Synthesis and DNA Cleavage Properties of Triazacrown Derivatives

New metal‐free DNA cleaving reagent 1 , 1,4,7‐triazacrown (TACN) both with aminoethyl, hydroxyethyl side arms and a planar anthraquinone linked by an alkyl (1,6‐hexamethylene) spacer has been synthesized and characterized by NMR and MS spectrometry. For comparison, the corresponding aminoethyl, hydroxyethyl triazacrown derivative 2 without the anthraquinone has also been synthesized. DNA‐binding properties via fluorescence and CD spectroscopy indicate that the binding affinity of 1 with DNA is much stronger than that of 2 . Agarose gel electrophoresis was used to assess plasmid pUC19 DNA cleavage. Kinetic data of DNA cleavage promoted by 1 , 2 and parent triazacrown (TACN) 3 under physiological condition give the 15‐fold and 234‐fold rate acceleration of compound 1 over 2 and parent triazacrown 3 . Radical scavenger inhibition study suggests that DNA cleavage promoted by 1 may be a non‐oxidative pathway through the transphosphorylation and then hydrolysis. The dramatic rate acceleration is due not only to the anthraquinone moiety of compound 1 intercalating into DNA base pairs via stacking interaction, but also the cooperative catalysis of the nucleophilic hydroxyl and the electrophilic ammonium group for the cleavage of phosphodiester of DNA.     

Steric and Electronic Effects, Enantiospecificity, and Reactive Orientation in DNA Binding/Cleaving by Substituted Derivatives of [SalenMn(III)](+)

Twenty-six derivatives of [SalenMn(III)](+) (1) bearing halogen, nitro, amino, ether, alkyl, or aryl substituents on the aromatic rings and/or at the imine positions or containing 1,3-propylene-, 1,2-phenylene-, 1,2-cyclohexane-, or 1,2-diphenylethylenediamine in place of ethylenediamine as the bridging moiety have been synthesized. The DNA binding/cleaving properties of these complexes in the presence of terminal oxidants have been examined using DNA affinity cleaving techniques. Active derivatives produced DNA cleavage from the minor groove at sites containing multiple contiguous A:T base pairs. For aryl-substituted derivatives, DNA cleavage efficiency was found to vary with both the identity and position of attachment of substituents. The precise patterns of cleavage at A:T target sites varied with the position of attachment of substituents, but not with the identity of the substituents. The results suggest that substituents alter specificity through both steric and electronic effects. The 3,3'-difluoro and -dichloro derivatives produced cleavage patterns that match those of the parent complex, suggesting that the activated form of 1 produces cleavage from an orientation in which the concave edge of the complex faces away from the floor of the DNA minor groove. Bridge modifications yield complexes with reduced DNA cleaving activity relative to 1. DNA cleaving efficiency was found to vary with both the structure and stereochemistry of the bridge. Cleavage efficiency for the complex derived from (R,R)-cyclohexanediamine was 5 times greater than that for the (S,S) enantiomer. Cleavage patterns produced by the enantiomeric complexes at A:T rich target sites were different, demonstrating enantiospecific recognition and cleavage of right-handed double-helical DNA.     

Interaction with plasmid DNA of Hoechst-TACN conjugates

ABSTRACT

A new family of conjugates between the Hoechst minor groove binder and the TACN metal ion ligand connected through hydrophobic alkyl or more hydrophilic oxyethyl linkers of different length has been prepared. The linkers are connected to the convex side of the Hoechst skeleton thus forcing the TACN ligand to exit the minor groove and interact with the phosphate backbone of DNA. The conjugates preserve the binding mode of Hoechst with an affinity influenced by the nature of the linker, the more hydrophobic being the more efficient. Coordination of Cu(II) or Zn(II) poorly affect these parameters. Nevertheless, the Zn(II) complex bearing a C6 linear alkyl linker induced a modest but reproducible acceleration of the hydrolytic cleavage of DNA which can be ascribed to the ability of the conjugate to deliver the hydrolytic subunit close to the DNA phosphodiester bonds.     

Supramolecular assemblies of a new series of gemini-type schiff base amphiphiles at the air/water interface: in situ coordination, interfacial nanoarchitectures, and spacer effect

Great interest has been devoted to the gemini amphiphiles because of their unique properties. In this article, we report some interesting properties of the interfacial films formed by a series of newly designed gemini amphiphiles containing the Schiff base moiety. This novel series of gemini amphiphiles with their Schiff base headgroups linked by a hydrophobic alkyl spacer (BisSBC18Cn, n = 2, 4, 6, 8, 10) could be spread to form stable monolayers and coordinated with Cu(Ac)(2) in situ in the monolayer. The alkyl spacer in the amphiphiles has a great effect on the regulation of the properties of the Langmuir monolayers. A maximum limiting molecular area was observed for the monolayers of the gemini amphiphile with the spacer length of hexa- or octamethylene groups. Both the monolayers on water and on the aqueous Cu(Ac)(2) subphase were transferred onto solid substrates, and different morphologies were observed for films with different spacers. Nanonail and tapelike morphologies were observed for amphiphile films with shorter spacers (n = 2 and 4) on the water surface. Wormlike morphologies were observed for gemini films with longer spacers of C(8) and C(10) when coordinated with Cu(Ac)(2). An interdigitated layer structure was supposed to form in the multilayer films transferred from water or the aqueous Cu(Ac)(2) subphase.     

新型有机小分子DNA切割试剂的合成

根据活性基团的协同催化原理,设计合成了有机小分子核酸切割剂1-(N-胍乙基)-4-(N-羟乙基)哌嗪盐酸盐(4),并通过核磁共振和液相色谱-质谱联用技术对其结构进行了表征.利用琼糖凝胶电泳研究了pH值对其切割pUC 19 DNA效率的影响,通过自由基猝灭实验研究其切割DNA的反应类型.运用密度泛函理论,利用Gaussian软件进行了理论计算,研究其裂解DNA的反应方式.研究结果表明,在pH=7.2时化合物4的裂解效率最高,且能通过非氧化还原反应以磷酯转移的方式裂解DNA的磷酸二酯键.     

PHOTOCLEAVAGE OF DNA: IRRADIATION OF QUINONE-CONTAINING REAGENTS CONVERTS SUPERCOILED TO LINEAR DNA

Irradiation (350 nm) of air-saturated solutions of reagents containing an anthraquinone group linked to quaternary alkyl ammonium groups converts supercoiled DNA to circular and to linear DNA. Generation of linear DNA does not occur by accumulation of numerous single-strand cuts but by coincident-site double-strand cleavage of DNA. Irradiation forms the triplet state of the anthraquinone, which reacts either by hydrogen atom abstraction from a sugar of DNA or by electron transfer from a base of the DNA. Subsequent reactions result in chain scission. The quinone is apparently reformed after this sequence and reirradiation leads to double-strand cleavage.     

2-[1-(4-甲酰氨基苯基乙酰氧)烷基]-1,4-二羟基-9,10-蒽醌类衍生物的 合成及其抗肿瘤作用研究

为寻找抗肿瘤作用强、毒性低并且对癌细胞具有靶向性的新蒽醌类化合物, 合成了未见报道的12个2-[1-(4-甲酰氨苯基乙酰氧)烷基]-1,4-二羟基-9,10-蒽醌类衍生物, 分别用L1210癌细胞进行细胞毒性实验及小鼠S180腹水癌做了体内抗肿瘤实验. 实验结果表明, 蒽醌侧链中引入对甲酰氨基苯乙酰基后细胞毒性增强. 随着侧链碳链数的增加细胞毒性随之逐渐减小, 当烷基侧链中的碳数超过7以上时, 细胞毒性消失. 当侧链R基为苯环时与脂肪烃链或环己基相比细胞毒性更大, 说明芳香环对癌细胞具有更强的抑制作用. S180小鼠抗肿瘤实验结果表明, 蒽醌侧链中引入对甲酰氨基苯甲酰基后活性无显著性变化.     

Dimeric liquid crystalline compounds having a central malonic acid moiety: effect of the length of the spacers and terminal chains

We have studied the liquid crystalline properties of two new series of dimeric compounds consisting of a central malonic acid moiety, polymethylene spacers, and Schiff's base mesogens. In the first series we changed the length of the spacers with the terminal chain fixed as the butoxy group; in the second series we changed the length of the terminal alkyl or alkoxy groups while keeping the spacers fixed as decamethylene groups. In the first series, as the length of the spacer increased, the tendency to form smectic phases grew. In the second series, changing the alkyl terminal chain to the alkoxy terminal group raised the melting and isotropization temperatures. Increasing the length of the terminal group diminished the temperature range for the higher temperature smectic phase. The smectic phases are assigned to be smectic A and crystal smectic E phases.     

Dimeric liquid crystalline compounds having a central malonic acid moiety: effect of the length of the spacers and terminal chains

We have studied the liquid crystalline properties of two new series of dimeric compounds consisting of a central malonic acid moiety, polymethylene spacers, and Schiff's base mesogens. In the first series we changed the length of the spacers with the terminal chain fixed as the butoxy group; in the second series we changed the length of the terminal alkyl or alkoxy groups while keeping the spacers fixed as decamethylene groups. In the first series, as the length of the spacer increased, the tendency to form smectic phases grew. In the second series, changing the alkyl terminal chain to the alkoxy terminal group raised the melting and isotropization temperatures. Increasing the length of the terminal group diminished the temperature range for the higher temperature smectic phase. The smectic phases are assigned to be smectic A and crystal smectic E phases.     

Interfacial assembly of a series of cinnamoyl-containing bolaamphiphiles: spacer-controlled packing, photochemistry, and odd-even effect

A series of bolaamphiphiles with 4-hydroxycinnamoyl head groups and different length of the alkyl spacers (n = 6-12) were designed to investigate their photochemistry in the organized films obtained from the air/water interface. It has been found that both the length and odd-even number of the spacers can finely tune the molecular packing as well as the photochemistry. When the spacer length was changed from 6 to 12 methylene units, the assemblies changed from J aggregate to H aggregate. The molecules with even-numbered polymethylene spacer tend to form three-dimensional nanorod structure at the air/water interface. For the assembly of derivatives with odd-numbered spacers, diverse morphologies such as nanospirals and nanofibers were observed depending on the chain length and the surface pressures. The different packing of bolaamphiphiles could subsequently affect the photochemistry of the cinnamoyl groups in the organized films. The spacer effect in the assembly can be understood from the cooperation between H-bond of the phenolic hydroxyl and the amide groups, π-π stacking as well as the hydrophobic interactions of the alkyl spacer. A packing model was proposed to explain the phenomenon.     

Tuning the activity of Zn(II) complexes in DNA cleavage: clues for design of new efficient metallo-hydrolases

The hydrolytic ability toward plasmid DNA of a mononuclear and a binuclear Zn(II) complex with two macrocyclic ligands, containing respectively a phenanthroline (L1) and a dipyridine moiety (L2), was analyzed at different pH values and compared with their activity in bis( p-nitrophenyl)phosphate (BNPP) cleavage. Only the most nucleophilic species [ZnL1(OH)]+ and [Zn2L2(OH)2]2+, present in solution at alkaline pH values, are active in BNPP cleavage, and the dinuclear L2 complex is remarkably more active than the mononuclear L1 one. Circular dichroism and unwinding experiments show that both complexes interact with DNA in a nonintercalative mode. Experiments with supercoiled plasmid DNA show that both complexes can cleave DNA at neutral pH, where the L1 and L2 complexes display a similar reactivity. Conversely, the pH-dependence of their cleavage ability is remarkably different. The reactivity of the mononuclear complex, in fact, decreases with pH while that of the dinuclear one is enhanced at alkaline pH values. The efficiency of the two complexes in DNA cleavage at different pH values was elucidated by means of a quantum mechanics/molecular mechanics (QM/MM) study on the adducts between DNA and the different complexed species present in solution.     

Double-helical dinuclear bis(dipyrromethene) complexes formed by self-assembly

Bis(dipyrromethene) ligands linked by an alkyl spacer between beta and beta' positions are shown to give helical dimers or monomers, dependent upon the length of the alkyl linker, upon complexation. Ligands consisting of methylene, ethylene, and propylene linkers -(CH(2))(n)()- (n = 1, 2, and 3) give helical dimers, while longer linking chains (n = 4, 5, or 6) give monomers or mixtures of dimers and monomers. X-ray crystal structures of the dimeric zinc complexes (n = 1, 2, and 3) reveal that the angles between dipyrromethene planes and the extent of helicity in the complexes differ as the length of the linker varies. The extent of helicity was assessed and found to be dependent upon the length and, specifically, the conformational preferences of the alkyl spacer unit. The presence of an ethylene linker gave complexes of greatest helicity. The use of a methylene spacer gave less helical structures upon complexation, while propylene spacers gave only slightly helical complexes. Our studies identify the crucial importance that the conformational preferences of the beta-beta' alkyl spacer group plays in the coordination algorithm of self-assembly to form dipyrromethene based complexes.     

Multiple Effects Tailoring the Self-organization Behaviors of Triphenylene Side-chain Liquid Crystalline Polymers <Emphasis Type="Italic">via</Emphasis> Changing the Spacer Length

Long-alkyl tail triphenylene (TP) side-chain liquid crystalline polymers (SCLCPs) with different spacer length (P-m-TP,m =2,3,4,6,8,which is the number of carbon atom in the flexible alkyl spacers) have been successfully synthesized via free radical polymerization.The differential scanning calorimetry (DSC),polarized light microscopy (POM),ultraviolet-visible spectroscopy (UV-Vis),wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) measurements were performed to investigate the influence of multiple effects on the self-organization behaviors of P-m-TP,including steric effect,decoupling effect and π-π stacking effect.The experimental results revealed that P-m-TP (m =2,3,4) formed the columnar phase which was developed by the TP moieties and the main chain as a whole,suggesting that the side-chains had strong steric effect even though the number of spacer length (m)exceeded 4.In addition,the clearing points (Tis) of the polymers were above 300 ℃.When m =6 and 8,the polymers displayed hexagonal columnar phase and exhibited the low Tis (91 and 80 ℃ respectively),originating from the self-assembly of triphenylene due to the decoupling effect and π-π stacking effect.This work offers a viable and inspiring pathway to control the phase transition temperature and phase structure of TP SCLCPs via simply tailoring the spacer length and increasing the alkyl tail length of TP.     

Clustering versus percolation in the assembly of colloids coated with long DNA

We report an experimental study in which we compare the self-assembly of 1 mum colloids bridged through hybridization of complementary single-stranded DNA (ssDNA) strands (12 bp) attached to variable-length double-stranded DNA spacers that are grafted to the colloids. We considered three different spacer lengths: long spacers (48 500 bp), intermediate length spacers (7500 bp), and no spacers (in which case the ssDNA strands were directly grafted to the colloids). In all three cases, the same ssDNA pairs were used. However, confocal microscopy revealed that the aggregation behavior is very different. Upon cooling, the colloids coated with short and intermediate length DNAs undergo a phase transition to a dense amorphous phase that undergoes structural arrest shortly after percolation. In contrast, the colloids coated with the longest DNA systematically form finite-sized clusters. We speculate that the difference is due to the fact that very long DNA can easily be stretched by the amount needed to make only intracluster bonds, and in contrast, colloids coated with shorter DNA always contain free binding sites on the outside of a cluster. The grafting density of the DNA decreases strongly with increasing spacer length. This is reflected in a difference in the temperature dependence of the aggregates: for the two systems coated with long DNA, the resulting aggregates were stable against heating, whereas the colloids coated with ssDNA alone would dissociate upon heating.     

Spacer‐Modulated Differentiation Between Self‐Assembly and Folding Pathways for Bichromophoric Merocyanine Dyes

We have synthesized a large series of bis(merocyanine) dyes with varying spacer unit and investigated in detail their self‐organization behavior by concentration‐ as well as solvent‐dependent UV/Vis spectroscopy. Our in‐depth studies have shown that the self‐organization of the present bis(merocyanine) dyes is subtly influenced by the nature of the spacer unit. The utilization of rigid spacers results in the formation of self‐associated bimolecular complexes with high binding strength, while flexible spacers drive the respective bichromophoric dyes to intramolecular folding. Our thorough investigations on the impact of alkyl spacer chain length on the folding tendency of the present series of bis(merocyanine) dyes revealed a biphasic behavior, that is, a steep increase of the folding tendency for the dyes containing C4 to C7 chains and then a gentle decrease for dyes with longer alkyl spacer chains as evidenced by free energy (ΔG) values for the folding of these dyes. Furthermore, analyses of aggregates’ optical properties based on exciton theory as well as quantum chemical calculations suggest a bimolecular aggregate structure for the dye possessing a rigid spacer and a rotationally twisted pleated structure for the bis(merocyanine) dyes having spacer units with less than seven carbon atoms, while the application of longer alkyl chain linkers (≥C7) provides enough flexibility to orient the chromophores in electrostatically most favored antiparallel fashion.     

Influence of spacer lengths on the properties of chiral triplet liquid crystals based on estradiol

A series of 3-[ω-(4-cyanobiphenyl-4'-yloxy)alkyl] ethers of estradiol 17-[ω(4-cyanobiphenyl-4'-yloxy)alkanoates] with variable spacers has been prepared as chiral triplet liquid crystals. The compounds show very broad range cholesteric phases and are transformed into cholesteric glasses at room temperature. They exhibit odd-even effects for their cholesteric-isotropic transition temperatures and the associated entropy changes as a function of spacer length. The odd-even effects are observed upon changing the parity of both the ester and of the ether spacer. The best ordering is observed for compounds with an even number of methylene groups both in the ester and the ether spacer. In these cases the three mesogen units are oriented more or less parallel when the alkyl spacers are in the all-trans-conformations. Odd-even effects are also observed for the selective reflection wavelength of the planar cholesteric phase, depending on the parity of both spacers. For several compounds with short spacers the selective reflection wavelength increases strongly with temperature, whereas for other compounds this is almost temperature independent.     

DNA cleavage by the photocontrolled cooperation of Zn(II) centers in an azobenzene-linked dizinc complex

We synthesized a new photoactive dinuclear zinc(II) complex by linking two zinc centers with a ligand containing an azobenzene chromophore and investigated the DNA cleavage activities of its trans and cis forms. The trans structure of the dinuclear zinc complex was determined by X-ray crystallography, where each zinc center is situated in an octahedral coordination environment comprised of three nitrogen atoms from the ligand and three oxygen atoms from two nitrate ions. The dinuclear zinc complex containing the azobenzene chromophore was photoisomerizable between the trans and cis forms. The binding affinities of the trans and cis complexes with calf thymus (CT)-DNA were similar. Although the DNA cleavage activity of the trans complex was negligible, the cis complex was able to cleave DNA. We attribute the efficient activity of the cis complex to the cooperation of the two closely located zinc centers and the inactivity of the trans complex to the two metal centers positioned far away from each other. The DNA cleavage activity of the cis complex exhibited a pH-dependent bell-shaped profile, which has been observed in the hydrolytic cleavage of DNA by zinc complexes. The DNA cleavage activity was not inhibited by a major groove binder, methyl green, but decreased significantly by a minor groove binder, 4',6-diamidino-2-phenylindole, indicating that the dinuclear zinc complex binds to the minor groove of DNA. The present work shows the importance of the cooperation of two zinc ions for hydrolytic DNA cleavage, which can be photoregulated by linking the two metal centers with a photoisomerizable spacer, such as an azobenzene chromophore.     

手性钌(Ⅱ)配合物对DNA的立体选择性断裂

八面体钌(Ⅱ)多吡啶配合物与双螺旋DNA插入结合后具有较强的结合能力,并且含有一个具有氧化一还原活性的中心金属离子．它们对氧化剂相对比较稳定,但对光比较敏感,因此可利用光辐射使之产生单线态氧或羟基自由基等而使DNA裂解．此外,这些配合物具有左手∧-和右手△-两种构型,与同样具有手性的DNA作用时,存在着立体选择性结合．并且在对DNA的断裂反应中也存在一定的立体选择性,可作为不同构型DNA的结构探针．     

Surface tension study of cationic gemini surfactants binding to DNA

Binding of cationic gemini surfactants alkanediyl-a-ω-bis(dimethyldodecylammonium bromides) with variable polymethylene spacer length ranging from 2 to 12 methylene groups to DNA in NaBr solution is investigated utilizing the tensiometry method. A simple method is presented for calculating the number of surfactant molecules bound to DNA. The results are evaluated in terms of the gemini surfactant spacer length, showing that gemini molecules with either short spacers (2 methylene groups) or long spacers are most efficiently adsorbed to DNA. A weak adsorption to DNA was found for gemini molecules with a medium spacer length (6 methylene groups in the spacer). The binding properties of cationic gemini surfactants as a function of spacer length are consistent with the results obtained by other experimental methods (dynamic light scattering measurements, fluorescence spectroscopy), indicating identical adsorption behaviour of gemini molecules as a function of the spacer length.