Synthesis,DNA-binding and cleavage studies of macrocyclic copper(II) complexes

Two macrocyclic copper(II) complexes, [CuL¹](ClO₄)₂ (L¹ = 2,6,9,13-tetraparacyclophane, a Schiff base) and [CuL²]Cl₂ [L² = 3,10-bis(2-benzyl)-1,3,5,8,10,13-hexaazacyclotetradecane] have been prepared and characterized by elemental analysis, u.v.–vis., i.r. and mass spectra. Absorption, fluorescence, circular dichroic spectra and viscosity experiments have been carried out on the interaction of the two complexes with calf thymus CT DNA. The results suggest that both complexes can bind to CT DNA by intercalation via the aromatic moiety ring in the macrocycle into the base pairs of DNA. [CuL¹](ClO₄)₂ binds to CT DNA more strongly than [CuL²]Cl₂. The position of the aromatic ring in the macrocycle plays an important role in deciding the extent of binding of the complexes to DNA. Significantly, the complexes have been found to be single-strand DNA cleavers in the presence of H₂O₂ or/and 2-mercaptoethanol.     

A bis(2,2′-Bipyridine) (Dipyrido[3, 2-a:2′ 3′-c]Phenazine-N4N5) Ruthenium(II)-Based Electrochemiluminescence Biosensor for Evaluation of DNA Damage

The electrochemiluminescence of bis(2, 2′-bipyridine) (dipyrido[3, 2-a:2′ 3′-c]phenazine-N₄N₅) ruthenium(II) ([Ru(bpy)₂(dppz)]²⁺) was used to monitor deoxyribonucleic acid (DNA) charge transfer with tri-n-propylamine as a coreactant. This system was used to measure damage to DNA induced by perfluorooctanoic acid. Fifteen-base pairs of double-stranded DNA with a thiol group at the 5′ end position were covalently bonded to a gold electrode. An electrochemiluminescence sensor was then constructed by incubating the modified gold electrode in [Ru(bpy)₂(dppz)]²⁺ solution for 30 min. For comparison, single-stranded DNA, well-matched double-stranded DNA, and single base-mismatched double-stranded DNA were assembled on the gold surface. The results showed that the electrochemiluminescence behavior of the DNA sensors were unique. The electrochemiluminescence decreased when the [Ru(bpy)₂(dppz)]²⁺-DNA ECL sensor was incubated in a perfluorooctanoic acid solution. The damage to DNA caused by perfluorooctanoic acid was monitored using a combination of DNA charge transfer theory and the interaction between DNA and [Ru(bpy)₂(dppz)]²⁺. The detection limit for perfluorooctanoic acid was 1 × 10^?12 mol/L. [Ru(bpy)₂(dppz)]²⁺ was shown to be a sensitive electrochemiluminescence sensor for the determination of DNA damage.     

Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase

Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg²⁺ cofactor with Mn²⁺ or Co²⁺. Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF₄⁻ and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn²⁺ and Co²⁺ in localizing the ATP cofactor in large oligomeric protein assemblies. ³¹P PCSs induced in the Co²⁺-containing sample are then used to localize the DNA phosphate groups on the Co²⁺ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.     

Selective,pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives

The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (K_b=10⁵−10⁶ M⁻¹) to representative quadruplex forming oligonucleotides 22AG , c-myc , c-kit , and a2 , than to duplex calf thymus (ct) DNA (K_b=5-7×10⁴ M⁻¹). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (K_b=1.2×10⁶ M⁻¹), whereas the binding constant towards ct DNA is lower (K_b=3.9×10³ M⁻¹) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φ_fl=0.01) and quadruplex DNA (Φ_fl=0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.     

Synthesis,spectroscopic/electrochemical characterization and DNA interaction study of novel ferrocenyl‐substituted porphyrins

We report the synthesis and characterization of two new meso‐ferrocenylporphyrins, with the ferrocenyl unit attached at the para position of a C₆F₄ group by a C? N bond with ? NH(CH₂)₂NH? ( 2a ) and ? NH(CH₂)₄NH? ( 2b ) spacers. Compounds 2a and 2b were characterized through elemental analyses, electrospray ionization high‐resolution mass spectrometry, ¹H NMR, UV–visible and fluorescence spectroscopies, electrochemistry and spectroelectrochemistry. The free base porphyrin 2 was included for comparison purposes. The binding ability of 2 and the porphyrin derivatives 2a and 2b with calf thymus DNA was determined using UV–visible and fluorescence spectroscopies. The results suggest that the interaction of these systems most probably occurs through π‐stacking by non‐classical modes involving the partial insertion of the C₆F₅ ring between adjacent base pairs on DNA and possible hydrogen interaction with the aliphatic ? NH(CH₂)_nNH? (n = 2 or 4) groups with calf thymus DNA. Moreover, we also demonstrate that porphyrins generate singlet oxygen species and show good photostability after irradiation.     

Synthesis,crystal structure,DNA binding,and oxidative cleavage activity of copper(II)-bipyridyl complexes containing tetraalkylammonium groups

Two copper(II) complexes of disubstituted 2,2′-bipyridine (bpy = 2, 2′-bipyridine) with tetraalkylammonium groups, [Cu(L¹)₂Br](ClO₄)₅·2H₂O (1) and [Cu(L²)₂Br](ClO₄)₅·H₂O (2) (L¹ = [4, 4′-(Et₃NCH₂)₂-bpy]²⁺, L² = [4, 4′-((n-Bu)₃NCH₂)₂-bpy]²⁺), have been synthesized and characterized. X-ray crystallographic study of 1 indicates that Cu(II) is a distorted trigonal bipyramidal or square pyramid. DNA binding of both complexes was studied by UV spectroscopic titration. In the presence of reducing reagents, the cleavage of plasmid pBR322 DNA mediated by both complexes was investigated and efficient oxidative cleavage of DNA was observed. Mechanistic study with reactive oxygen scavengers indicates that hydrogen peroxide and singlet oxygen participate in DNA cleavage.     

Review: Synthesis,characterization, and DNA-binding properties of Ru(II) molecular “light switch” complexes

This article presents recent progress in our laboratory on the interactions of Ru(II) polypyridyl complexes with calf thymus DNA (CT-DNA). Mixed polypyridyl Ru(II) complexes [Ru(L)₄(AIP)]²⁺ and [Ru(L)₄PyIP]²⁺, where L is 4-amino pyridine and pyridine (AIP?=?2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline; PyIP?=?2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]phenanthroline), have been synthesized and characterized by elemental analysis, and physicochemical methods such as ESI-MS, UV-Vis, IR, and NMR spectroscopic techniques. Electronic absorption titrations, fluorescence spectroscopy, viscosity measurements, and salt-dependent studies of CT-DNA in the presence of incremental amounts of all four Ru(II) complexes clearly demonstrate that all four complexes bind to DNA by intercalation. The DNA-binding affinities of these complexes follow the order [Ru(4-APy)₄(PyIP)]^2+?>?[Ru(Py)₄PyIP]^2+?>?[Ru(4-APy)₄(AIP)]^2+?>?[Ru(Py)₄AIP]²⁺. Irradiation of pBR 322 DNA with these complexes results in nicking of the plasmid DNA. All four complexes were screened for antimicrobial activity. All complexes also exhibited DNA “light switch” properties. These results suggest that both ancillary ligand and intercalative ligand influence the binding of these complexes to DNA.     

DNA cleavage activities of two dinuclear copper coordination polymers

The DNA cleavage activities of two coordination polymers of Robson-type macrocycles, {[Cu₄L¹(4,4′-bipy)₂](ClO₄)₄·H₂O}_∞ (1) and {[Cu₄L²(4,4′-bipy)₄](ClO₄)₄·2CH₃CN·2H₂O}_∞ (2) (where H₂L¹ and H₂L² are the [2 + 2] condensation products of 1,3-diaminopropane with 2,6-diformyl-4-methylphenol and 2,6-diformyl-4-fluorophenol, respectively), have been studied. The interactions of the complexes with calf thymus-DNA were investigated by UV–vis spectroscopy, CD spectroscopy, and gel electrophoresis. The binding constants of 1 and 2 are 7.2 × 10⁴ and 2.1 × 10⁵ M^?1, respectively. The complexes exhibit DNA cleavage activity, with the cleavage process involving oxidative cleavage of DNA.     

Label-free detection of DNA molecules on the dendron based self-assembled monolayer by electrochemical impedance spectroscopy

We report preparation of a novel platform for effective DNA hybridization and its application to the detection of single mismatched DNA. Cone-shaped dendrimer molecules have been immobilized on the gold surface at equidistance, 3.1 nm, from each other with a probe DNA molecule attached to the top of each dendrimer so that enough space would be secured for effective hybridization. This arrangement allows each probe DNA molecule to form a natural DNA double helix upon hybridization with a target DNA molecule. The single nucleotide polymorphism at either the central or end position of the 25-mer target DNA has been shown to be effectively discriminated against on this platform from each other as well as from a complementary DNA by electrochemical impedance measurements. We also report adverse effects exerted by probe ions, Fe(CN)₆^3−/4−, on DNA hybridization reactions. The significance of the results for the use in DNA analysis is discussed.     

Structure of the Complex of [Ru(tpm)(dppz)py]2+ with a B‐DNA Oligonucleotide—A Single‐Substituent Binding Switch for a Metallo‐Intercalator

We report the synthesis of three new complexes related to the achiral [Ru(tpm)(dppz)py]²⁺ cation (tpm=tripyridazole methane, dppz=dipyrido[3,2‐a:2′,3′‐c]phenazine, py=pyridine) that contain an additional single functional group on the monodentate ancillary pyridyl ligand. Computational calculations indicate that the coordinated pyridyl rings are in a fixed orientation parallel to the dppz axis, and that the electrostatic properties of the complexes are very similar. DNA binding studies on the new complexes reveal that the nature and positioning of the functional group has a profound effect on the binding mode and affinity of these complexes. To explore the molecular and structural basis of these effects, circular dichroism and NMR studies on [Ru(tpm)(dppz)py]Cl₂ with the octanucleotides d(AGAGCTCT)₂ and d(CGAGCTCG)₂, were carried out. These studies demonstrate that the dppz ligand intercalates into the G²–A³ step, with {Ru(tpm)py} in the minor groove. They also reveal that the complex intercalates into the binding site in two possible orientations with the pyridyl ligand of the major conformer making close contact with terminal base pairs. We conclude that substitution at the 2‐ or 3‐position of the pyridine ring has little effect on binding, but that substitution at the 4‐position drastically disrupts intercalative binding, particularly with a 4‐amino substituent, because of steric and electronic interactions with the DNA. These results indicate that complexes derived from these systems have the potential to function as sequence‐specific light‐switch systems.     

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one Ru^II, through the DNA base‐pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear Ru^II compounds and DNA. We report a structural NMR study on the binuclear Ru^II intercalator Λ,Λ‐B (Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺; bidppz=11,11′‐bis(dipyrido[3,2‐a:2′,3′‐c]phenazinyl, bipy = 2,2′‐bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]₂. Threading of Λ,Λ‐B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ‐B is trapped in a well‐defined surface‐bound state consisting of an eccentric minor‐groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ‐B. Molecular dynamics simulations show that this minor‐groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru²⁺ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ‐B with natural calf thymus DNA. The present minor‐groove binding mode is proposed to represent the initial surface interactions of binuclear Ru^II compounds prior to intercalation into AT‐rich DNA.     

The glycosyl C1′—N9 bond of deoxyadenosine and deoxyguanosine: response to electrophilic attacks on the purinic nitrogen atoms

Self-consistent-field computations shed light on two relevant conformations of deoxyadenosine (dA) and deoxyguanosine (dG): one with a pseudoequatorial C_1′N₉ glycosyl bond and the other, a slightly more stable one, with its C_1′N₉ bond in a bisectional orientation. In dA, both the N₃ and N₇ nitrogens are plausible sites for electrophilic attack, but only N₇ is a plausible site in dG. The addition of H⁺, CH₃ ⁺, C₂H₅ ⁺ or tert-C₄H₉ ⁺ onto N₇ does not provoke notable structural modifications and leaves the base of dA and dG in an antiperiplanar (or nearly antiperiplanar) position with respect to the sugar C_1′O_4′ bond, but N₃ additions cause the base to adopt a synperiplanar or strongly chiral position. This produces strong interactions between the purine and deoxyribose moieties, whose relief could aid the eventual cleavage of the glycosyl bond of dA. Addition of a radical cation onto N₇ reduces the dissociation energy of the glycosyl bond by an estimated 8 kcal mol⁻¹ in dA and 4 kcal mol⁻¹ in dG – a bond weakening likely to concur to a depurination of DNA induced by radical cations. Received: 13 September 1999 / Accepted: 3 February 2000 / Published online: 21 June 2000     

碳链长度对芳香异羟肟酸二烃基锡配合物与5’-AMP或DNA相互作用的影响

选择体外筛选活性强的Bu₂Sn(4-FC₆H₄C(O)NHO)₂和活性弱的有机锡化合物Me₂Sn(4-FC₆H₄C(O)NHO)₂为模型,利用高分辨¹H NMR和³¹P NMR 技术比较研究这两个有代表性的有机锡化合物与DNA的基本组成单元5’-AMP在不同时间、不同条件下的作用模式并用紫外法进一步研究其与DNA的相互作用。结果显示,具有不同碳链的有机锡化合物与5’-AMP相互作用明显不同,含较长碳链的Bu₂Sn(4-FC₆H₄C(O)NHO)₂与5’-AMP的作用明显强于Me₂Sn(4-FC₆H₄C(O)NHO)₂,Me₂Sn(4-FC₆H₄C(O)NHO)₂分子可能只与5’-AMP的磷酸骨架静电结合,与整个分子作用较弱,而含丁基的Bu₂Sn(4-FC₆H₄C(O)NHO)₂可能除了与磷酸骨架静电结合,也与疏水碱基具有超分子相互作用而更有利于与5’-AMP稳定结合。Bu₂Sn(4-FC₆H₄C(O)NHO)₂的长链有机配体在与DNA的作用模式上发挥了重要作用。     

DNA binding and photocleavage specificities of a group of tricationic metalloporphyrins

The interactions of 5,10,15-tris(1-methylpyridinium-4-yl)-20-(4-hydroxyphenyl)porphyrinatozinc(II) Zn[TMPyHP]³⁺ (2) along with Cu[TMPyHP]³⁺ (3), Co[TMPyHP]⁴⁺ (4), Mn[TMPyHP]⁴⁺ (5) and the free base porphyrin H₂[TMPyHP]³⁺ (1) with duplex DNA have been studied by using a combination of absorption, fluorescence titration, surface-enhanced Raman spectroscopy (SERS), induced circular dichroism (ICD) spectroscopy, thermal DNA denaturation, viscosity measurements as well as gel electrophoresis experiment. Their binding modes and intrinsic binding constants (K_b) to calf DNA (CT DNA) were comparatively studied and were found significantly influenced by different metals coordinated with the porphyrin plane. Except 3, which has four-coordination structure at the metal, all the metal derivatives showed non-intercalative DNA-binding mode and lower K_b than the free base porphyrin 1, most probably due to the steric hindrance results from the axial ligands of the inserted metals which are five or six-coordination structures. Meanwhile, the insertion of metals into cationic porphyrin greatly removed the self-aggregation of the metal-free porphyrins, and thus fully enhanced the singlet oxygen (¹O₂) productivities in the DNA photocleavage experiments. Therefore, these metalloporphyrins have comparable DNA cleavage ability with the free base porphyrin.     

Biosensor for Hepatitis B Virus DNA PCR Product and Electrochemical Study of the Interaction of Di(2,2′‐bipyridine)osmium(III) with DNA

The strategy for electrochemical detection of HBV DNA PCR product (181 bps) was designed by covalently immobilizing single‐stranded HBV DNA on preoxidized glassy carbon electrode surface. The immobilization of single stranded DNA was verified by AC impedance spectra. The following hybridization reaction on surface was evidenced by electrochemical methods using [Os(bpy)₂Cl₂]⁺ as an electroactive indicator. The interactions of [Os(bpy)₂Cl₂]⁺ with calf thymus single and double stranded DNA immobilized on preoxidized glassy carbon electrodes were studied. [Os(bpy)₂Cl₂]⁺ could bind preferentially to the duplex DNA by intercalating to base pairs. The intrinsic binding constant of [Os(bpy)₂Cl₂]⁺ with calf thymus DNA was calculated to be 1.21×10⁴ M^?1. Using [Os(bpy)₂Cl₂]⁺ as an electrochemical hybridization indicator, the HBV DNA sensor has been used to detect qualitatively target HBV DNA in solution with high sensitivity and selectivity.     

Study on the Interaction of Vitamin B12 with DNA by Spectroscopy and Electrochemical Methods

The Interaction between vitamin B₁₂ (VB₁₂) and fish sperm DNA was investigated in physiological buffer (pH 7.4) using the methylene blue (MB) dye as a spectral probe by spetcrophotometery, viscosity measurements and cyclic voltammetry. The apparent binding constant of vitamin B₁₂ with DNA was found to be 3.2×10⁵ mol⁻¹·L. The voltammetric behavior of vitamin B₁₂ has been investigated at glassy carbon electrode using cyclic voltammetry. Thermodynamic parameters including ΔH⁰, ΔS⁰ and ΔG⁰ for the interaction between VB₁₂ and DNA have determined as −2.3×10⁴, 27.54 and −3.1×10⁴J·mol⁻¹·K⁻¹ respectively. One indication of DNA binding mode with VB₁₂ was the change in viscosity when a small molecule associates with DNA. The diffusion coefficients of VB₁₂ in the absence (D₀)_f and presence of DNA (D₀)_b was calculated as 5.04×10⁻⁶ and 1.13×10⁻⁶ cm²·s⁻¹ respectively. The results indicated that vitamin B₁₂ can bind to DNA and the major binding mode was intercalative binding.     

Synthesis and crystal structure of the first dinuclear zinc complex containing 1,4,7-triazacyclononane and biological properties of the protonated ligand

Abstract

A new binuclear complex, [Zn₂L₂Cl₄]·2H₂O {L?=?N-aldehyde-N-(4-(benzyloxy)benzyl)-1,4,7triazacyclononane}, was synthesized and characterized by X-ray, elemental analysis, infrared and electronic spectroscopy, and mass spectrometry. The central ion is bridged by the L and lies in a tetrahedral configuration with Zn···Zn distance of 6.283 Å. The complex crystallizes in the triclinic space group Pī. ESI-MS of the complex indicates that the protonated ligand HL⁺ is the active species. The interaction of HL⁺ with calf thymus–DNA (CT–DNA) and bovine serum albumin (BSA) was studied by means of various spectroscopic methods, which revealed that HL⁺ could interact with CT–DNA through groove-binding mode and could quench the intrinsic fluorescence of BSA in a static quenching process. DNA–cleavage experiments indicate that HL⁺ exhibits efficient DNA–cleavage activity in the presence of H₂O₂, hydroxyl radical (HO^?) may serve as the major cleavage active species, and the pseudo-Michaelis–Menten kinetic parameters (K_cat, K_M, V_max); 2.47?h^?1, 2.70?×?10^?4 M and 6.68?×?10^?4 Mh^?1.     

4‐Nitroindazole: Its Ambiguous Nature in Oligonucleotide Base Pairing and the Influence of the Glycosylation Position on the Duplex Stability

Oligonucleotides incorporating the regioisomeric 4‐nitroindazole N¹‐ and N²‐(2′‐deoxy‐β‐D ‐ribofuranosides) 7 and 8 were synthesized and their base‐pairing properties investigated. For solid‐phase synthesis, the phosphoramidites 11 and 12 were prepared. Oligonucleotides containing the building block 7 or 8 show ambiguous base pairing. Duplexes have similar T_m values when the modified bases are positioned opposite to the four canonical DNA constituents. The glycosylation position of the regioisomeric 4‐nitroindazole nucleosides has very little influence on the duplex stability.     

Ultrasensitive determination of DNA sequences by flow injection chemiluminescence using silver ions as labels

We presented a new strategy for ultrasensitive detection of DNA sequences based on the novel detection probe which was labeled with Ag⁺ using metallothionein (MT) as a bridge. The assay relied on a sandwich-type DNA hybridization in which the DNA targets were first hybridized to the captured oligonucleotide probes immobilized on Fe₃O₄@Au composite magnetic nanoparticles (MNPs), and then the Ag⁺-modified detection probes were used to monitor the presence of the specific DNA targets. After being anchored on the hybrids, Ag⁺ was released down through acidic treatment and sensitively determined by a coupling flow injection–chemiluminescent reaction system (Ag⁺–Mn²⁺–K₂S₂O₈–H₃PO₄–luminol) (FI–CL). The experiment results showed that the CL intensities increased linearly with the concentrations of DNA targets in the range from 10 to 500 pmol L⁻¹ with a detection limit of 3.3 pmol L⁻¹. The high sensitivity in this work may be ascribed to the high molar ratio of Ag⁺–MT, the sensitive determination of Ag⁺ by the coupling FI–CL reaction system and the perfect magnetic separation based on Fe₃O₄@Au composite MNPs. Moreover, the proposed strategy exhibited excellent selectivity against the mismatched DNA sequences and could be applied to real samples analysis.