A far-red fluorescent probe for selective G-quadruplex DNA targeting

The development of rapid and simple approaches for detection of G-quadruplex DNA structures has attracted significant attention to disclose their diverse physiological and pathological functions. Thiazole orange (TO) is a common fluorescence probe used for the detection of G-quadruplexes. However, it still suffers from some common problems like non-selective for G-quadruplex and emission in the lower wavelength region of spectrum, thus hampering its further applications. Probes with turn-on fluorescence in the far-red region are highly sought-after due to minimal auto-fluorescence and cellular damage. In this paper, we described a far-red fluorescent probe (L-1) by introducing an amine group into styrylquinolinium scaffold. The experimental results indicated that L-1 exhibited significant fluorescence enhancement when treated with G-quadruplexes but retained weak fluorescence in the presence of duplex DNAs. In addition, this probe also displayed higher binding affinity for parallel G-quadruplexes. The characteristics of L-1 were further investigated with UV–vis spectrophotometry, fluorescence, circular dichroism, KI quenching, FID assay and molecular docking to validate optical photophysical properties, as well as the selectivity, sensitivity and detailed binding mode toward G-quadruplex DNAs.     

Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting

Pyrrole-imidazole (Py-Im) polyamides are a class of programmable minor-groove binders that recognize pre-determined DNA double helixes with high affinity and specificity. This review summarized the recent advances of Py-Im polyamides from their synthesis to applications via various modifications at the molecular level.     

Binding of distamycin A to UV-damaged DNA

We have found that distamycin A can bind to DNA duplexes containing the (6-4) photoproduct, one of the major UV lesions in DNA, despite the changes, caused by photoproduct formation, in both the chemical structure of the base moiety and the local tertiary structure of the helix. A 20-mer duplex containing the target site, AATT.AATT, was designed, and then one of the TT sequences was changed to the (6-4) photoproduct. Distamycin binding to the photoproduct-containing duplex was detected by CD spectroscopy, whereas specific binding did not occur when the TT site was changed to a cyclobutane pyrimidine dimer, another type of UV lesion. Distamycin binding was analyzed in detail using 14-mer duplexes. Curve fitting of the CD titration data and induced CD difference spectra revealed that the binding stoichiometry changed from 1:1 to 2:1 with photoproduct formation. Melting curves of the drug-DNA complexes also supported this stoichiometry.     

Design and synthesis of novel thiazole-containing cross-linked polyamides related to the antiviral antibiotic distamycin

A family of naturally occurring oligopeptides includes netropsin, distamycin, anthelvencin, kikumycin B, amidinomycin, and norformycin. Netropsin (I) and distamycin (II) express their biological activities by targeting specific sequences of chemical functionalities in the minor groove of DNA. Both netropsin and distamycin can be regarded as polyamide chains in which each alpha-carbon has been replaced by a five-membered pyrrole ring. The repeat distance in such an augmented polyamide chain is almost the same as the distance from one base pair to the next along the floor of a minor groove within beta-DNA. In this paper we report the synthesis of 16-21 cross-linked polyamides containing a thiazole heterocyclic ring bearing the active functionalites NH(2), NHCHO, or H. 16 and 17 were synthesized by DCC and HOBt catalyzed reaction of 5 with 14 and 15, while the formylation products 18 and 19 were obtained by coupling the formylated 4-methyl-thiazolated acid 6 with 14 and 15. The deaminated compounds 20 and 21 were obtained by the coupling of 5-trichloroacetyl-4-methylthiazole 7 synthesized from 4-methylthiazole. All the six cross-linked polyamides 16-21 were tested for their DNA gyrase inhibition. The studies have shown these polyamides have better sequence recognition and a greater percentage of inhibition than the corresponding monomers. The compound 17 shows complete inhibition of gyrase at 0.5 microM concentration as compared to the naturally occurring distamycin at 1.0 microM.     

Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures

The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4. A selected NDI was able to significantly impair the growth of melanoma cells by causing telomere dysfunction and down-regulation of telomerase expression. These findings points to our hybrid ligand-alkylating NDIs as possible tools for the development of novel targeted anticancer therapies.     

Synthesis of carboranyl polyamines for DNA targeting

Three groups of internal and terminal N-substituted carboranyl spermidines/spermines were synthesized as potential BNCT agents for the treatment of malignant tumors.     

A DNA G-quadruplex converts SOD1 into fibrillar aggregates

Nucleic acids with G4 elements play a role in the formation of aggregates involved in intracellular phase transitions. Our previous studies suggest that different forms of DNA could act as an accelerating template in Cu/Zn superoxide dismutase (SOD1) aggregation. Here, we examined the regulation of formation and cytotoxicity of the SOD1 aggregates by single-stranded 12-mer deoxynucleotide oligomers (dN)₁₂ (N = A, T, G, C; ssDNAs) under acidic conditions. The ssDNAs can be divided into two groups based on their roles in SOD1 binding, exposure of hydrophobic clusters in SOD1, accelerated formation, morphology and cytotoxicity of SOD1 aggregates. G-quadruplexes convert SOD1 into fibrillar aggregates as a template, a fact which was observed for the first time in the nucleic acid regulation of protein aggregation. Moreover, the fibrillar or fibril-like SOD1 species with a G-quadruplex provided by (dG)₁₂ were less toxic than the amorphous species with (dN)₁₂ (N = A, T). This study not only indicates that both morphology and cytotoxicity of protein aggregates can be regulated by the protein-bound DNAs, but also help us understand roles of nucleic aid G-quadruplexes in the formation of aggregates and membraneless organelles involved in intracellular phase transitions.     

Synthesis of polyamides through active diesters

Polycondensation reactions of active diesters including several aromatic or heterocyclic nuclei with hexamethylenediamine were carried out in order to investigate the enhancement of reactivity of active diesters for nucleophilic replacement to form polyamide for synthesis of polyamides under moderate condition. These active diesters easily induce polycondensation reaction in solutions, forming polyamides at room temperature. Solvents have a considerable influence on the rate of the polycondensation. The reactivity of these active diesters toward aminolysis is strongly controlled by the structure of the alcohol formed. The reactivity enhancement of active ester group toward amine could be attributed either to the polarization of carbonyl group or to the resonance effect of the alkoxy group.     

邻菲罗啉衍生物与G-四链体DNA的识别

设计合成了一种新型邻菲罗啉衍生物,用IR,<'1>H-NMR,<'13>C-NMR和质谱进行了结构表征.在包含100mM NaCl的Tris-HCl(pH 7.4)缓冲溶液中,利用荧光共振能量转移熔点(FRET-melting)分析以及紫外可见光谱研究了此化合物对人端粒G-四链体DNA(AG<,3>T<,2>AG<,3...     

Synthesis of inherently dissymmetric polyamides,

The preparation of polyamides from derivatives of optically active biphenic acid is described. The diacid chlorides chosen were 2,2′-dinitro-6,6′-dimethylbiphenyl-4,4′-dicarbonyl chloride and 2,2′-dichloro-6,6′-dimethylbiphenyl-4,4′-dicarbonyl chloride, the diamines were phenyldiamines (o-, m-, p-) piperazine, trans-2,5-dimethylpiperazine, and 1,2-piperaazolidine. Polymerization was carried out by the method of interfacial polycondensation. The polymers of aromatic diamines were insoluble in common organic solvents but soluble in dimethylformamide containing 5% lithium chloride, triesters of phosphoric acid, and methanesulfonic acid. The polymers of aliphatic diamines were also insoluble in common organic solvents but soluble in trifluoroethanol. All polymers had melting points higher than 280°C.     

Synthesis and characterization of Schiff-base-containing polyamides

A series of new Schiff base polyamides（PAs） were synthesized by polycondensation of benzilbisthiosemicarbazone diamine（LH₆） with different commercially available aliphatic and aromatic diacid chlorides. The monomer and all the PAs were characterized by FTIR,¹H-NMR,and elemental analysis.The prepared polyamides showed inherent viscosities in the range of 0.30-0.36 dL/g in DMF at 25℃,indicating their moderate molecular weight.The PAs were completely soluble in aprotic polar solvents such as dimethylformamide（DMF）,N-methylpyrolidone（NMP）, tetrachloroethane（TCE）,dimthylsulfoxide（DMSO） and also in H₂SO₄ and partially soluble in THF,acetone and chloroform at room temperature.Thermal analysis showed that these PAs were practically amorphous and exhibited 10%weight loss above 220℃.     

Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands

The folding of the single-stranded 3' end of the human telomere into G-quadruplex arrangements inhibits the overhang from hybridizing with the RNA template of telomerase and halts telomere maintenance in cancer cells. The ability to thermally stabilize human telomeric DNA as a four-stranded G-quadruplex structure by developing selective small molecule compounds is a therapeutic path to regulating telomerase activity and thereby selectively inhibit cancer cell growth. The development of compounds with the necessary selectivity and affinity to target parallel-stranded G-quadruplex structures has proved particularly challenging to date, relying heavily upon limited structural data. We report here on a structure-based approach to the design of quadruplex-binding ligands to enhance affinity and selectivity for human telomeric DNA. Crystal structures have been determined of complexes between a 22-mer intramolecular human telomeric quadruplex and two potent tetra-substituted naphthalene diimide compounds, functionalized with positively charged N-methyl-piperazine side-chains. These compounds promote parallel-stranded quadruplex topology, binding exclusively to the 3' surface of each quadruplex. There are significant differences between the complexes in terms of ligand mobility and in the interactions with quadruplex grooves. One of the two ligands is markedly less mobile in the crystal complex and is more quadruplex-stabilizing, forming multiple electrostatic/hydrogen bond contacts with quadruplex phosphate groups. The data presented here provides a structural rationale for the biophysical (effects on quadruplex thermal stabilization) and biological data (inhibition of proliferation in cancer cell lines and evidence of in vivo antitumor activity) on compounds in this series and, thus, for the concept of telomere targeting with DNA quadruplex-binding small molecules.     

Synthesis and spectral study of a novel distamycin conjugate

The ¹H and ¹³C NMR resonances for a novel distamycin conjugate, 3‐[1‐methyl‐4‐[1‐methyl‐4‐[1‐methyl‐4‐[N¹‐[5‐methyl‐2,4(1H,3H)pyrimidinedione]acetylamino]pyrrole‐2‐carboxamido]pyrrole‐2‐carboxamido]pyrrole‐2‐carboxamido]propionamidine hydrochloride ( 1 ), were assigned, using the concerted application of one‐ and two‐dimensional NMR techniques including nuclear Overhauser effect difference, DEPT, HMQC and HMBC experiments. Copyright © 2003 John Wiley & Sons, Ltd.     

The natural product prodigiosin binds G-quadruplex DNA

Prodigiosin, a metabolite isolated from Serratia bacteria, is a potent anti-cancer agent. The goal of this research was to determine if prodigiosin could bind to G-quadruplex DNA. We found by using UV–vis spectroscopy that the G-quadruplex K⁺√d[TG₄T]₄, but not the single-stranded Li⁺√d[TG₄T], increased the water solubility of prodigiosin. In addition, we found that prodigiosin's fluorescence was strongly enhanced in the presence of K⁺√d[TG₄T]₄, further evidence for quadruplex-ligand binding. Using ¹H and ³¹P NMR experiments, we confirmed that prodigiosin binds at the 3′-end of K⁺√d[TG₄T]₄. Saturation transfer difference NMR experiments, done by irradiating the G5 H8 signal in K⁺√d[TG₄T]₄, indicated specific interactions between the G-quadruplex and prodigiosin's A and B rings. This study raises the possibility that G-quadruplex DNA may well be a target for the anti-cancer agent prodigiosin.     

Synthesis and preliminary evaluation of novel analogues of quindolines as potential stabilisers of telomeric G-quadruplex DNA

Telomeric DNA is a potential selective target for cancer therapy since the tumour-associated enzyme telomerase regulates telomere maintenance in most cancer cells. The 3′ single-stranded ends of telomeric DNA can be folded into quadruplex structures by appropriate small molecules. We describe the preparation of a new class of 2,7-disubstituted 10H-indolo[3,2-b]quinolines with enhanced selectivity for the stabilisation of quadruplex DNA compared to duplex DNA, and also the preparation of a key intermediate for the synthesis of trisubstituted quindolines.     

Synthesis of semiaromatic polyamides based on decanediamine

<正>Long chain semiaromatic polyamides were synthesized by the reactions of decanediamine with various aromatic diacids and characterized by Fourier transform infrared spectroscopy(FT-IR) and nuclear magnetic resonance(~1H-NMR). The thermal behaviors were determined by differential scanning calorimetry(DSC) and thermogravimetric analysis(TGA). The solubility,dynamic mechanical,physical and mechanical properties of the polyamides have also been investigated.The resultant polyamides have intrinsic viscosity ranging from 1.7 dL/g to 2.1 dL/g.Their melting temperatures range from 305℃to 343℃,and the glass transition temperatures fall in the range of 125-130℃.The tensile strength of the polyamides is above 100 MPa.     

Synthesis and characterization of norbornane-containing cardo polyamides

A new diamine, 2,2-bis[4-(4-aminophenoxy)phenyl]norbornane (BAPN), containing both ether and norbornane cardo groups, was synthesized in three steps started from norcamphor. A series of cardo polyamides were obtained by the direct polycondensation of BAPN and various aromatic dicarboxylic acids in N-methyl-2-pyrrolidinone (NMP) using triphenyl phosphite and pyridine as condensing agents. Polyamides had inherent viscosities in the range of 0.82–1.58 dL g⁻¹, and were readily soluble in polar aprotic solvents such as NMP, N,N-dimethylacetamide (DMAc) and N,N-dimethylformamide and dimethyl sulfoxide. These polymers were cast in DMAc solution into transparent, flexible, and tough films that were further characterized by X-ray and mechanical analysis. All the polymers were amorphous, and the polyamide films had a tensile strength range of 71–89 MPa, an elongation at break range of 5–9%, and a tensile modulus range of 2.0–2.3 GPa. Polyamides showed glass transition temperatures in the range of 256–296°C as measured by DSC and thermogravimetric analysis indicated no weight loss below 450°C in nitrogen and air atmosphere. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 2791–2794, 1999