Solution Structure of a Parallel-Stranded Oligoisoguanine DNA Pentaplex Formed by d(T(iG)(4) T) in the Presence of Cs(+) Ions

What a pentaplexing situation: Isoguanine (iG) is an isomer of guanine, where the positions of the C2 amino group and the C6 carboxy group are swapped. iG can self-assemble into pentads in the presence of alkali metal cations. Cs(+) ions were found to stabilize a pentaplex of d(T(iG)(4) T). Solution NMR studies of this pentaplex in the presence of Cs(+) ions (or Na(+) , K(+) , Rb(+) , or NH(4) (+) cations) demonstrate its stability and structure.     

Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules

The polaron might play an important role in the process of charge migration through duplex DNA stack. In the present work, we investigate properties of hole polarons in DNA molecules containing identical base pairs, such as poly(G)-poly(C) and poly(A)-poly(T), An extended tight-binding model (extended Su-Schrieffer-Heeger model), which involves the effect of an electric field in the direction of DNA stack, will be introduced. The transfer integral and electron-phonon coupling parameters in this model are obtained according to ab initio calculation for different base pair dimers. Calculations reveal that the polaron in poly(A)-poly(T) has a wider shape and a higher mobility under a specific electric field than that in poly(G)-poly(C) DNA stack.     

Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

In this study, using QM/QTAIM calculations in the continuum with ε = 1 under normal conditions, we have revealed for the first time the nondissociative A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions. It was established that they proceed via the essentially nonplanar transition states (С₁ symmetry) through the intermediates, which are wobbled conformers (С₁ symmetry) theoretically predicted in our previous work (Brovarets’ et al., Frontiers in Chemistry, 2018, 6:8, 10.3389/fchem.2018.00008) of the classical А·Т DNA base pairs—Watson–Crick А·Т(WC), reverse Watson–Crick А·Т(rWC), Hoogsteen А·Т(Н) and reverse Hoogsteen А·Т(rН). At this, the A·T(H)↔A·T(rWC) and A·T(WC)↔A·T(rH) conformational transformations are controlled by the transition states (TSs) stabilized by the participation of the intermolecular (T)N3H···N6(A) H‐bond (∼3.70 kcal·mol⁻¹) between the imino group N3H of T and pyramidilized amino group N6H₂ of A. Gibbs free energies of activation for these processes consist 12.22 and 11.11 kcal·mol⁻¹, accordingly, under normal conditions. TSs, which control the A·T(WC)↔A·T(rWC) and A·T(H)↔A·T(rH) conformational transitions are stabilized by the participation of the intermolecular (T)N3H···N6(A) H‐bond (5.82 kcal·mol⁻¹) and bifurcating intermolecular (T)N3H···N6(A) (5.00) and (T)N3H···N7(A) (0.61 kcal·mol⁻¹) H‐bonds, accordingly. Notably, in these two TSs amino group N6H₂ of A is significantly pyramidilized; Gibbs free energies of activation for these reactions are 19.07 and 19.71 kcal·mol⁻¹, accordingly.     

Structure and cytotoxicity of zinc (II) and cobalt (II) complexes based on 1,3,5‐tris(1‐imidazolyl) benzene

Three novel complexes, [Zn (tib)₂·(H₂O)₂]·(NO₃)₂ ( 1 ), [Co (tib)₂]·2NO₃ ( 2 ) and [Co₂(tib)₂(btc)]·H₂O ( 3 ) [H₄btc = 1,2,4,5‐benzenetetracarboxylic acid; H₂tib = 1,3,5‐tris(1‐imidazolyl)benzene], were synthesized and characterized by single‐crystal X‐ray, IR and elemental analysis. The interaction of these complexes with FS‐DNA (fish sperm DNA) was monitored, and binding constants were determined using UV/Vis, which revealed that they have the ability to bind to FS‐DNA. DNA‐binding constants (K) for the three complexes were 2.2 × 10⁴ m ^?1, 0.7 × 10⁴ m ^?1 and 0.09 × 10⁴ m ^?1, respectively. The interaction capacity of the complexes with FS‐DNA has been investigated by fluorescence spectroscopy. Stern–Volmer quenching plot values for complexes 1 , 2 and 3 were 0.3784, 0.1028 and 0.076, respectively. The viscosity measurement suggested that complexes 1 , 2 and 3 interact with DNA in an intercalation mode. In addition, anti‐cancer activities of these complexes investigated through MTT assays in vitro indicated that the complexes showed good cytotoxic activity against cancer cell lines. Cytotoxic activity of test complexes against two different cancer cell lines (HeLa and KB cells) showed significant cancer cell inhibition rates. Flow cytometry experiments and morphological apoptosis studies showed that the complexes induced apoptosis of HeLa tumor cell lines. Finally, a further molecular docking technique was employed to confirm the binding of the complexes toward the molecular target DNA.     

Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

DNA binding and nuclease activity of cationic iron(IV) and manganese(III) corrole complexes

Cationic meso(4‐N‐methylpyridyl)‐based metallocorroles, μ‐oxo iron corrole dimer ( 1b ) and manganese corrole monomer ( 2b ), were synthesized and characterized. The interactions of these two metal corrole complexes with CT‐DNA were studied by UV–visible, fluorescence and circular dichroism spectroscopic methods, as well as by viscosity measurements. The results revealed that 1b interacts with CT‐DNA in a difunctional binding mode, i.e. non‐classical intercalation and outside groove binding with H‐aggregation, while 2b can interact with CT‐DNA via an outside groove binding mode only. The binding constants K_b of 1b and 2b were 4.71 × 10⁵ m ^?1 and 2.17 × 10⁵ m ^?1, respectively, indicating that 1b can bind more tightly to CT‐DNA than 2b . Furthermore, both complexes may cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide or tert‐butyl hydroperoxide (TBHP), albeit 1b exhibited a little higher efficiency. The inhibitor tests suggested that singlet oxygen and high‐valent (oxo)iron(VI) corrole or (oxo)manganese(V) corrole might be the active intermediates responsible for the oxidative DNA scission. Copyright © 2014 John Wiley & Sons, Ltd.     

Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA

Cationic porphyrin derivatives such as meso-tetrakis(4-N-methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO(5) system was due to an oxidative attack, within the minor groove of B-DNA, at the C5' or C1' carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5'-TCGTCAAACCGC)-d(5'-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5'.     

Novel Cr (III), Fe (III) and Ru (III) Vanillin Based Metallo‐Pharmaceuticals for Cancer and Inflammation Treatment: Experimental and Theoretical Studies

In this study, three novel complexes comprising trivalent Cr (III), Fe (III) and Ru (III) with imine ligand derived from 2‐amino‐3‐hydroxypyridine and o‐vanillin (H₂L) have been synthesized and characterized via wide range of spectroscopic and analytical tools such as ¹H NMR and ¹³C NMR, infrared (IR) and UV–Vis spectrophotometry, conductivity and magnetic measurements. The obtained results along with DFT data confirmed a 1:1 (metal: ligand) stoichiometry with non‐planner geometries for the three complexes. The binding action and the docking study of the prepared metal‐complexes to calf thymus DNA was also studied by absorption spectra and viscosity technique, which revealed that the three complexes interact strongly with DNA through intercalative binding mode. Significantly, these metal‐imine complexes showed strong and efficient anti‐inflammatory and antimicrobial activities against various gram‐positive (Microccus luteus), gram‐negative (Escherichia coli and Serratia marcescence) bacteria, and three strains of fungus. Moreover, all complexes exhibited more potent cytotoxicity effect on the outgrowth of different types of carcinoma cells, including human colon (HCT‐116 cell line), breast (MCF‐7 cell line), and hepatic cellular (HepG‐2), than the clinically‐proven Vinblastine standard.     

From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations

It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set results, estimated from calculations with the family of polarization-consistent pcS-n basis sets. This implies that the remaining basis set error of the aug-cc-pVTZ-J basis set is very similar in DFT and CCSD(T) calculations. As the aug-cc-pVTZ-J basis set is significantly smaller, CCSD(T)/aug-cc-pVTZ-J calculations allow in combination with affordable DFT/pcS-n complete basis set calculations the prediction of nuclear shieldings at the CCSD(T) level of nearly similar accuracy as those, obtained by fitting results obtained from computationally demanding pcS-n calculations at the CCSD(T) limit. A significant saving of computational efforts can thus be achieved by scaling inexpensive CCSD(T)/aug-cc-pVTZ-J calculations of nuclear isotropic shieldings with affordable DFT complete basis set limit corrections.     

Copper(II)–Girard's T complex as a promising anti‐tumor agent

A copper(II) complex was evaluated for its anti‐tumor activity. Firstly, electrophoretic studies were applied on the complex. These studies revealed the binding of the complex to calf thymus DNA, leading to a delay in electrophoretic mobility of the DNA molecule. Secondly, spectroscopic data pointed out that the λ_max of DNA was shifted to a longer wavelength, which was accompanid by a hyperchromic shift. Moreover, the λ_max of copper(II) complex was shifted to a shorter wavelength. The favorable reaction conditions between the DNA molecule and the copper(II) complex were studied. Thirdly, The effects of the ligand and the Cu(II) ion were tested separately on the DNA molecule by electrophoresis technique. Furthermore, the fluorescence quenching of DNA bound ethidium ion by Cu(II)‐Girard's T complex was noticed. The IR spectral data of DNA before and after the reaction with the copper(II) complex indicated that the interaction takes place through the carbonyl group of DNA nucleobases. Finally, a significant increase in the mean survival of EAC (Ehrlich ascites carcinoma) tumor‐bearing mice was observed when treated with the copper(II) complex. The tumor volume was also significantly reduced (p < 0.0001). Electrophoretic studies showed that the DNA pattern extracted from EAC cells of tumor‐bearing mice was affected after treatment with the copper(II) complex. Flow cytometric studies showed that this complex may be taken into consideration in seeking novel anti‐tumor agents. Copyright © 2010 John Wiley & Sons, Ltd.     

Dicoumarol complexes of Cu(II), Fe(II) and Fe(III): preparation,characterization, in‐vitro antibacterial and DNA binding activity

3‐3′‐Benzylidenebis[4‐hydroxycoumarin] or 4‐nitro,3‐3′‐benzylidenebis[4‐hydroxycoumarin] or 4‐methoxy,3‐3′‐benzylidenebis[4‐hydroxycoumarin] and their complexes with Cu(II), Fe(II) and Fe(III) were synthesized and characterized using ¹H‐NMR, ¹³C‐NMR, IR spectra, electronic spectra, magnetic measurements and elemental analyses. The ligands, metal salts, complexes, control and standard drug were tested for their in‐vitro antibacterial activity against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Salmonella typhi, and Serratia marcescens. The metal complexes exhibit good activity against bacterial strains compared with parental compounds and moderate compared with the standard drug (ciprofloxacin). In‐vitro DNA‐binding activity was carried out using agarose gel electrophoresis. The synthesized compounds show effective DNA‐binding activity. Copyright © 2007 John Wiley & Sons, Ltd.     

基于聚硫堇膜对DNA杂交的直接电化学检测

In this work, the application of a conducting polymer, poly（thionine）, modified electrode as matrix to DNA immobilization as well as transducer to label-free DNA hybridization detection was introduced. The electropolymerization of thionine onto electrode surface was carried out by a simple two-step method, which involved a preanodization of glassy carbon electrode at a constant positive potential in thionine solution following cyclic voltammetry scans in the solution. Electrochemical detection was performed by differential pulse voltammetry in the electroactivity potential domain of poly（thionine）. The resulting poly（thionine） modified electrode showed a good stability and electroactivity in aqueous media during a near neutral pH range. Additionally, the pendant amino groups on the poly（thionine） chains enabled poly（thionine） modified electrode to immobilize phosphate group terminated DNA probe via covalent linkage. Hybridization process induced a clear decrease in poly（thionine） redox current, which was corresponding to the decrease in poly（thionine） electroactivity after double stranded DNA was formed on the polymer film. The detection limit of this electrochemical DNA hybridization sensor was 1.0 × 10^-10mol/L. Compared with complementary sequence, the hybridization signal values of 1-base mismatched and 3-base mismatched samples were 63.9% and 9.2%, respectively.