New transition metal complexes of 9,10‐phenanthrenequinone p‐toluyl hydrazone Schiff base: Synthesis,spectroscopy, DNA and HSA interactions,antimicrobial, DFT and docking studies

The new complexes of Cu (II) and Ni (II) of a tridentate Schiff base ligand derived from 9,10‐phenanthrenequinone and p‐toluic hydrazide have been synthesized and characterized by elemental analysis, electrical conductometry, FT‐IR, Mass, NMR and UV–Vis. The DFT calculations were carried out at B3LYP/6‐31G*(d) level for the determination of the optimized structure of the ligand and its complexes. The as‐synthesized compounds were screened for their antimicrobial activity. Also, their binding behavior with fish salmon‐DNA (FS‐DNA) and human serum albumin (HSA) were studied by different kinds of spectroscopic and molecular modeling techniques. The fluorescence data at different temperatures were applied in order to estimate the thermodynamics parameters of interactions of ligand and its complexes with DNA and HSA. The results showed that the as‐made compounds could bind to FS‐DNA and HSA via the groove binding as the major binding mode. According to molecular docking calculation and competitive binding experiments, these compounds bind to the minor groove of DNA and hydrophobic residues located in the subdomain IB of HSA. In addition, the molecular docking results kept in good consistence with experimental data.     

Guanidiniocarbonylpyrrole–Aryl Derivatives: Structure Tuning for Spectrophotometric Recognition of Specific DNA and RNA Sequences and for Antiproliferative Activity

We present a systematic study of different guanidiniocarbonylpyrrole‐aryl derivatives designed to interact with DNA or RNA both through intercalation of an aromatic moiety into the base stack of the nucleotide and through groove binding of a guanidiniocarbonylpyrrole cation. We varied 1) the size of the aromatic ring (benzene, naphthalene, pyrene and acridine), 2) the length and flexibility of the linker connecting the two binding groups, and 3) the total number of positive charges present at different pH values. The compounds and their interactions with DNA and RNA were studied by UV/Vis, fluorescence and CD spectroscopy. Antiproliferative activities against human tumour cell lines were also determined. Our studies show that efficient interaction with, for example, DNA requires a significantly large aromatic ring (pyrene) connected through a flexible linker to the pyrrole moiety. However, a positive charge, as in 12 , is also needed. Compound 12 allows for base‐pair‐selective recognition of ds‐DNA at physiological pH values. The antiproliferative activities of these compounds correlate with their binding affinities towards DNA, suggesting that their biological effects are most probably due to DNA binding.     

Interpolyelectrolyte reactions in solutions of polycarboxybetaines, 2: influence of alkyl spacer in the betaine moieties on complexing with polyanions

Series of polycarboxybetaines (PCB-n) of pyridiniocarboxylate structure with the same degree of polymerization but differing in the number, n, of methylene groups in the alkyl spacer between charges in the betaine moieties, n = 1, 2, 3, 4, 5, and 8, were synthesized. The utility of PCB-n as positively charged components of polyelectrolyte complexes was elucidated by potentiometry, turbidimetry, and fluorescence spectroscopy. Affinity of PCB-n to the pyrenyl-tagged poly(methacrylic) acid (PMAA) or DNA was judged from the stability of the corresponding polyelectrolyte complexes in water-salt solutions at different pH values as monitored by fluorescence quenching techniques. At pH = 9.0, PCB-1 formed the least stable complexes due to strong interaction of charged groups positioned in close proximity in the betaine moieties. The increase in n resulted in the irregular change of the affinity. Thus, as expected, PCB-2 formed noticeably more stable complexes than PCB-1. However, PCB-3 and, in particular, PCB-4 revealed weaker affinity to PMAA or DNA that is attributed to formation of stable ion pairs between charges in the betaine rings. At neutral and slightly acidic pH values binding of all PCB-n except PCB-1 was drastically enhanced due to protonation of PCB-n carboxylic groups that occurred with a DeltapH shift of 2-3 units to higher values as compared with the protonation of free PCB-n. The ability of added polyanion to compete with the betaine carboxylic groups in binding with the pyridinium groups was supported by potentiometric titration of PCB-n mixtures with sodium poly(styrenesulfonate): for n > or = 2, the binding of the polyanion-competitor also shifted protonation of carboxylic groups to higher values with DeltapH of more than 2 units. Practical ramifications of the revealed role of the alkyl spacer in polyelectrolyte complexation as well as the pH-induced stabilization of the complexes that occurs under enzyme-friendly conditions might extend to areas of biotechnology, specifically in bioseparation and gene delivery.     

2,6-二(2'-咪唑啉-2'-基)吡啶合铬(Ⅲ)的合成及其与DNA的相互作用

在微波辐射和无催化剂条件下,由吡啶2,6-二甲酸与乙二胺反应合成了2,6-二(2'-咪唑啉-2'-基)吡啶(L),采用常规加热法合成其配合物[CrL2][NO3]3。用核磁共振、红外光谱、元素分析、热重分析和摩尔电导率测试技术对其进行表征分析。通过紫外吸收光谱和黏度测试,分别考察了配体及配合物与DNA的键合常数及其作用方式。结果表明,配体L以氢键和沟面作用方式与DAN键合,而配合物以氢键和静电作用模式与DNA键合。密度泛函理论(DFT)计算结果较好的解释了L及[CrL2]3+与DNA的相互作用模式。     

Synthesis and molecular modelling of double-functionalised nucleosides with aromatic moieties in the 5'-(S)-position and minor groove interactions in DNA zipper structures

A series of six double-functionalised nucleosides, in which aromatic moieties were inserted into the 5'-(S)-C-position, were synthesised and incorporated into DNA duplexes. The aromatic moieties were thymine-1-yl, phenyl, 1,2,3-triazol-1-yl, 1,2,3-triazol-4-yl, 4-(uracil-5-yl)-1,2,3-triazol-1-yl and 4-phenyl-1,2,3-triazol-1-yl. The DNA duplexes were studied with UV melting curves, CD spectroscopy and molecular modelling. The results showed that the aromatic moieties in some cases interact in the minor groove forming DNA zipper structures. The strongest specific interaction was found between two thymines or between a thymine and a phenyl group in a crossed (-3)-zipper motif (i.e., with two base pairs interspacing the modifications). Modelling revealed that the interaction is aromatic stacking across the minor groove. Also, the extended uracil-triazole moiety demonstrated zipper contacts in the minor groove as well as binding to the floor of the groove.     

Interactions of Phenanthroline Compounds with i-Motif DNA

The interactions of each of three phenanthroline derivatives 1, 2 and 3 with the human telomeric/-motif DNA were investigated. The results suggest these compounds are potent binders. The compounds could stabilize the structure of i-motif DNA by π-π stacking. Moreover, the binding constants of the compounds with/-motif DNA were （2.71-8.12）×10^4 L·mol^-1, and the binding stoichiometry ratio was 1：1. CD studies reveal that the binding by phenanthroline comoounds perturbs the conformation of i-motif DNA.     

4-(1H-1,2,4-三唑-1-亚甲基)苯甲酸过渡金属配合物的合成、结构、抑菌活性及DNA裂解活性

Three novel transitionmetal compounds [Cu_0.5L]_n (1), {[Ni(L)₂·(H₂O)₂]·(H₂O)₂}_n(2), and {[Co(L)₂·(H₂O)₂]· (H₂O)₂}_n (3), were hydrothermally synthesized with 4-(1H-1,2,4-triazol-1-ylmethyl) benzoic acid (HL) and characterized by infrared spectroscopy, elemental analyses, single-crystal X-ray diffraction, thermal analyses, UV-Vis spectroscopy, and fluorescence spectroscopy. Structural analyses reveal that compound 1 features a one-dimensional (1D) chain, while isomorphic 2 and 3 exhibit a three-dimensional (3D) network structure with interchain hydrogen-bonding. Antifungal activities tests reveal that 1 has the highest antifungal effect on the five fungi (Fusarium graminearum, Vasa mali, Macrophoma kawatsukai, Colletotrichum gloeosporioides, and Alternaria alternate) among the three compounds. Furthermore, DNA cleavage experiments indicate that compound 1 has more efficient DNA (pUC 18) cleavage activity than compounds 2 and 3. The binding properties of the three compounds with DNA were also investigated by absorption. The results show that the three compounds can intercalate into DNA, and the interaction of compound 1 is the strongest.     

Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model

Neomycin is the most effective aminoglycoside (groove binder) in stabilizing a DNA triple helix. It stabilizes TAT, as well as mixed base DNA triplexes, better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (in the presence of salt), without any effect on the DNA duplex. (1) Triplex stabilization by neomycin is salt dependent (increased KCl and MgCl(2) concentrations decrease neomycin's effectiveness, at a fixed drug concentration). (2) Triplex stabilization by neomycin is pH dependent (increased pH decreases neomycin's effectiveness, at a fixed drug concentration). (3) CD binding studies indicate approximately 5-7 base triplets/drug apparent binding site, depending upon the structure/sequence of the triplex. (4) Neomycin shows nonintercalative groove binding to the DNA triplex, as evident from viscometric studies. (5) Neomycin shows a preference for stabilization of TAT triplets but can also accommodate CGC(+) triplets. (6) Isothermal titration calorimetry (ITC) studies reveal an association constant of approximately 2 x 10(5) M(-)(1) between neomycin and an intramolecular triplex and a higher K(a) for polydA.2polydT. (7) Binding/modeling studies show a marked preference for neomycin binding to the larger W-H groove. Ring I/II amino groups and ring IV amines are proposed to be involved in the recognition process. (8) The novel selectivity of neomycin is suggested to be a function of its charge and shape complementarity to the triplex W-H groove, making neomycin the first molecule that selectively recognizes a triplex groove over a duplex groove.     

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.     

A Programmed DNA Marker Based on Bis(4‐ethynyl‐1,8‐naphthalimide) and Three‐Methane‐Bridged Thiazole Orange

Two large conjugated naphthalimide derivatives with or without three‐methane‐bridged thiazole orange (TO3; i.e., compounds 1 a and 2 a , respectively) were designed and synthesized. The fluorescence of the naphthalimide group in compound 1 a at λ=532 nm initially decreased and that for the TO3 group at λ=655 nm increased sequentially upon adding Salmon testes (St) DNA. In contrast, without the TO3 group, the fluorescence intensity of compound 2 a monotonously decreased in response to the addition of DNA. The non‐monotonic change in the fluorescence for compound 1 a could be divided into two linear sections with two different wavelengths in the range of 0<R_{b/ 1 a} <1.2 and 1.2 <R_{b/ 1 a} <6.0 (R_{b/ 1 a} =[base pair]/[ 1 a ]). Thus, compound 1 a can be regarded as a programmed responding molecule for DNA, which can semi‐quantitatively determine the concentration of DNA over a large concentration range from the standard fluorescence curve of compound 1 a at different wavelengths when bound with DNA. Furthermore, the binding modes of compounds 1 a and 2 a with StDNA were studied by using CD spectroscopy and melting temperature (T_m) testing. The results showed that compound 1 a interacts with StDNA through multi‐interactions including weak intercalation, weak minor groove binding, and inter‐dye interactions, whereas compound 2 a bound with DNA through simultaneous intercalation and minor groove binding.     

Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove

A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH₃)₃]₂) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.     

Synthesis,Crystal Structure and DNA Binding Studies of α,α'-Bis(3,5-bismethyl-1-pyrozolyl)-carbene-acetyl-isopropenyl Hydrazine

The title compound α,α'-bis(3,5-bismethyl-pyrozole-N-yl)-carbene-acetyl-isopro- penyl hydrazine (C16H22N6O, Mr = 314.40) has been prepared. It was characterized by elemental analysis as well as IR, MS, 1H-NMR and 13C-NMR spectra. Its crystal structure was determined by single-crystal X-ray diffraction, getting the following data: triclinic, space group P1 with a = 6.9734(16), b = 10.773(3), c = 12.001(3) , α = 75.311(4), β = 82.695(4), γ = 77.143(4)o, Z = 2, V = 847.9(3) 3, Dc = 1.231 g/cm3, F(000) = 336 and μ(MoKα) = 0.082 mm-1 (λ = 0.71073 ). The results of crystal structure determination show that there exist intermolecular and intramolecular hydrogen bonds, resulting in a two-dimensional supramolecular framework of the title compound. The binding of the title compound to DNA was investigated by absorption, emission, and viscosity measurements. The title compound shows absorption hyperchromicity accompanied by a blue shift at about 254 nm. The binding constant Kb for the title compound has been determined to be 1.89 × 104 M-1 from absorption measurements. The addition of the title compound to DNA pretreated with EB causes appreciable reduction in the emission intensity, indicating that the DNA-bound EB fluorophore is partially replaced by the title compound. The value of K is 3.093 × 104 M-1. The relative viscosity of DNA decreased with the addition of the title compound. Results suggest that the title compound binds to DNA with a non-classical intercalative or groove interaction mode. The observed efficient nuclease activity of the title compound is interesting and may have further influences on the chemistry of DNA minor groove binders. Keywords: α,α'-bis(3,5-bismethyl-pyrozole-N-yl)-carbene-acetyl-isopropenyl, preparation, crystal structure, DNA binding     

Synthesis, DNA-binding, cleavage, and cytotoxic activity of new 1,7-dioxa-4,10-diazacyclododecane artificial receptors containing bisguanidinoethyl or diaminoethyl double side arms

Novel 1,7-dioxa-4,10-diazacyclododecane artificial receptors with two pendant aminoethyl (3) or guanidinoethyl (4) side arms have been synthesized. Spectroscopy, including fluorescence and CD spectroscopy, of the interactions of 3, 4, and their copper(II) complexes with calf thymus DNA indicated that the DNA binding affinity of these compounds follows the order Cu(2+)-4>Cu(2+)-3>4>3, and the binding constants of Cu(2+)-3 are Cu(2+)-4 are 7.2x10(4) and 8.7x10(4) M(-1), respectively. Assessment by agarose gel electrophoresis of the plasmid pUC 19 DNA cleavage activity in the presence of the receptors showed that the complexes Cu(2+)-3 and Cu(2+)-4 exhibit powerful supercoiled DNA cleavage efficiency. Kinetic data of DNA cleavage promoted by Cu(2+)-3 and Cu(2+)-4 under physiological conditions fit to a saturation kinetic profile with kmax values of 0.865 and 0.596 h(-1), respectively, which give about 10(8)-fold rate acceleration over uncatalyzed supercoiled DNA. This acceleration is due to efficient cooperative catalysis of the copper(II) center and the functional (diamino or bisguanidinium) groups. In-vitro cytotoxic activities toward murine melanoma B16 cells and human leukemia HL-60 cells were also examined: Cu(2+)-4 shows the highest activity with IC(50) values of 1.62x10(-4) and 1.19x10(-5) M, respectively.     

Synthesis, Crystal Structure and DNA Binding Studies of α,α'-Bis(3,5-bismethyl-1-pyrozolyl)- carbene-acetyl-isopropenyl Hydrazine

The title compound α,α'-bis(3,5-bismethyl-pyrozole-N-yl)-carbene-acetyl-isopro-penyl hydrazine (C16H22N6O, Mr = 314.40) has been prepared. It was characterized by elemental analysis as well as IR, MS, 1H-NMR and 13C-NMR spectra. Its crystal structure was determined by single-crystal X-ray diffraction, getting the following data: triclinic, space group P1 with a = 6.9734(16), b = 10.773(3), c = 12.001(3) A, α = 75.311(4), β = 82.695(4), γ = 77.143(4)°, Z = 2, V = 847.9(3) A3, Dc : 1.231 g/cm3, F(000) = 336 and μ(MoKα) = 0.082 mm-1 (λ = 0.71073 A). The results of crystal structure determination show that there exist intermolecular and intramolecular hydrogen bonds, resulting in a two-dimensional supramolecular framework of the title compound. The binding of the title compound to DNA was investigated by absorption, emission, and viscosity measurements. The title compound shows absorption hyperchromicity accompanied by a blue shift at about 254 nm. The binding constant Kb for the title compound has been determined to be 1.89 × 104 M-1 from absorption measurements. The addition of the title compound to DNA pretreated with EB causes appreciable reduction in the emission intensity, indicating that the DNA-bound EB fluorophore is partially replaced by the title compound. The value of K is 3.093 × 104 M-1. The relative viscosity of DNA decreased with the addition of the title compound. Results suggest that the title compound binds to DNA with a non-classical intercalative or groove interaction mode. The observed efficient nuclease activity of the title compound is interesting and may have further influences on the chemistry of DNA minor groove binders.     

Synthesis and thermal denaturation studies of novel 2'-O,3'-C-linked bicyclic oligonucleotides with a methoxy or a piperazino group facing the major groove of nucleic acid duplexes

With the aim of evaluating duplex stabilities of oligonucleotides (ONs) with major groove facing functionalities, two novel 2'-O,3'-C-linked bicyclic nucleoside phosphoramidite building blocks were synthesized by routes involving regioselective O-methylation or piperazine attachment using carbonyldiimidazole coupling chemistry. The novel monomers were incorporated into 9-mer mixed base ONs and the thermal stability toward complementary single stranded DNA and RNA was evaluated by thermal denaturation experiments. O-methylated ONs confirmed the applicability of the functionalized bicylic sugar unit for attachment of groups facing the major groove and satisfactory binding properties towards the RNA complement were observed. For the piperazino modified ONs, experiments were performed in aqueous buffers with low (40 mM) and medium (110 mM) salt concentrations, at pH 5 and pH 7. A change from a medium to a low salt concentration induced a significant relative increase in the thermal stability of modified duplexes toward both DNA and RNA complements, which suggests protonation of the piperazino group under the experimental conditions applied.     

Simulation of interactions between DNA and diglycerides

Calculations by molecular mechanics methods showed that diglycerides containing stearic, oleic, linoleic, or linolenic acids can bind to DNA. The binding energy of diglycerides to the DNA minor groove is higher than that to the major groove. The bond energies of diglycerides to DNA were calculated as the sums of the contributions of the binding energies between DNA and two fatty acid residues. These energies depend on the structure of the fatty acid and the nucleotide composition of DNA and vary from 20 to 120 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1741–1744, August, 2008.     

荧光猝灭法研究氟比洛芬与DNA相互作用

采用荧光光谱法和紫外光谱法, 在生理条件下(pH=7.40)对氟比洛芬(FP)与脱氧核糖核酸(DNA)的作用方式进行了研究.证实了氟比洛芬通过沟槽结合方式与DNA发生相互作用.实验表明, DNA与氟比洛芬的相互作用为静态猝灭过程,测得结合常数为5.53×10~5 L·mol~(-1),结合位点数为1.12.     

Guanidiniocarbonyl-pyrrole-aryl conjugates as nucleic acid sensors: switch of binding mode and spectroscopic responses by introducing additional binding sites into the linker

Two novel guanidiniocarbonyl pyrrole-pyrene conjugates 3 and 4 as spectroscopic probes for ds-polynucleotides were synthesized and their interaction with different ds-DNAs/RNAs studied. Compared to a previously reported first set of conjugates (1 and 2) the significant extension and increased rigidity of the central part of the structure resulted in a switch of DNA binding mode from intercalative (previously studied derivatives 1 and 2 with a nonbinding and flexible linker) to minor groove binding of the two novel guanidiniocarbonyl-pyrrole-pyrene conjugates 3 and 4. These two compounds interact strongly with ds-DNAs, but only weakly with ds-RNA. The newly incorporated heterocyclic moieties within the central part of the structure of 3 and 4 were able to control by steric and hydrogen-bonding effects the alignment of the molecules within various, structurally different forms of DNA minor grooves, whereby even small differences in the position of the attached pyrene within the groove were reflected in different fluorimetric responses. In addition, 3 and 4 revealed intriguing in vitro selectivity among various human tumour cell lines.     

新型双核配合物的形成、与DNA的作用机制及荧光性质研究

利用紫外、荧光和粘度等方法研究了含不同配体的钌(II)配合物[Ru(phen)₂CImP]^2＋(CImP＝3,4-二羟基-咪唑并[4,5-i][1,10]邻菲咯啉)和[Ru(phen)₂TPPZ]^2＋(TPPZ＝四吡啶[3,2-a:2',3'-c:3',2'-h:2',3'-j]吩嗪)与DNA的作用机制, 并研究了配合物与Zn^2＋配合后荧光性质变化. 结果表明[Ru(phen)₂TPPZ]^2＋与DNA以插入模式作用, 而[Ru(phen)₂CImP]^2＋与DNA则以沟面结合模式作用. 向配合物溶液中滴加Zn^2＋后, 配合物[Ru(phen)₂TPPZ]^2＋和[Ru(phen)₂CImP]^2＋均可以与Zn^2＋形成双核配合物[Ru(phen)₂(TPPZ)Zn]^4＋和[Ru(phen)₂(CImP)Zn]^4＋, 配合物的荧光减弱. 与DNA作用后, 配合物仍可以与Zn^2＋配位形成双核配合物, 但[Ru(phen)₂(TPPZ)Zn]^4＋保持插入模式与DNA作用, 配合物的荧光减弱. 而[Ru(phen)₂(CImP)Zn]^4＋与DNA则由沟面结合改为插入结合, 配合物的荧光增强.