaction of trace metal ions, viz. Mn^II, Co^II, Ni^II, Cu^II, Zn^II and Cd^II with adenine (A) as primary ligand and 5-halouracils, viz. 5-bromouracil (5BrU) and 5-iodouracil (5IU) as secondary ligands (L) has been studied at 25±0.1°C and at constant ionic strength (=0.1M NaNO₃), in an aqueous medium using Bjerrum–Calvin's pH-titration technique as adopted by Irving and Rossotti for binary (ML), and by Chidambaram and Bhattacharya for ternary (MAL) systems respectively. The experimental pH-titration data were analyzed with the aid of the BEST computer program in order to evaluate formation constants of various intermediate complex species formed in binary and ternary systems involving nucleobases (viz. A, 5BrU and 5IU). The relative stability of each ternary complex was compared with that of the corresponding binary complexes in terms of logK values.     

Formate-driven catalysis and mechanism of an iridium–copper complex for selective aerobic oxidation of aromatic olefins in water

A hetero-dinuclear Ir^III–Cu^II complex with two adjacent sites was employed as a catalyst for the aerobic oxidation of aromatic olefins driven by formate in water. An Ir^III–H intermediate, generated through formate dehydrogenation, was revealed to activate terminal aromatic olefins to afford an Ir-alkyl species, and the process was promoted by a hydrophobic [Ir^III–H]-[substrate aromatic ring] interaction in water. The Ir-alkyl species subsequently reacted with dioxygen to yield corresponding methyl ketones and was promoted by the presence of the Cu^II moiety under acidic conditions. The Ir^III–Cu^II complex exhibited cooperative catalysis in the selective aerobic oxidation of olefins to corresponding methyl ketones, as evidenced by no reactivities observed from the corresponding mononuclear Ir^III and Cu^II complexes, as the individual components of the Ir^III–Cu^II complex. The reaction mechanism afforded by the Ir^III–Cu^II complex in the aerobic oxidation was disclosed by a combination of spectroscopic detection of reaction intermediates, kinetic analysis, and theoretical calculations.

A hetero-dinuclear Ir^III–Cu^II complex with two adjacent sites was employed as a catalyst for the aerobic oxidation of aromatic olefins driven by formate and promoted by a hydrophobic interaction in water.     

Transition metal complexes with a polydentate Schiff base derived from 3-formylsalicylic acid and 1,2-bis(o-aminophenylthio)ethane

The reaction of 3-formylsalicylic acid with 1,2-bis(o-aminophenylthio)ethane yielded a Schiff base with eight donor centres N₂S₂O₄ of which the inner compartment is of an N₂S₂O₂ type and the outer is of the O₂O₂ type. The base forms several mononuclear homo- and hetero-dinuclear complexes: e.g. mononuclear Cu^II, Ni^II and dinuclear Cu^II, Ni^II, UO₂ ^VI complexes. Hetero-dinuclear complexes {[M]M}, where M = the inner metal ion Cu^II, Ni^II and M = the outer metal ion Pd^II, UO₂ ^VI are also reported. The complexes were characterised by elemental analyses, spectral, thermal and magnetic measurements. Dicopper and dinickel complexes exhibit subnormal magnetic moments showing spin pairing between two metal centres, via the phenolato oxygen, whereas other mono-copper and mono-nickel complexes (both mononuclear and hetero-dinuclear) show the expected magnetic behaviour for 1e and 2e, respectively. The e.s.r. spectra of copper complexes also support the above behaviour.     

Artificial metallo-DNA towards discrete metal arrays

DNA shows promise as a provider of a structural basis for the “bottom-up” fabrication of functionalized molecular building blocks. In particular, the replacement of hydrogen-bonded DNA base pairing for alternative one could possibly provide a novel tool for re-engineering DNA as well as for biological applications. This review describes our recent approaches to metal-based strategy directed towards self-assembled metal arrays within DNAs. Recently, we reported the synthesis of a series of artificial oligonucleotides, d(5′-G H _nC-3′) (n = 1-5), using hydroxypyridone nucleobases ( H ) as flat bidentate ligands. Right-handed double helices of the oligonucleotides, nCu²⁺·d(5′-G H _nC-3′)₂ (n = 1-5), are quantitatively formed through Cu²⁺-mediated alternative base pairing ( H -Cu²⁺- H ), where the Cu²⁺ ions are aligned along the helix axes inside the duplexes with the Cu²⁺-Cu²⁺ distance of 3.7 ± 0.1 Å. The Cu²⁺ ions are coupled in a ferromagnetic manner with one another through unpaired d electrons to form magnetic chains. This strategy represents a new method for self-assembled metal arrays in a predesigned fashion, leading to the possibility of metal-based molecular devices such as molecular magnets and wires.     

Development of a Metal‐Ion‐Mediated Base Pair for Electron Transfer in DNA

A new C‐nucleoside structurally based on the hydroxyquinoline ligand was synthesized that is able to form stable pairs in DNA in both the absence and the presence of metal ions. The interactions between the metal centers in adjacent Cu^II‐mediated base pairs in DNA were probed by electron paramagnetic resonance (EPR) spectroscopy. The metal–metal distance falls into the range of previously reported values. Fluorescence studies with a donor–DNA–acceptor system indicate that photoinduced charge‐transfer processes across these metal‐ion‐mediated base pairs in DNA occur more efficiently than over natural base pairs.     

A DNA Structure Containing AgI‐Mediated G:G and C:C Base Pairs

Metal‐mediated base pairs have been extensively utilized in many research fields, including genetic‐code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag^I is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C‐Ag^I‐C pairs and the first reported G‐Ag^I‐G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag^I‐mediated base‐pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy‐metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence‐dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between Ag^I and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.     

The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N‐aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)₂, and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non‐modified PNA duplex adopts a P‐type helical structure similar to that of previously characterized PNAs. The atomic‐level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P‐type helical structure, its flexibility is relatively high. For example, the base‐pair rise in the bipyridine‐containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π‐stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl‐modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.     

A novel silver(i)-mediated DNA base pair

We have generated a novel silver(I)-mediated unnatural DNA base pair consisting of two 2,6-bis(ethylthiomethyl)pyridine nucleobases SPy. This metallo-base pair has a remarkably high pairing stability and selectivity which rivals that of the natural base pairs dA:dT and dC:dG. UV-melting experiments revealed that the dSPy:dSPy self-pair can replace natural base pairs at multiple sites and still form stable DNA duplexes.     

Electrochemical synthesis and magnetic studies of neutral transition metal imidazolates and pyrazolates

Summary The single-step electrochemical synthesis of neutral transition metal complexes of imidazole, pyrazole and their derivatives has been achieved at ambient temperature. The metal was oxidized in an Me₂CO solution of the diazole to yield complexes of the general formula: [M(Iz)₂] (where M = Co, Ni, Cu, Zn; Iz = imidazolate); [M(MeIz)₂] (where M = Co, Ni, Cu, Zn; MeIz = 4-methylimidazolate); [M(PrⁱIz)₂] (where M = Co, Ni, Cu, Zn; PrⁱIz = 2-isopropylimidazolate); [M(pyIz)_n] (where M = Co^III, Cu^II, Zn^II; pyIz = 2-(2-pyridyl)imidazolate); [M(Pz)_n] (where M = Co^III, Ni^II, Cu^II, Zn^II; Pz = pyrazolate); [M(ClPz)_n] and [M(IPz)_n] (where M = Co^III, Ni^II, Cu^II, Zn^II; ClPz = 4-chloropyrazolate; IPz = 4-iodopyrazolate); [M(Me₂Pz)_n] (where M = Co^II, Cu^I, Zn^II; Me₂Pz = 3,5-dimethylpyrazolate) and [M(BrMe₂Pz)_n] (where M = Co^II, Ni^II, Cu^I, Zn^II; BrMe₂Pz = 3,5-dimethyl-4-bromopyrazolate). Vibrational spectra verified the presence of the anionic diazole and electronic spectra confirmed the stereochemistry about the metal centre. Variable temperature (360-90 K) magnetic measurements of the cobalt and copper chelates revealed strong antiferromagnetic interaction between the metal ions in the lattice. Data for the copper complexes were fitted to a Heisenberg (S= ) model for an infinite one-dimensional linear chain, yielding best fit values of J=–62––65cm^–1 andg = 2.02–2.18. Data for the cobalt complexes were fitted to an Ising (S= ) model with J=–4.62––11.7cm^–1 andg = 2.06–2.49.     

Synthesis,spectral, redox and antimicrobial activities of Schiff base complexes derived from 1-phenyl-2,3-dimethyl-4-aminopyrazol-5-one and acetoacetanilide

Novel terdentate neutral complexes of Cu^II, Ni^II, Co^II, Mn^II, Zn^II, Cd^II, Hg^II, VO^II, ZrO^II and UO₂ ^II have been prepared using a Schiff base derived from 1-phenyl-2,3-dimethyl-4-aminopyrazol-5-one (4-aminoantipyrine) and acetoacetanilide. The structural features of the chelates have been confirmed by microanalytical data, i.r., u.v.–vis., ¹H-n.m.r., e.s.r. and mass spectral techniques. Electronic absorption and i.r. spectra of the complexes indicate an octahedral geometry around the central metal ion, except for the VO^II and ZrO^II complexes which show square pyramidal geometry. The monomeric and neutral nature of the complexes are confirmed from their magnetic susceptibility and low conductance values. The cyclic voltammogram of the copper complex in MeCN at 300 K shows a quasi-reversible peak for the couple Cu^II/Cu^III at Ep_c = 0.47 and Ep_a = 0.61 V versus Ag/AgCl and two irreversible peaks for Cu^II Cu^I and Cu^I Cu⁰ reduction at Ep_c = –0.63 and – 0.89 V respectively. The e.s.r. spectra of copper and vanadyl complexes in DMSO solution at 300 K and 77 K were recorded and their salient features are reported. The molecular orbital coefficients (², ²) were calculated for complexes. The antimicrobial activity of the ligand and its complexes have been extensively studied on microorganisms such as Staphylococcus aureus, Klebsiela pneumoniae, Bacillus subtillis, Escherichia coli, Citrobacter ferundii and Salmonella typhi. Most of the complexes have higher activities than that of the free ligand.