Discrimination Between 8‐Oxo‐2′‐Deoxyguanosine and 2′‐Deoxyguanosine in DNA by the Single Nucleotide Primer Extension Reaction with Adap Triphosphate

The adenosine derivative of 2‐oxo‐1,3‐diazaphenoxazine (Adap) exhibits a superb ability to recognize and form base pairs with 8‐oxo‐2′‐deoxyguanosine (8‐oxo‐dG) in duplex DNA. In this study, the triphosphate of Adap (dAdapTP) was synthesized and tested for single nucleotide incorporation into primer strands using the Klenow Fragment. The efficiency of dAdapTP incorporation into 8‐oxo‐dG‐containing templates was more than 36‐fold higher than with dG‐containing templates, and provides better discrimination than does the incorporation of natural 2′‐deoxyadenosine triphosphate (dATP). The selective incorporation of dAdapTP into 8‐oxo‐dG templates was therefore applied to the detection of 8‐oxo‐dG in human telomeric DNA sequences extracted from H₂O₂‐treated HeLa cells. The enzymatic incorporation of dAdapTP into 8‐oxo‐dG‐containing templates may provide a novel basis for sequencing oxidative DNA damage in the genome.     

(Nitro‐κN)[2‐(phenyldiazenyl‐κN2)pyridine‐κN](2,2′:6′,2′′‐terpyridine‐κ3N)ruthenium(II) tetrafluoroborate

The Ru—N bond distances in the title complex, [Ru(NO₂)(C₁₁H₉N₃)(C₁₅H₁₁N₃)]BF₄ or [Ru(NO₂)(tpy)(azpy)]BF₄, [tpy is 2,2′:6′,2′′‐ter­pyridine and azpy is 2‐(phenyl­azo)­pyridine], are Ru—N_py 2.063 (4), Ru—N_azo 2.036 (4), Ru—N_nitro 2.066 (3) Å, and Ru—N_tpy 2.082 (4), 1.982 (3) and 2.074 (4) Å. The azo N atom is trans to the nitro group. The azo N=N bond length is 1.265 (5) Å, which is the shortest found in such complexes to date. This indicates a multiple bond between Ru and the N atom of the nitro group, and π‐­backbonding [dπ(Ru) π*(azo)] is decreased.     

Silver Ions in Non‐canonical DNA Base Pairs: Metal‐Mediated Mismatch Stabilization of 2′‐Deoxyadenosine and 7‐Deazapurine Derivatives with 2′‐Deoxycytidine and 2′‐Deoxyguanosine

Novel silver‐mediated dA?dC, dA*?dC, and dA*?dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA). 7‐Deazapurine nucleosides enforce silver ion binding and direct metal‐mediated base pair formation to their Watson–Crick face. New phosphoramidites were prepared from 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA, which contain labile isobutyryl protecting groups. Solid‐phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher T_m values) were observed for oligonucleotide duplexes with non‐canonical dA*?dC and dA?dC pairs in the presence of silver ions. The stability of the silver‐mediated base pairs was pH dependent. Silver ion binding was not observed for the dA?dG mismatch but took place when mismatches were formed between 7‐deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.     

DNA Interactions of the Functionalized (Mixed Polypyridine)ruthenium(II) Complex Bis(2,2′‐bipyridine‐κN1,κN1′)(methyl dipyrido[3,2‐a : 2′,3′‐c]phenazine‐11‐carboxylate‐κN4,κN5)ruthenium(2+) ([Ru(bpy)2(dppz‐11‐CO2Me)]2+)

A novel polypyridine ligand, dipyrido[3,2‐a:2′,3′‐c]phenazine‐11‐carboxylic acid methyl ester (=dppz‐11‐CO₂Me), and its ruthenium(II) complex, [Ru(bpy)₂(dppz‐11‐CO₂Me)]²⁺ ( 1 ), were synthesized and characterized. The binding properties of this complex to calf‐thymus DNA (CT‐DNA) were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that the complex binds to DNA in an intercalative mode and serves as a molecular ‘light switch’ for DNA. When irradiated at 365 nm, the complex 1 promoted the photocleavage of plasmid pBR‐322 DNA.     

μ‐Acetato‐1:2κ2O:O′‐diacetato‐1κ2O,O′;2κO‐bis(di‐2‐pyridylamine)‐1κ2N,N′;2κ2N,N′‐isothiocyanato‐2κN‐dicopper(II)

In the title dinuclear acetate‐bridged complex, [Cu₂(C₂H₃O₂)₃(NCS)(C₁₀H₉N₃)₂], the two Cu atoms are five‐coordinated, with a basal plane consisting of two N atoms of a di‐2‐pyridylamine (dpyam) ligand and two O atoms of two different acetate ligands. The axial positions of these Cu atoms are coordinated to N and O atoms from thio­cyanate and acetate mol­ecules, respectively, leading to a distorted square‐pyramidal geometry with τ values of 0.30 and 0.22. Both Cu^II ions are linked by an acetate group in the equatorial–equatorial positions and have syn–anti bridging configurations. Hydrogen‐bond inter­actions between the amine H atom and the coordinated and uncoordinated O atoms of the acetate anions generate an infinite one‐dimensional chain.     

μ‐2,2′,6,6′‐Tetramethyl‐4,4′‐bipyridine‐κ2N1:N1′‐bis[(diethylenetriamine‐κ3N,N′,N′′)palladium(II)] tetranitrate

The title compound, [Pd₂(C₄H₁₃N₃)₂(C₁₄H₁₆N₂)](NO₃)₄, comprises discrete tetracationic dumbbell‐type dinuclear complex molecules and noncoordinating nitrate anions. Two Pd(dien)²⁺ moieties (dien is diethylenetriamine) are joined by the rigid linear exo‐bidentate bridging 2,2′,6,6′‐tetramethyl‐4,4′‐bipyridine ligand to form the dinuclear complex, which lies across a centre of inversion in the space group P2₁/n, so that the rings in the 2,2′,6,6′‐tetramethyl‐4,4′‐bipyridine bridging ligand are parallel. In the crystal, the primary and secondary amino groups of the dien ligand act as hydrogen‐bond donors towards the nitrate anions to form a three‐dimensional hydrogen‐bond network.     

The Thermal N9/N7 Isomerization of N2‐Acylated 2′‐Deoxyguanosine Derivatives in the Melt and in Solution

The protected 2′‐deoxyguanosine derivatives 5a – c undergo N⁹→N⁷ isomerization in the melt and in solution. The rate of isomerization is much faster than in the case of the corresponding ribonucleosides and occurs even in the absence of a catalyst. In the melt (195°, 2 min), the N²,3′‐O,5′‐O‐tris(4‐toluoyl) derivative 5b and the N²‐acetyl‐3′,5′‐bis‐O‐[(tert‐butyl)dimethylsilyl] derivative 5c gave anomeric mixtures of the N⁷‐isomers 9b / 10b (43%) and 9c / 10c (55%), respectively. In addition, the N⁹‐α‐D ‐anomers 8b and 8c were obtained. Different from 5b , the isomerization of peracetylated 5a resulted in low yields. Compound 5b was also prone to isomerization performed in solution (toluene, 100°, 5 min; chlorobenzene, 120°, 5 min), furnishing the N⁷‐regioisomers in 24–53% yield. The highest yield of the N⁹→N⁷ isomerization occurred in the presence of 2‐deoxy‐3,5‐di‐O‐(4‐toluoyl)‐α‐D ‐erythro‐pentofuranosyl chloride.     

[N,N′‐Bis(3‐aminopropyl)ethylenediamine‐κ4N,N′,N′′,N′′′](trithiocyanurato‐κ2N,S)zinc(II) ethanol solvate

In the crystal structure of the title compound, [N,N′‐bis(3‐­amino­propyl)­ethyl­enedi­amine‐κ⁴N,N′,N′′,N′′′][1,3,5‐triazine‐2,4,6(1H,3H,5H)‐tri­thionato(2−)‐κ²N,S]­zinc(II) ethanol sol­vate, [Zn(C₈H₂₂N₄)₂(C₃HN₃S₃)]·C₂H₆O, the Zn^II atom is octa­hedrally coordinated by four N atoms [Zn—N = 2.104 (2)–2.203 (2) Å] of a tetradentate N‐donor N,N′‐bis(3‐­amino­propyl)­ethyl­enedi­amine (bapen) ligand and by two S and N atoms [Zn—S = 2.5700 (7) Å and Zn—N = 2.313 (2) Å] of a tri­thio­cyanurate(2−) (ttcH²⁻) dianion bonded as a bidentate ligand in a cis configuration. The crystal structure of the compound is stabilized by a network of hydrogen bonds.     

2‐Substituted dATP Derivatives as Building Blocks for Polymerase‐Catalyzed Synthesis of DNA Modified in the Minor Groove

2′‐Deoxyadenosine triphosphate (dATP) derivatives bearing diverse substituents (Cl, NH₂, CH₃, vinyl, ethynyl, and phenyl) at position 2 were prepared and tested as substrates for DNA polymerases. The 2‐phenyl‐dATP was not a substrate for DNA polymerases, but the dATPs bearing smaller substituents were good substrates in primer‐extension experiments, producing DNA substituted in the minor groove. The vinyl‐modified DNA was applied in thiol–ene addition and the ethynyl‐modified DNA was applied in a CuAAC click reaction to form DNA labelled with fluorescent dyes in the minor groove     

Chlorido[N,N′‐dibenzyl‐N′′‐(trichloroacetyl)phosphoramidato‐κ2O,O′](1,10‐phenanthroline‐κ2N,N′)copper(II)

In the title complex, [Cu(C₁₆H₁₆Cl₃N₃O₂P)Cl(C₁₂H₈N₂)], the Cu^II cation presents a square‐pyramidal environment, where the CuO₂N₂ base is formed by two O atoms from carbonyl and phosphoryl groups, and by two N atoms from a 1,10‐phenanthroline molecule. A coordinated Cl atom occupies the apex. N—H...Cl hydrogen bonds link the molecules into one‐dimensional chains. The trichloromethyl group is rotationally disordered over two positions, with occupancies of 0.747 (7) and 0.253 (7).     

Bis[(dihydrogen pyrophosphato‐κ2O,O′)(2,2′:6′,2′′‐terpyridine‐κ3N,N′,N′′)copper(II)] 4.5‐hydrate

The title copper complex, [Cu(H₂P₂O₇)(C₁₅H₁₁N₃)]₂·4.5H₂O, consists of two very similar independent Cu(Tpy)H₂P₂O₇ monomeric units (Tpy is 2,2′:6′,2′′‐terpyridine) plus four and a half water molecules of hydration, some of which are disordered. Tpy units bind through the usual triple bite via their N atoms, and the H₂P₂O₇²⁻ anions coordinate through two O atoms from two different phosphate units. Each independent CuN₃O₂ chromophore can be described as a slightly deformed square pyramid, with one of them having a sixth, semicoordinated, O atom from a centrosymmetrically related CuN₃O₂ unit in a weakly bound second apical position suggesting an octahedral environment for the cation and weak dimerization of the molecule. The two independent complex molecules are connected via two strong O—H...O interactions between the phosphate groups to form hydrogen‐bonded dinuclear units, further linked into [111] columns, resulting in a very complex three‐dimensional supramolecular structure through a variety of classical and nonclassical hydrogen bonds, as well as π–π interactions.     

μ‐{N,N′‐Bis[2‐(dimethyl­amino)ethyl]oxamidato(2–)}‐1κ2O,O′:2κ4N,N′,N′′,N′′′‐bis­(4,4′‐dimethyl‐2,2′‐bipyridine‐1κ2N,N′)dinickel(II) bis­(perchlorate)

In the crystal structure of the title complex, [Ni₂(C₁₀H₂₀N₄O₂)(C₁₂H₁₂N₂)₂](ClO₄)₂ or [Ni(dmaeoxd)Ni(dmbp)₂](ClO₄)₂ {H₂dmaeoxd is N,N′‐bis­[2‐(dimethyl­amino)ethyl]oxamide and dmbp is 4,4′‐dimethyl‐2,2′‐bipyridine}, the deprotonated dmaeoxd²⁻ ligand is in a cis conformation and bridges two Ni^II atoms, one of which is located in a slightly distorted square‐planar environment, while the other is in an irregular octa­hedral environment. The cation is located on a twofold symmetry axis running through both Ni atoms. The dmaeoxd²⁻ ligands inter­act with each other via C—H⋯O hydrogen bonds and π–π inter­actions, which results in an extended chain along the c axis.     

Bis(di‐2‐pyridylamine‐κ2N2,N2′)(nitrato‐κ2O,O′)nickel(II) nitrate

<!?tpct=26.8pt>In the ionic title compound, [Ni(NO₃)(C₁₀H₉N₃)₂]NO₃, the central Ni^II atom exhibits cis‐NiN₄O₂ octahedral coordination with three chelating ligands, viz. one nitrate anion and two di‐2‐pyridylamine (dpya) molecules. A second nitrate group acts as a counter‐ion. The complex cations and the nitrate anions are also linked by N—H...O hydrogen bonds. The compound was prepared in two different reproducible ways: direct synthesis from Ni(NO₃)₂ and dpya yielded systematically twinned crystals (the twinning law is discussed), while single crystals were obtained unexpectedly from the Ni(NO₃)₂/dpya/maleic acid/NaOH system.     

The twinned crystal structure of μ‐2,2′‐bipyrimidine‐1κ2N1,N1′:2κ2N3,N3′‐bis­{tris­[4,4,4‐trifluoro‐1‐(2‐thienyl)butane‐1,3‐dionato‐κ2O,O′]terbium(III)} ethyl acetate solvate

The title compound, [Tb₂(C₂₄H₁₂F₉O₆S₃)₂(C₈H₆N₄)]·C₄H₈O₂, has two terbium(III) centers bridged by the polyazine ligand 2,2′‐bipyrimidine (bpm), which is distorted from planarity by 7.0 (2)°. The terminal ligand 4,4,4‐trifluoro‐1‐(2‐thienyl)­butane‐1,3‐dione (tta) is bidentate, coordinating through the two O atoms, while the bridging ligand is bis‐bidentate, coordinating through four equivalent N atoms. Both the complex and the ethyl acetate solvent mol­ecules are dis­ordered. The structure was refined as a non‐merohedral twin.     

catena‐Poly[[[aqua(ethylenediamine‐κ2N,N′)(nitrato‐κO)copper(II)]‐μ‐4,4′‐dithiodipyridine‐κ2N:N′] nitrate monohydrate]

The title compound, {[Cu(NO₃)(C₂H₄N₂)(C₁₀H₈N₂S₂)(H₂O)]NO₃·H₂O}_n, is composed of a one‐dimensional linear coordination polymer involving cis‐protected copper(II) ions and a 4,4′‐dithiodipyridine bridging ligand. The polymeric chains run along the c‐axis direction. N—H...O and O—H...O hydrogen bonds involving the coordinating amine groups, nitrate ions and water molecules, as well as cocrystallized noncoordinating nitrate ions and water molecules, generate a three‐dimensional structure.     

catena‐Poly[[μ‐hexa­nedioato‐1κO1:2κO6‐bis­[aqua­(5‐carboxy­penta­noato‐κO)copper(II)]]‐di‐μ‐4,4′‐bipyridine‐1κN:1′κN′;2κN:2′κN′]

In the title compound, [Cu₂(C₆H₈O₄)(C₆H₉O₄)₂(C₁₀H₈N₂)₂(H₂O)₂]_n, the square‐pyramidally coordinated Cu atoms are bridged by both 4,4‐bipyridine and adipate ligands into ladder‐­like chains, with exo‐orientated 5‐carboxypentan­oate ligands pendant from both side rails. Half of the adipate ligand is related to the other half by inversion symmetry. Inter­chain O—H⋯O hydrogen bonds from the aqua ligands to the carbonyl O atoms of the 5‐carboxy­penta­noate ligands are responsible for the formation of two‐dimensional grid‐like (4,4)‐networks, which complete a twofold inter­penetration.     

Poly[(N,N‐dimethylformamide‐κO)(μ3‐4,4′‐ethylenedibenzoato‐κ5O,O′:O′:O′′,O′′′)(pyrazino[2,3‐f][1,10]phenanthroline‐κ2N8,N9)lead(II)]

In the title Pb^II coordination polymer, [Pb(C₁₆H₁₀O₄)(C₁₄H₈N₄)(C₃H₇NO)]_n, each Pb^II atom is eight‐coordinated by two chelating N atoms from one pyrazino[2,3‐f][1,10]phenanthroline (L) ligand, one dimethylformamide (DMF) O atom and five carboxylate O atoms from three different 4,4′‐ethylenedibenzoate (eedb) ligands. The eedb dianions bridge neighbouring Pb^II centres through four typical Pb—O bonds and one longer Pb—O interaction to form a two‐dimensional structure. The C atoms from the L and eedb ligands form C—H...O hydrogen bonds with the O atoms of eedb and DMF ligands, which further stabilize the structure. The title compound is the first Pb^II coordination polymer incorporating the L ligand.     

(1H‐Pyrazole‐κN2)(2,2′:6′,2′′‐terpyridine‐κ3N,N′,N′′)platinum(II) bis(perchlorate) nitromethane monosolvate

The reaction between [PtCl(terpy)]·2H₂O (terpy is 2,2′:6′,2′′‐terpyridine) and pyrazole in the presence of two equivalents of AgClO₄ in nitromethane yields the title compound, [Pt(C₃H₄N₂)(C₁₅H₁₁N₃)](ClO₄)₂·CH₃NO₂, as a yellow crystalline solid. Single‐crystal X‐ray diffraction shows that the dicationic platinum(II) chelate is square planar with the terpyridine ligand occupying three sites and the pyrazole ligand occupying the fourth. The torsion angle subtended by the pyrazole ring relative to the terpyridine chelate is 62.4 (6)°. Density functional theory calculations at the LANL2DZ/PBE1PBE level of theory show that in vacuo the lowest‐energy conformation has the pyrazole ligand in an orientation perpendicular to the terpyridine ligand (i.e. 90°). Seemingly, the stability gained by the formation of hydrogen bonds between the pyrazole NH group and the perchlorate anion in the solid‐state structure is sufficient for the chelate to adopt a higher‐energy conformation.     

(2,2′‐Biquinoline‐κ2N,N′)bis(nitrato‐κ2O,O′)copper(II)

In the title monomer, [Cu(NO₃)₂(C₁₈H₁₂N₂)], the six‐coordinated Cu^II atom lies on a twofold axis which bisects one of the ligands (a chelating biquinoline) and duplicates the remaining ligand, a chelating nitrate. The latter binds in a very asymmetric way, consistent with a Jahn–Teller distortion in the coordination polyhedron which, due to the triple chelation, is extremely distorted and difficult to describe in terms of any regular model.