Design of a hairpin polyamide, ZT65B, for targeting the inverted CCAAT box (ICB) site in the multidrug resistant (MDR1) gene

A novel hairpin polyamide, ZT65B, containing a 3-methylpicolinate moiety was designed to target the inverted CCAAT box (ICB) of the human multidrug resistance 1 gene (MDR1) promoter. Binding of nuclear factor-Y (NF-Y) to the ICB site upregulates MDR1 gene expression and is, therefore, a good target for anticancer therapeutic agents. However, it is important to distinguish amongst different promoter ICB sites so that only specific genes will be affected. All ICB sites have the same sequence but they differ in the sequence of the flanking base pairs, which can be exploited in the design of sequence-specific polyamides. To test this hypothesis, ten ICB-containing DNA hairpins were designed with different flanking base pairs; the sequences ICBa and ICBb were similar to the 3'-ICB site of MDR1 (TGGCT). Thermal-denaturation studies showed that ZT65B effectively targeted ICBa and ICBb (DeltaTM=6.5 and 7.0 degrees C) in preference to the other DNA hairpins (<3.5 degrees C), with the exception of ICBc (5.0 degrees C). DNase I-footprinting assays were carried out with the topoisomerase IIalpha-promoter sequence, which contains five ICB sites; of these, ICB1 and ICB5 are similar to the ICB site of MDR1. ZT65B was found to selectively bind ICB1 and ICB5; footprints were not observed with ICB2, ICB3, or ICB4. A strong, positive induced ligand band at 325 nm in CD studies confirmed that ZT65B binds in the DNA minor groove. The selectivity of ZT65B binding to hairpins that contained the MDR1 ICB site compared to one that did not (ICBd) was confirmed by surface-plasmon studies, and equilibrium constants of 5x10(6)-1x10(7) and 4.6x10(5) M-1 were obtained with ICB1, ICB5,and ICB2 respectively. ZT65B and the previously published JH37 (J. A. Henry, et al. Biochemistry 2004, 43, 12 249-12 257) serve as prototypes for the design of novel polyamides. These can be used to specifically target the subset of ubiquitous gene elements known as ICBs, and thereby affect the expression of one or a few proteins.     

可检测Fe~(3+)的萘酰亚胺席夫碱荧光探针的合成及性质研究

通过醛胺缩合反应,合成了一种萘酰亚胺席夫碱荧光探针(L)。探针L的分子结构通过1H NMR进行了鉴定。紫外-可见吸收光谱和荧光发射光谱测试结果表明探针L可选择性识别Fe~(3+)离子,并且具有可视化识别特点。     

NBD‐Based Green Fluorescent Ligands for Typing of Thymine‐Related SNPs by Using an Abasic Site‐Containing Probe DNA

The binding behavior of green fluorescent ligands, derivatives of 7‐nitrobenzo‐2‐oxa‐1,3‐diazole (NBD), with DNA duplexes containing an abasic (AP) site is studied by thermal denaturation and fluorescence experiments. Among NBD derivatives, N¹‐(7‐nitrobenzo[c][1,2,5]oxadiazol‐4‐yl)propane‐1,3‐diamine (NBD‐NH₂) is found to bind selectively to the thymine base opposite an AP site in a DNA duplex with a binding affinity of 1.52×10⁶ M ^?1. From molecular modeling studies, it is suggested that the NBD moiety binds to thymine at the AP site and a protonated amino group tethered to the NBD moiety interacts with the guanine base flanking the AP site. Green fluorescent NBD‐NH₂ is successfully applied for simultaneous G>T genotyping of PCR amplification products in a single cuvette in combination with a blue fluorescent ligand, 2‐amino‐6,7‐dimethyl‐4‐hydroxypteridine (diMe‐pteridine).     

Rational Design,Synthesis, and DNA Binding Properties of Novel Sequence‐Selective Peptidyl Congeners of Ametantrone

Natural and synthetic compounds characterized by an anthraquinone nucleus represent an important class of anti‐neoplastic agents, the mechanism of action of which is related to intercalation into DNA. Ametantrone (AM) is a synthetic 9,10‐anthracenedione bearing two (hydroxyethylamino)ethylamino residues at positions 1 and 4; along with other anthraquinones and anthracyclines, it shares a polycyclic intercalating moiety and charged side chains that stabilize DNA binding. All these drugs elicit adverse side effects, which represent a challenge for antitumor chemotherapy. In the present work the structure of AM was augmented with appropriate groups that target well‐defined base pairs in the major groove. These should endow AM with DNA sequence selectivity. We describe the rationale for the synthesis and the evaluation of activity of a new series of compounds in which the planar anthraquinone is conjugated at positions 1 and 4 through the side chains of AM or other bioisosteric linkers to appropriate dipeptides. The designed novel AM derivatives were shown to selectively stabilize two oligonucleotide duplexes that both have a palindromic GC‐rich hexanucleotide core, but their stabilizing effects on a random DNA sequence was negligible. In the case of the most effective compound, the 1,4‐bis‐[Gly‐(L ‐Lys)] derivative of AM, the experimental results confirm the predictions of earlier theoretical computations. In contrast, AM had equal stabilizing effects on all three sequences and showed no preferential binding. This novel peptide derivative can be classified as a strong binder regarding the sequences that it selectively targets, possibly opening the exploitation of less cytotoxic conjugates of AM to the targeted treatment of oncological and viral diseases.     

新型双发色团固体激光染料薄膜的光稳定性研究

利用UV－Vis吸收光谱仪和光化学反应器研究了新型双发色团固体激光染料薄膜的光降解动力学。研究结果表明：双发色团固体激光染料薄膜 的光褪色反应遵循假一级动力学衰减。在PRNAM系列共聚物（N－烯丙基－若丹明19、N－[2-丙烯酸基）乙基]-1,8-萘酰亚胺和甲基丙烯酸甲酯的共聚物）中萘酰亚胺基团通过聚合物碳链与若丹明基团的氮原子相连；而在PRNM系列共聚物（若丹明19的烯丙基酯、N-[(2-丙烯酸基）乙基]-1,8,-萘酰亚胺和甲基丙烯酸甲酯的共聚物）中则是与若丹明基团的酯基相连。PRNAM系列共聚物的光稳定性优于PRNM和PRM（若丹明19的烯丙基酯和甲基丙烯酸甲酯的共聚物）系列的光稳定性。     

Gold(I) N‐Heterocyclic Carbene Complexes with Naphthalimide Ligands as Combined Thioredoxin Reductase Inhibitors and DNA Intercalators

Organometallic conjugates consisting of a gold(I) N‐heterocyclic carbene (NHC) moiety and a naphthalimide were prepared and investigated as cytotoxic agents that interact with both DNA and the disulfide reductase enzyme thioredoxin reductase (TrxR). The complexes were potent DNA intercalators related to their naphthalimide partial structure, inhibited TrxR as a consequence of the incorporation of the gold(I) moiety, and triggered efficient cytotoxic effects in MCF‐7 breast and HT‐29 colon adenocarcinoma cells. Strong effects on tumor cell metabolism were noted for the most cytotoxic complex, chlorido[1‐(3′‐(4′′‐ethylthio‐1′′,8′′‐naphthalimid‐N′′‐yl))‐propyl‐3‐methyl‐imidazol‐2‐ylidene]gold(I) ( 4 d ). In conclusion, the conjugation of naphthalimides with gold(I) NHC moieties provided a useful strategy for the design of bioorganometallic anticancer agents with multiple modes of action.     

Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase

Glycosylphosphatidylinositol (GPI) anchoring is a common post- translational modification of extracellular eukaryotic proteins. Attachment of the GPI moiety to the carboxyl terminus (omega-site) of the polypeptide occurs after proteolytic cleavage of a C-terminal propeptide. In this work, the sequence pattern for GPI-modification was analyzed in terms of physical amino acid properties based on a database analysis of annotated proprotein sequences. In addition to a refinement of previously described sequence signals, we report conserved sequence properties in the regions omega - 11...omega - 1 and omega + 4...omega + 5. We present statistical evidence for volume-compensating residue exchanges with respect to the positions omega - 1...omega + 2. Differences between protozoan and metazoan GPI-modification motifs consist mainly in variations of preferences to amino acid types at the positions near the omega-site and in the overall motif length. The variations of polypeptide substrates are exploited to suggest a model of the polypeptide binding site of the putative transamidase, the enzyme catalyzing the GPI-modification. The volume of the active site cleft accommodating the four residues omega - 1...omega + 2 appears to be approximately 540 A3.      

Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif

I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.     

An electrochemical study of neutral red-DNA interaction

Electrochemical methods were used to investigate the interaction of neutral red (NR) with double-stranded calf thymus DNA, in solution as well as using a DNA-modified glassy carbon (GC-DNA) electrode. The results were compared with those obtained from bare glassy carbon (GC) electrode. The formal potential of NR was more positive when GC-DNA electrode was used although the rate of heterogeneous electron transfer is as high as that of using GC electrode. GC-DNA electrode enables preconcentration of NR for chosen times on the electrode surface, despite the fact that the mass transfer effects in the thin DNA layer adsorbed on the surface was still observed using cyclic voltammetry and electrochemical impedance spectroscopy techniques. Parameters, such as the diffusion coefficient of NR, binding site size in base pairs and the ratio of the binding constants for the oxidized and reduced forms of the bound species were obtained. A binding isotherm for NR at GC-DNA electrode was obtained from coulometric titrations and gave an affinity constant equal to 2.76 × 10⁴ L mol⁻¹. From the studies of the interaction in solution, the diffusion coefficient of free and DNA-bound NR, binding constant and binding site size of the DNA-NR complex was also obtained simultaneously by non-linear fitting analysis of voltammetric data.     

对Fe3+和草酸具有荧光“关-开”功能的喹啉衍生物

通过8-羟基喹啉-2-甲醛与水杨酰肼的缩合反应,合成了一种喹啉席夫碱衍生物荧光分子探针(L)。经FT-IR、1H NMR、13C NMR、ESI-MS表征,确定了探针L的分子结构。利用吸收和荧光光谱研究了探针L的识别性能。在DMSO溶液中,探针L与Fe3+能够形成1:1型配合物L-Fe,表观结合常数为4.6 × 104 L/mol。利用该配合物的形成导致的探针荧光猝灭,能够在常见金属离子中高选择性识别Fe3+,检出限为6.8 × 10-8 mol/L。进一步以L-Fe复合物为探针,实现了对草酸的高选择性荧光增强识别,检出限为1.3 × 10-7 mol/L。该方法可用于蔬菜中草酸的检测。     

An Isocytidine Derivative with a 2‐Amino‐6‐methylpyridine Unit for Selective Recognition of the CG Interrupting Site in an Antiparallel Triplex DNA

Sequence‐specific recognition of duplex DNA mediated by triple helix formation offers a potential basis for oligonucleotide therapy and biotechnology. However, triplex formation is limited mostly to homopurine strands, due to poor stabilization at CG or TA base pairs in the target duplex DNA sequences. Several non‐natural nucleosides have been designed for the recognition of CG or TA base pairs within an antiparallel triplex DNA. Nevertheless, problems including low selectivity and high dependence on the neighboring bases remain unsolved. We thus synthesized N²‐arylmethyl isodC derivatives and incorporated them into triplex‐forming oligonucleotides (TFOs) for the selective recognition of the CG base pair within antiparallel triplex DNA. It was shown that an isodC derivative bearing a 2‐amino‐6‐methylpyridine moiety (AP‐isodC) recognizes the CG base pair with high selectivity in antiparallel triplex DNA irrespective of the flanking base pairs.     

Dyeing and fastness properties of polyamide fabrics using some acid‐based monoazo disperse dyes

A series of monoazo disperse dyes derived from naphthalimide containing butyric acid has been applied on polyamide fabrics. The build up and dyeing properties of these dyes such as leveling property, wash, light, perspiration for alkaline and acidic conditions, and rubbing fastnesses on polyamide fabrics have been investigated. The results showed that the applied dyes are capable of producing red to bluish red hues on polyamide fabrics. Because of the presence of both carboxylic acid and hydroxyl groups on the molecular structure of Dye 3, it showed desired and more strength in respect to other used dyes. Comparing the build up of these dyes to commercial dyes such as disperse red 60 and disperse red 73 revealed that most of the used dyes have higher build up in comparison to the commercial ones. Measurement of fastness properties of dyed samples indicated that they have good wash (4–5), rubbing (4), perspiration (4–5), and heat fastnesses (4–5) and they possess less than moderate light fastness (3–4) on polyamide fabrics. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011.     

Light Triggers the Antiproliferative Activity of Naphthalimide-Conjugated (η6-arene)ruthenium(II) Complexes

We report the synthesis and characterization of three half-sandwich Ru(II) arene complexes [(η⁶-arene)Ru(N,N′)L][PF₆]₂ containing arene = p-cymene, N,N′ = bipyridine, and L = pyridine meta- with methylenenaphthalimide (C1), methylene(nitro)naphthalimide (C2), or methylene(piperidinyl)naphthalimide (C3). The naphthalimide acts as an antenna for photoactivation. After 3 h of irradiation with blue light, the monodentate pyridyl ligand had almost completely dissociated from complex C3, which contains an electron donor on the naphthalimide ring, whereas only 50% dissociation was observed for C1 and C2. This correlates with the lower wavelength and strong absorption of C3 in this region of the spectrum (λ_max = 418 nm) compared with C1 and C2 (λ_max = 324 and 323 nm, respectively). All the complexes were relatively non-toxic towards A549 human lung cancer cells in the dark, but only complex C3 exhibited good photocytoxicity towards these cancer cells upon irradiation with blue light (IC₅₀ = 10.55 ± 0.30 μM). Complex C3 has the potential for use in photoactivated chemotherapy (PACT).     

Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide

We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py−Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py−Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py−Im polyamide as a molecular tool to modulate the formation of DNA assemblies.     

Glycine fluoromethylketones as SENP-specific activity based probes

We report here the synthesis and biochemical properties of a new peptidyl activity-based probe 1 for SUMO proteases, SENPs. The activity-based probe has at its C terminus a glycine-derived fluoromethylketone moiety as a reactive group designed to target the active-site cysteine of SENPs. Based on a study of the interactions between SENPs and SUMOs, we introduced further design elements that allow the activity-based probe to selectively target SENPs at low micromolar to high nanomolar concentrations. Moreover, 1 out-competes SUMO1 from the reversible SUMO1-SENP1 complex, thus suggesting that 1 and SUMO1 share a common binding site on SENP1.     

The synthesis,crystal structure and photophysical properties of three novel naphthalimide dyes

Three new naphthalimide derivatives containing an electron-donor moiety (carbazole), 4-carbazolyl-N-methyl-1,8-naphthalimide, 4-carbazolyl-N-cyclohexyl-1,8-naphthalimide and 4-carbazolyl-N-phenyl-1,8-naphthalimide were synthesized and crystal structures confirmed. Crystallographic data revealed that the interplanar angles (θ) of the carbazole and naphthalimide moieties were, respectively, 70.7° and 66.5°. The UV–vis absorption and photoluminescent spectra of the systems in n-hexane, CHCl₃, tetrahydrofuran and CH₂Cl₂ were investigated. The lowest absorption band of the naphthalimide molecular centered at 400–420 nm was assigned to charge-transfer transition with emission at ≈440 nm in n-hexane and at ≈560 nm in CH₂Cl₂.