O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron

Tetrahedron DNA structures were formed by the assembly of three-way junction ( TWJ ) oligonucleotides containing O⁶-2′-deoxyguanosine-alkylene-O⁶-2′-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2′-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O⁶-alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.     

Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.     

A Click Chemistry Approach to Developing Molecularly Targeted DNA Scissors

Nucleic acid click chemistry was used to prepare a family of chemically modified triplex forming oligonucleotides (TFOs) for application as a new gene-targeted technology. Azide-bearing phenanthrene ligands—designed to promote triplex stability and copper binding—were ‘clicked’ to alkyne-modified parallel TFOs. Using this approach, a library of TFO hybrids was prepared and shown to effectively target purine-rich genetic elements in vitro. Several of the hybrids provide significant stabilisation toward melting in parallel triplexes (>20 °C) and DNA damage can be triggered upon copper binding in the presence of added reductant. Therefore, the TFO and ‘clicked’ ligands work synergistically to provide sequence-selectivity to the copper cutting unit which, in turn, confers high stabilisation to the DNA triplex. To extend the boundaries of this hybrid system further, a click chemistry-based di-copper binding ligand was developed to accommodate designer ancillary ligands such as DPQ and DPPZ. When this ligand was inserted into a TFO, a dramatic improvement in targeted oxidative cleavage is afforded.     

Organotin(IV) complexes of NSAID,ibuprofen, X-ray structure of Ph3Sn(IBF), binding and cleavage interaction with DNA and in vitro cytotoxic studies of several organotin complexes of drugs

This study encompasses the synthesis and characterization of organotin(IV) derivatives of non-steroidal anti-inflammatory drug ibuprofen (IBF), viz. [(Me₃Sn)(IBF)] ( 1 ), [(Bu₃Sn)(IBF)] ( 2 ), [Ph₃Sn(IBF)] ( 3 ), {[Me₂Sn(IBF)]₂O}₂ ( 4 ) and [Bu₂Sn(IBF)₂] ( 5 ). The crystal structure of complex 3 , [Ph₃Sn(IBF)], indicates a highly distorted tetrahedral (td) geometry with anisobidentate mode of coordination of the carboxylate group with tin atom, and a similar structure has been proposed for other two triorganotin(IV) derivatives. Moreover, the DFT (density functional theory) calculation and other studies have verified a dimer distannoxane type of structure for complex 4 , {[Me₂Sn(IBF)]₂O}₂. Complex 5 has been found to exhibit a highly distorted octahedral geometry around the tin atom. To investigate the DNA binding profile of the synthesized complexes, viscosity measurement, UV–vis and fluorescence titrations were performed, which revealed an intercalative type of binding with DNA for IBF and complex 5 and external binding in case of the complexes 1 and 2 ; complexes 3 and 4 could not be studied owing to their insufficient solubility in tris buffer. Plasmid DNA fragmentation studies of IBF and complexes 1 , 2 and 5 indicate that they cleaved the pBR322 plasmid potentially. Further, the drugs IBF {2-[4-(2-methylpropyl)phenyl]propanoic acid}, MESNA (sodium 2-mercaptoethane-sulfonate), warfarin [2H-1-benzopyran-2-one,4-hydroxy-3-(3-oxo-1-phenylbutyl)], sulindac (2-{5-fluoro-1-[(4-methanesulfinylphenyl) methylidene]-2-methyl-1H-inden-3-yl}acetic acid) and their corresponding organotin(IV) complexes 1–19 (complexes 6–19 were synthesized/reported previously) were screened in vitro for cytotoxicity against human cancer cell lines viz. DU145 (prostate cancer), HCT-15 (colon adenocarcinoma), Caco-2 (colorectal adenocarcinoma), MCF-7 (mammary cancer), LNCaP (androgen-sensitive prostate adenocarcinoma) and HeLa (cervical cancer), through MTT reduction assay and the cause of cell death was investigated through acridine orange/ethidium bromide staining of cells and DNA fragmentation assay. The probable structure–cytotoxicity relationship is also discussed. The major role of apoptosis along with small necrosis was also validated by flow cytometry assay using annexin V–fluorescein isothiocyanate and propidium iodide analysis.     

Synthesis and characterization studies of 3-formyl chromone Schiff base complexes and their application as antitumor,antioxidant and antimicrobial

A novel Schiff base namely (E)-3-((2,6-dihydroxypyrimidin-4-ylimino)methyl)-4H-chromen-4-one and its Co (II), N (II)i, Cu (II) and Cd (II) complexes have been synthesized and proved by elemental analysis, molar conductance, thermal analysis (TGA), Inductive Coupled plasma (ICP), magnetic moment measurements, X-ray powder diffraction, IR, EI-mass,¹H NMR, ¹³C NMR,UV–Vis. and ESR spectral studies. On the basis of these data, it is evident that the Schiff base acts as bidentate via oxygen atom of carbonyl group and azomethine nitrogen atom for Co (II) complex; monobasic bidentate ligand for Ni (II), Cu (II) and Cd (II) complexes via oxygen atom of hydroxyl group and nitrogen atom of pyrimidine ring. The results showed all complexes have octahedral geometry. The average particle size of the ligand and its complexes were found to be 1.010–0.343 nm. The pharmacological action (antioxidant, antimicrobial and anticancer) of the prepared compounds is studied. The antitumor activity of the ligand and its metal complexes is evaluated against human liver carcinoma (HEPG2) cell. The data displayed the Co (II) complexes strong cytotoxicity where IC₅₀ values of Co (II) complex and 5-fluorouracil (stander drug) are 9.33 and 7.86 μg/ml respectively. The Co (II) and Cd (II) complexes have antibacterial activity more than ampicillin (stander drug). The interaction of the synthesized compounds with calf-thymus DNA (CT-DNA) has been performed via absorption spectra and viscosity technique. The DNA- binding constants have been determined.     

Water Soluble Nickel – metformin ternary complexes: Thermal,DNA binding and molecular docking studies

The Nickel (II) complexes [Ni(Cl)₂(metf)(o-phen)] (1), [Ni(Cl)₂(metf)(opda)] (2) , [Ni(Cl)₂(metf)(en)] (3) , [Ni(Cl)₂(metf)(2,2'-bipy)] (4) , (metf = metformin, o-phen = ortho-phenanthroline, opda = ortho-phenylenediamine, en = ethylenediamine, 2–2′ bipy = 2–2′ bipyridyl) were synthesized and characterized using LC–MS, elemental analysis, molar conductance measurements, TGA-DTA, IR spectroscopy, magnetic moment measurements and electronic spectroscopy. The central Ni²⁺ was found to be in octahedral geometry. The DNA interaction of these complexes have been studied by UV–visible absorption studies, fluorescence emission technique and viscosity measurement. The complexes showed absorption hyperchromism in UV–visible spectra with calf thymus DNA. The binding constants from UV–visible absorption studies were 7.42 × 10⁴, 0.74 × 10⁴, 3.19 × 10⁴, 5.9 × 10⁴ M⁻¹ for 1 , 2 , 3 and 4 , respectively and Stern-Volmer quenching constants from fluorescence studies were 0.16, 0.41, 0.23, 0.18, respectively. Viscosity measurements revealed that the binding of the complexes with DNA could be surface binding, mainly due to groove binding. The highest DNA cleavage activity of the complexes is recorded for complex 1 . The complexes were docked in to B-DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP* GP*TP*CP*GP*GP*T)-3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software. C Docker Intectraction energy of 1 , 2 , 3 and 4 complexes is 32.027, 31.427, 35.393 and 30.521 respectively. The highest docking score is seen for complex 3 .     

Tridentate Schiff base and 4,4′-bipyridine coordinated di/polynuclear Cu (II) complexes: Synthesis,crystal structure,DNA/protein binding and catecholase activity

4,4′-bipyridine bridged two Cu (II) complexes, [Cu₂L¹₂(4,4′-bipy)(H₂O)₂](ClO₄)₂ ( 1 ) and [Cu₂L²₂(4,4′-bipy)]_n·(2H₂O)_n ( 2 ) (where, HL¹ = 2-[(3-methylamino-propylimino)-methyl]-phenol, H₂L² = 3-[(2-hydroxy-3-methoxy-benzylidene)-amino]-propionic acid, and 4,4′-bipy = 4,4′-bipyridine) have been synthesized and characterized by single crystal structure determination, mass spectrometry, FT-IR, electronic absorption, and emission spectroscopy. Complex 1 is dinuclear cationic compound and counter balanced by perchlorate anion, whereas complex 2 possesses 1D poly-nuclear structure. Both the complexes crystallize in monoclinic system with P2₁/c space group and the copper centers possess square pyramidal geometry. H-bonding, C-H···π, π···π interactions results the formation of two dimentional supramolecular structure for both the complexes. Interactions of complexes with bovine serum albumins (BSA) and human serum albumins (HSA) have been studied by using electronic absorption and emission spectroscopic technique. The calculated values of binding constants (K_b) are (9.22 ± 0.26) × 10⁵ L mol⁻¹ ( 1 -BSA), (7.19 ± 0.16) × 10⁵ L mol⁻¹ ( 1 -HSA), (5.05 ± 0.20) × 10⁵ L mol⁻¹ ( 2 -BSA) and (3.56 ± 0.25) × 10⁵ L mol⁻¹ ( 2 -HSA). The mechanism of serum albumins-complex interactions have been investigated by fluorescence lifetime measurement. Fluorescence spectroscopic studies indicate that both the complexes interact with calf thymas-DNA. Catecholase activity of the complexes has been studied in methanol using 3,5-di-tert-butylcatechol (3,5-DTBC) as substrate and the result show that both the complexes are active for catalytic oxidation of 3,5-DTBC to 3,5-di-tert-butylquinone (3,5-DTBQ) in presence of molecular oxygen. Calculated values of turnover numbers are 71.81 ± 1.04 h⁻¹ and 69.45 ± 0.74 h⁻¹ for 1 and 2 , respectively.     

Synthesis,characterization, DNA binding,cytotoxicity and molecular docking properties of three novel butterfly-like complexes with nitrogen-containing heterocyclic ligands

Three novel complexes, namely [Nd·L₁·HCOO·(H₂O)₄] ( 1 ), [Pr·L₁·HCOO·(H₂O)₄] ( 2 ) and [In·L₂·Cl·(H₂O)₂] ( 3 ) (L₁ = 1,1-bis(5-(pyrazin-2-yl)-1,2,4-triazol-3-yl)methane, L₂ = 1,1-bis(5-(pyrazin-2-yl)-1,2,4-triazol-3-yl)ketone), were synthesized and characterized. The molecular structures of 1 – 3 were confirmed using single-crystal X-ray diffraction. All three obtained complexes are zero-dimensional and connected to each other by hydrogen bonds. In 1 and 2 the metal is surrounded by nine donors and 3 has seven coordination sites. The interaction of 1 – 3 with calf thymus DNA (CT-DNA) was explored using UV absorption spectra and fluorescence spectra. The intrinsic binding constants of 1 – 3 with CT-DNA are about 1.9 × 10⁴, 1.4 × 10⁴ and 1.1 × 10⁴, respectively. Stern–Volmer quenching plots of 1 – 3 have slopes of 0.1508, 0.134 and 0.1205, respectively. The ability of these complexes to cleave pBR322 plasmid DNA was demonstrated using gel electrophoresis assay. Apoptosis studies of the three novel complexes showed a significant inhibitory effect on HeLa cells. Furthermore, MTT assays were used to evaluate the anticancer activity of the three complexes. The cytotoxicity study indicated that complex 1 possesses a higher inhibitory rate of HeLa cells than the other complexes. Especially, the efficacy of 1 was shown to be the highest for cisplatin at 24 h. A further molecular docking technique was introduced to understand the binding of the complexes toward the target DNA.     

Mirror-Image Oligonucleotides: History and Emerging Applications

As chiral molecules, naturally occurring d -oligonucleotides have enantiomers, l -DNA and l -RNA, which are comprised of l -(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d -counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l -oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d -oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d - and l -oligonucleotides to form contiguous Watson–Crick base pairs with each other has ultimately led to the perception that l -oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l -oligonucleotides, while overcoming (and even exploiting) their inability to Watson–Crick base pair with the natural polymer. Herein, a brief history of l -oligonucleotide research is presented and emerging l -oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.     

Electrochemical Signal Enhancer Fabricated Using Lysine‐rich Peptide for Ultrasensitive Electrochemical DNA Biosensor Analysis

Here we present a novel design of electrochemical signal enhancer to increase the detection sensitivity of electrochemical DNA biosensors. The key element of this enhancer is a lysine‐rich peptide (LRP). Its C‐terminal is conjugated with a planer molecule, being able to intercalate into the base pairs of probe‐target duplexes. The lysine residues of LRP are covalently linked with electrochemical signal indicators, acting as an assembly of electrochemical signal indicators. Experimental results proved the feasibility of the novel design. We have examined the effects of the numbers of lysine residues and the hybridization conditions on the detection sensitivity. The optimization procedures have led to significant sensitivity enhancement, and the LOD (limit of detection) has been determined to be 1.4 amol. This enhancer demonstrates advantages of easy operation, simple instrumentation, and high exemption from environmental influence.