Berenil Complexation with a Nucleic Acid Triple Helix

Abstract

The interaction of berenii molecule, a minor groove binding drug, with T-A-T triple helix and A-T double helix was studied using circular dichroism spectroscopy and thermal denaturation. The triple helix was made by an oligonucleotide (dA)₁₂?x-(dT)₁₂?x-(dT)₁₂, where x is a hexaethylene glycol chain bridged between the 3′ phosphate of one strand and the 5′ phosphate of the following strand. This oligonucleotide is able to fold back on itself to form a very stable triplex. Circular dichroism spectroscopy demonstrates that berenil can bind to the triple helical structure. Spectral analysis shows that in the same ionic strength the drug bound to a double-stranded structure exhibits a conformation and an environment close to those observed in triple-stranded structure. The influence of the ionic strength on the interaction between the berenil molecule and the 36-mer is clearly demonstrated. We showed that when no NaCl salt is added in the buffer the triplex form of (dA)₁₂?x-(dT)₁2-x-(dT)₁₂ is stabilized by berenil whereas it is destabilized slightly by the dye when NaCl concentration is 1 M.     

三链核酸稳定性和生物学功能的研究进展

近10年来三链核酸的研究发展迅猛,已经成为分子生物学和基因工程的一个前沿领域.综述了最近在三链核酸稳定性和生物学功能方面的研究进展.较为详细地讨论了影响三链稳定性的各种内源和外源因素如：寡聚脱氧核苷酸(ODN)的长短 、序列、碱基修饰、骨架结构以及温度、酸度、离子强度 、配基等,同时对三链核酸的生物学功能进行了初步的总结,这些功能包括：控制基因转录,保护靶序列防止酶切,充当分子剪刀进行特定位点切割等.     

Structure-Function Relationship of Three Triple-Helical Nucleic Acids

Abstract

The nucleic acid triplexes poly d(T)·poly d(A)·poly d(T), poly (U)·poly (A)·poly (U), and poly (I)·poly (A)·poly (I) display a sort of continuity between each other. However, their morphologies present their own individuality which, considering those of their parent duplexes, are quite unexpected. This comparison helps to understand triplex structure-function relationship. While helical parameters are functions of the sugar pucker, low values of WC and Hoogsteen base-pair propellers is commonplace for triplexes and the Hoogsteen base-pair geometry monitors the effects of the interstrand phosphates charge-charge repulsion.

Synopsis

The nucleic acid triplexes poly d(T)·poly d(A)·poly d(T), poly(U)·poly(A)·poly(U), and poly (I)·poly (A)·poly (I) present distinct morphologies. Considering those of their parent duplexes, they are also quite unexpected.     

New chelate complexes of trivalent Y and lanthanides (Eu, Ho, Yb) with a triazene N-oxide: Synthesis, structural characterization and luminescence properties

Deprotonated 3-(4-nitrophenyl)-1-phenyltriazene N-oxide reacts with YCl₃·6H₂O and LnCl₃·6H₂O (Ln = Eu, Ho, Yb) to give the monoclinic chelate complexes [Y{O₂N(C₆H₄)NNN(O)Ph}₄](Et₃NH)·H₂O (1) (Ph = C₆H₅; Et = C₂H₅) and [Ln^III{O₂N(C₆H₄)NNN(O)Ph}₄](Et₃NH)·H₂O·{CH₃OH∗} {Ln^III = Eu (2), Ho (3), Yb∗ (4), in which the metal centers present a square antiprismatic configuration. As already observed for hydrated ammonium complexes of triazene-oxides ligands with (C₆H₄)−NO₂ groups, multiple, effective O···H and N···H interactions hold the species in supramolecular 3D assemblies. The optical and the luminescent properties of the triazene-oxide europium complex 2 are also presented and fully discussed.     

Iron(III) complexes: Preparation,characterization, antibacterial activity and DNA-binding

Iron(III) have been combined to well known quinolones (ciprofloxacin) and some Schiff bases with the help of coordination approach. Characterization of these compounds have been done using elemental analysis, magnetic measurements, thermogravimetric analysis, IR, UV-VIS, ¹H NMR and ¹³C NMR spectral investigation. Analytical studies suggest that the iron(III)-quinolone complexes assume a six-coordinated dimeric distorted octahedral geometry. All the compounds show a good antibacterial activity against broad range of bacteria like Bacillus cereus, Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Salmonella typhi and Serratia marcescens, whereas no significant inhibition towards growth of fungal strains like Aspergillus Niger, Aspergillus flavus and Lasiodiplodia theobromae. Analyses of all these compounds show effective sperm herring DNA inhibition.     

两种核酸染料染色效果的比较研究

用前染和后染两种不同的染色方法,研究比较SYBRGreenI和溴化乙锭(EB)两种核酸染料对凝胶中DNA的染色效果和灵敏度,及SYBRGreenI取代EB用于常规凝胶中核酸染色的可能性。结果表明,用前染法染色SYBRGreenI对琼脂糖凝胶中的核酸染色效果与EB相当;用后染法染色前者要优于后者,可显示5ng以下的DNA条带,在完全相同的操作条件下,其染色DNA条带背景清晰,灵敏度较高。因此,无致突变性新型染料SYBRGreenI可替代强致突变性染料EB用于检测凝胶中DNA片段大小、含量等,从而减少由于使用EB带来的环境污染和人体健康危害。     

The high-energy intraconfigurational spin-forbidden bands in the spectra of quadrate chromium(III) complexes

The high-energy intraconfigurational spin-forbidden bands expected in the region of 20 000 cm⁻¹ have been uncovered in the spectra of a number of trans-diacidobis(ethylenediamine) chromium(III)complexes. These bands have been fitted to the quadrate components of the cubic transition ⁴A_2g → ²T_2g including spin-orbit interaction. Two interconfigurational spin-forbidden bands in the spectrum of trans-[Cr(en)₂(dmf)₂](ClO₄)₃ have been uncovered and interpretted.     

New binuclear model compounds for the study of the 4f-4f exchange interaction

Two new homobinuclear 4f-4f complexes, [Ln^III(L)₃]₂, (Ln=Pr 1; Gd 2) have been synthesized (L⁻=2,6-diformyl-4-methylphenolato). The crystallographic investigation of 1 reveals centrosymmetric binuclear entities with the metallic centers connected by two of the anionic ligands. The praseodymium ions are bridged by the phenoxo oxygen atoms. One carbonyl group of a bridging molecule is coordinated to one Pr(III) ion, while the other one is coordinated to the second Pr(III) ion. The other four L⁻ ions act as terminal chelated ligands, through the phenoxo oxygen atom and one carbonyl group. The distance between the Pr(III) ions within the binuclear entity is 4.0711(4) Å. The supramolecular solid-state architecture is sustained by a system of π-π interactions. The cryomagnetic study of 2 reveals a very weak antiferromagnetic interaction between the Gd(III) ions (J=−0.053 cm⁻¹, ).     

简化核酸提取过程在病原体核酸检测中的应用现状和发展趋势

简化核酸提取过程相较于经典的试剂盒法和全自动核酸提取技术,凭借其简便的操作步骤、便携易用的仪器设备和简单的人员培训等优势在病原体核酸检测中得到广泛应用,为实现病原体核酸的快速检测和现场检测(Point-of-care testing,POCT)奠定了良好的基础。本文比较了不同的核酸提取方法,对简化核酸提取过程的方法学进行综述,讨论其在病原体核酸检测领域中的应用现状,并展望其发展趋势。     

Syntheses of linear-type S-bridged trinuclear complexes composed of heavy d metal ions and 2-aminoethanethiolate: comparative characterization by X-ray diffraction, spectroscopy and electrochemistry

The S-bridged trinuclear complexes composed of heavy d⁶ metal ions, [Rh^III{M(aet)₃}₂]³⁺ (M=Ir^III(1), Rh^III(2); aet = 2-aminoethanethiolate), have been prepared by the reactions of fac(S)-[M(aet)₃] with RhCl₃ · 3H₂O. The complexes were separated into meso (1a, 2a) and rac (1b, 2b) isomers by SP-Sephadex C-25 column chromatography. 1b and 2b were optically resolved by the column chromatographic method and characterized by CD spectroscopy. Crystal structures of 1a, 1b and 2a were determined by X-ray diffraction, and it was found that they consist of linear-type trinuclear structures. The central Rh(III) ion in the present complexes has d⁶ electronic configuration with the non-degenerated A-type cubic field term, and showed long Rh?M distances, acute S-M-S angles and obtuse Rh-S-M angles. These are in contrast with the complexes having the degenerated T-type cubic field term such as [M^′{M(aet)₃}₂]ⁿ⁺ (M^′=V^III, Mo^IV and Re^III, M=Ir^III, Rh^III, n=3 or 4). All the isomers have been comparatively characterized and discussed in solid state and the solution for spectrochemical and electrochemical properties.     

Synthesis, DNA-binding and photocleavage studies of cobalt(III) mixed-polypyridyl complexes: [Co(phen)(2)(dpta)](3+) and [Co(phen)(2)(amtp)](3+)

Two novel cobalt(III) mixed-polypyridyl complexes [Co(phen)(2)(dpta)](3+) and [Co(phen)(2)(amtp)](3+) (phen=1,10-phenanthroline, dpta=dipyrido-[3,2-a;2',3'-c]- thien-[3,4-c]azine, amtp=3-amino-1,2,4-triazino[5,6-f]1,10-phenanthroline) have been synthesized and characterized. The interaction of these complexes with calf thymus DNA was investigated by spectroscopic, cyclic voltammetry, and viscosity measurements. Results suggest that the two complexes bind to DNA via an intercalative mode. Moreover, these Co(III) complexes have been found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365nm. The mechanism studies reveal that hydroxyl radical (OH()) is likely to be the reactive species responsible for the cleavage of plasmid DNA by [Co(phen)(2)(dpta)](3+) and superoxide anion radical (O(2)(-)) acts as the key role in the cleavage reaction of plasmid DNA by [Co(phen)(2)(amtp)](3+).     

A new example of a tetranuclear iron(III) cluster containing the [Fe4O2] core: preparation, X-ray crystal structure, magnetochemistry and Mössbauer study of [Fe4O2(O2CMe)6(N3)2(phen)2]

Two synthetic procedures have been employed that allow access to the new tetranuclear cluster [Fe₄O₂(O₂CMe)₆(N₃)₂(phen)₂] (1), where phen is 1,10-phenanthroline. Complex 1 · 3MeCN displays an unusual structural asymmetry (observed for the second time) in its [Fe₄O₂]⁸⁺ core that can be considered as a hybrid of the bent (butterfly) and planar dispositions of four metal ions seen previously in such compounds with transition metals. Complex 1 has been characterized by variable-temperature magnetic susceptibility studies, and by IR and variable-temperature ⁵⁷Fe Mössbauer spectroscopies. Magnetochemical data reveal a diamagnetic ground state (S=0) with antiferromagnetic body-body and body-wingtip interactions between the iron(III) ions of the butterfly core (J_bb=−11 cm⁻¹, J_wb=−70 cm⁻¹). Magnetochemical and Mössbauer studies on 1 show that its structural asymmetry has practically no influence on these properties compared with the more symmetric types.     

Synthesis, structural characteristics, DNA binding properties and cytotoxicity studies of a series of Ru(III) complexes

Four related ruthenium(III) complexes, with the formula mer-[RuCl₃(dmso)(N−N)] (dmso = dimethyl sulfoxide; N−N = 2,2′-bipyridine (1), 1,10-phenantroline (2), dipyrido[3,2-f:2′,3′-h]quinoxaline (3) and dipyrido[3,2-a:2′,3′-c]phenazine (4)), have been reported. Complexes 3 and 4 are newly synthesized and characterized by X-ray diffraction. The hydrolysis process of 1-4 has been studied by UV-vis measurement, and it has been found that the extension of the N−N ligands can increase the stability of the complexes. The binding of these complexes with DNA has been investigated by plasmid cleavage assay, competitive binding with ethidium bromide (EB), DNA melting experiments and viscosity measurements. The DNA binding affinity is increased with the extension of the planar area of the N−N ligands, and complex 4 shows an intercalative mode of interaction with DNA. The in vitro anticancer activities of these compounds are moderate on the five human cancer cell lines screened.     

Coordination polymers of Ln(III): Synthesis, characterization, catalytic and antimicrobial aspects

Coordination polymers of HEAP-ED with La(III), Pr(III), Nd(III), Sm(III), Gd(III), Tb(III) and Dy(III) metal ions have been synthesized and characterized by elemental analyses, electronic spectra, magnetic susceptibilities, FTIR, NMR, scanning electronic microscopy (SEM) and thermogravimetric analyses. Catalytic activity of selected coordination polymers was examined for pharmaceutical important organic synthesis. Antimicrobial activity of isolated Ln(III) coordination polymers against Escherichia coli, Bacillus subtilis, Staphylococcus aureus (bacteria) and Saccharomyces cerevisiae (yeast) were measured. It was observed from the study that the Ln(III) coordination polymers acted as an efficient and effective catalysts and antimicrobial agents.     

Towards a new attenuating compound: a potentiometric, spectrophotometric and NMR equilibrium study on Fe(III), Al(III) and a new tetradentate mixed bisphosphonate-hydroxypyridinonate ligand

Coordination properties toward Fe(III) and Al(III) of a mixed bisphosphonate-hydroxypyridinonate ligand are presented. Potentiometric, spectrophotometric and NMR results allowed to conclude that Fe(III) and Al(III) coordination takes place on the pyridinone moiety. The high steric hindrance prevents the possibility of simultaneous coordination of both groups to the same metal ion. Quantum mechanical calculations confirm this finding allowing to determine the minimal length of the linker necessary for a stable conformation of complexes in which Fe(III) is coordinated both by pyridinone and bisphosphonate groups.     

Triboluminescence and crystal structure of the centrosymmetric complex [Tb(NO3)2(Acac)(Phen)2]·H2O

The atomic structure of crystals of the complex [Tb(NO₃)₂(Acac)(Phen)₂]·H₂O, (AA – acetylacetonate anion, Phen – 1,10‐phenanthroline) characterized by an intensive luminescence and triboluminescence has been determined by means of an X‐ray structural analysis method. Centrosymmetric crystals have a monoclinic syngony: a = 11.2298(1), b = 9.6492(1), c = 13.2745(1) Å, β = 101.290(1), space group P2/n, Z = 2, ρ_calc = 1.790 g/cm³. The crystal structure is represented by individual С₂₉Н₂₅N₆O₉Tb complexes linked through van der Waals interactions with clearly expressed cleavage planes. The Tb(III) atom coordination polyhedron reflects the state of a distorted square antiprism. The structural aspects of the suggested model of formation of the triboluminescent properties were considered and the role of the cleavage planes discussed. Copyright © 2016 John Wiley & Sons, Ltd.     

Effect of substituents on complex stability aimed at designing new iron(III) and aluminum(III) chelators

The solution equilibria of iron(III) and aluminum(III) with two classes of hard ligands (catechol, salicylic acid and their nitro-derivatives) have been reliably studied by potentiometric, spectrophotometric and NMR spectroscopy. The effect of the nitro substituent on the binding properties of catechol and salicylic acid has been examined thoroughly. The inductive and resonance properties of the substituent that, as expected, lower the basicity of the phenolic and carboxylic groups, lead to a general decrease in both protonation and complex formation constants. This decrease causes an increase in pM of between 0.2 and 1.1 pM units for the nitro-substituted salicylates and of about 4 units for 4-nitrocatechol, with a significantly higher chelating efficacy. The influence of the substituent on catechol and salicylic acid is discussed in detail on the basis of conditional constants at pH 7.4.     

The structure of the dichromium compound Cr2(μ-OH)2(μ-3,5Cl2-form)2(η-3,5Cl2-form)2

With exposure to trace amounts of air and moisture, the Cr₂(II, II) complex Cr₂(μ-3,5Cl₂-form)₄, where 3,5Cl₂-form is [(3,5-Cl₂C₆H₃)NC(H)N(3,5-Cl₂C₆H₃)⁻], undergoes an oxidative addition reaction. Structural information from the X-ray crystal structure of the edge-sharing bioctahedral (ESBO) Cr₂(III, III) product Cr₂(μ-OH)₂(μ-3,5Cl₂-form)₂(η²-3,5Cl₂-form)₂ (1) indicates 1 has a significantly longer Cr–Cr distance [2.732(2) Å] than Cr₂(μ-3,5Cl₂-form)₄ [1.9162(10) Å], but the shortest Cr–Cr distance in an ESBO Cr₂(III, III) complex recorded to date.     

Preparation and characterization of manganese(III) halide derivatives of N,N′-bis(aminobenzylidene)-1,2-ethanediamine

The preparation and characterization of manganese(III) complexes containing the quadridenate ligand, N,N′-bis(aminobenzylidene)-1,2-ethanediamine (H₂amben), and its previously unreported analogue, N,N′-bis(2-amino-5-nitro-benzylidene)-1,2-ethanediamine (H₂nitroamben), are described. The new manganese(III) halide/pseudohalide complexes, Mn(amben)X · nH₂O and Mn(nitroamben)X · nH₂O (X = Cl, Br, I, NCS; n =  0.5 or 1), were isolated as red-brown, microcrystalline solids, which were characterized fully.     

Synthesis, structure and antitumor activity of [RhCl3(N-N)(DMSO)] polypyridyl complexes

The [RhCl₃(N-N)(DMSO)] complexes, the N-N being 2,2′-bipyridine (1), 1,10-phenanthroline (2), 4,7-diphenyl-1,10-phenanthroline (3), 4,4′-dimethyl-2,2′-bipyridine (4) and 1,10-phenanthroline-5,6-dione (5), have been synthesized and characterized with spectroscopic methods. The compounds 2-5 adopt mer- and complex 1fac-structure. The molecular and electronic structure studies of mer- and fac-complexes with bpy and phen ligands at the DFT B3LYP level with 3-21G^∗∗ basis set showed that mer-isomers are more stable. The cytostatic activity of the [RhCl₃(N-N)(DMSO)] complexes against Caco-2 and A549 tumor cells have been studied. Their antibacterial activity have also been investigated. It has been found that the very promising biological activity show complexes 2, 3 and 4.