Structure-function studies on a synthetic guanosine receptor that simultaneously binds Watson-Crick and Hoogsteen sites

[structure: see text] A series of receptors (11-16) designed to simultaneously bind the Watson-Crick and Hoogsteen sites of guanosine were synthesized, and their binding of guanosine tri-O-pentanoate (32) was probed via 1H NMR complexation studies in 5% DMSO-d6-chloroform-d. The guanosine receptors were synthesized with aminonaphthalene or aminoquinoline auxiliary groups tethered to N-4 of cytosine via a methylene or carbonyl group. A structure-function relationship was established allowing energetic contributions made by components of nucleoside analogues to be probed and more general design rules formulated that may guide the development of more efficacious DNA bases.     

Wavefunction and reactivity study of benzo[a]pyrene diol epoxide and its enantiomeric forms

Benzo[a]pyrene is a known carcinogen, which derives from fossil fuel combustion, cigarette smoke, and generic biomass combustion including traffic emissions. This potent carcinogen has a well-known mechanism of action, leading to the formation of adducts with the DNA, primarily at guanosine positions. The reactivity and chemistry of this notorious compound are, however, dependent on the electronic configuration of the biologically activated metabolite, the benzo[a]pyrene diol epoxide. The activated metabolite exists mainly as four isomers, which have particular chemical reactivities toward guanosine sites on the DNA. These isomers exert also a different carcinogenicity compared to one another, which is a feature that is conventionally attributed to their geometry. However, the reactivity and properties of the isomers are not fully defined, and a determination of these properties by wavefunction behavior is required. This study reports the electronic properties of the benzo[a]pyrene diol epoxide enantiomers, along with a detailed analysis of the energy landscape, geometry, and electronic configuration of the epoxide ring. The results show that the epoxide ring, the core of the reactivity, bears different properties at the level of wavefunction for each isomer. Each of the isomers has a distinct profile on the epoxide ring, in terms of hydrogen bonds and in terms of the non-covalent interaction between the diol groups and the epoxide. These profiles generate differential reactivities of epoxide group, which can be attributed to its local bond lengths, the electron localization function, and polarized bonds. Most interestingly, the quantum chemical calculations showed also that the epoxide ring is inclined more perpendicularly toward the angular ring plane for the more carcinogenic isomers, a feature which suggests a potential geometrical relationship between the inclination of the epoxide group and its interaction with the guanosine group upon adduct formation. Our results introduce novel and crucial information, which assist in understanding the mechanism of toxic potential of this known molecule, and display the strength and level of detail of applying quantum chemical methods to reveal the reactivity, energy properties, and electronic properties of a mutagen.     

Neutral loss and precursor ion scan tandem mass spectrometry for study of activated benzopyrene-DNA adducts

Methodology for detection of activated benzo[a]pyrene (B[a]P)–nucleoside adducts by liquid chromatography–tandem mass spectrometry is reported. Adducts of B[a]P-dihydrodiol epoxide (B[a]PDE) with guanosine and adenosine have been detected for the first time by use of precursor ion scan and neutral loss scan. B[a]P was then activated by use of UV irradiation and some of the products obtained have been identified by taking advantage of the information obtained for B[a]PDE. Photoactivation has also been carried out in the presence of hydrogen peroxide; this resulted in a higher yield of products with increased production of BaP diones. The reactivity of these compounds toward nucleosides has been tested. The proposed method was successfully used for detection of one stable guanosine–B[a]P dione adduct.     

Metallo-guanines and metallo-guanosines

Metallo-guanines of the type [M(G)₂·2H₂O] [M = Ni^II, Fe^II, Cu^II and UO₂ ^II; G = anionic guanine], [M(G)₂(GH)· H₂O] (M = Co^II and Mn^II; GH = neutral guanine), [Pd(G)₂]·2H₂O and [Zn(G)Cl]₂ have been isolated and characterised. Anionic guanine functions as a bidentate ligand and links through N(3) and N(9). E.p.r. data indicate that the Cu^II complex has a highly distorted octahedral structure. The magnetic susceptibility data suggest that the Co^II and Ni^II complexes possess pseudooctahedral geometry. Neutral guanines are probably unidentate and coordinate either through N(3) or N(9). The isolated guanosine complexes are of the types: [M(Gs)₂·H₂O] [M = Ni^II and Cu^II, Gs = anionic guanosine] [Pd(Gs)₂]·2H₂O and [UO₂(Gs)₂]. I.r. data indicate that guanosine also functions as a bidentate ligand, but coordinates through N(1) and C₂ — NH₂. The electronic absorption spectra of the complexes indicate that guanine is a stronger ligand than guanosine.     

Transient silylation of the guanosine O6 and amino groups facilitates N-acylation

[reaction: see text] The formation of a guanosine derivative silylated at both the O6 and amino groups was identified by (15)N NMR. This intermediate allows facile reaction with acetyl chloride or phenoxyacetyl chloride to give in high yield the corresponding N-protected guanosine derivatives, suitable for use in RNA synthesis. The acetyl and phenoxyacetyl amino protecting groups are, respectively, 4 and 230 times more labile than the isobutyryl group to methylamine/ethanol deprotection.     

Alkylation of nucleic acids and their components

Guanosine, cytidine, inosine, and thymine react with 4-[N-(-chloroethyl)-N-methylamino]-benzaldehyde to give 7-alkylguanosine, 3-alkylcytidine, 1-alkylinosine, and 1-alkylthymine, respectively. The order of reactivities of the nucleosides with respect to 4-[N-(-chloroethyl)-N-methylamino] benzaldehyde in 36% aqueous dioxane at 50°C and pH 5–6 is guanosine > inosine > cytidine > thymine. Inosine, cytidine, and thymine are 36%, 21%, and 13% as reactive as guanosine. Adenosine and uridine do not react under these conditions. The ratio of the rate constant for the alkylation of guanosine by 4-[N-(-chloroethyl)-N-methylamine]-benzaldehyde and the rate constant for the hydrolysis of the latter in 17% aqueous dioxane at 50° and pH 5–6 is 10.5±0.5 mole^–1. The alkylation of guanosine at pH 7.5 is accompanied by cleavage of the imidazole ring of the 7-alkylguanosine, which proceeds at a higher rate than the rate of the limiting step — ionization of 4-[N-(-chloroethyl)-N-methylamino]benzaldehyde. The transformations of the alkylated nucleosides in acids and alkalis were studied, and the rate constants of these transformations were determined.See [26] for communication III.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 109–116, January, 1972The authors thank D. G. Knorre for discussing the kinetic results of this research.     

Biosynthetic Production of [N2,1,3,7,9-15N]Guanosine and [1,3,7,9-15N]inosine and conversion into [N6,1,3,7,9-15N]adenosine for structure elucidation of RNA by heteronuclear NMR

A procedure was developed for the biosynthetic preparation of ¹⁵N-labelled guanosine and inosine through the action of a mutant Bacillus subtilis strain. Crude [N²,1,3,7,9-¹⁵N]guanosine and [1,3,7,9-¹⁵N]inosine were isolated from the culture filtrate by precipitation and anion-exchange chromatography (Scheme 1). No cell lysis and no enzymatic degradation was necessary. The per-isobutyrylated derivatives 1 and 2 were isolated from a complex mixture, purified by virtue of their different lipophilicity, and separated in three steps involving normal-and reversed-phase silica-gel chromatography. One litre of complex nutrient medium yielded 8.44 mmol of guanosine derivative and 2.84 mmol of inosine derivative with high average ¹⁵N enrichment (83.5 and 91.9 atom-%, resp.). [N⁶,1,3,7,9-¹⁵N]Adenosine ( 4 ) was obtained from 2′,3′,5′-tri-O-isobutyryl[1,3,7,9-¹⁵N]inosine ( 1 ) through the ammonolysis of its 1,2,4-triazolyl derivative with aqueous ¹⁵NH₃ (Scheme 2).     

Selective fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene by nucleotides

[reaction: see text] The fluorescence quenching of 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) by nucleotides has been studied. The quenching mechanism was analyzed on the basis of deuterium isotope effects, tendencies for exciplex formation, and the quenching efficiency in the presence of a molecular container (cucurbit[7]uril). Exciplex-induced quenching appears to prevail for adenosine, cytidine, and uridine, while hydrogen abstraction becomes competitive for thymidine and guanosine. Compared to other fluorescent probes, DBO responds very selectively to the type of nucleotide.     

Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides

Raman spectra are presented for nine crystals containing the guanosine residue and ten crystals containing the cytidine residue whose conformations are known from their X-ray crystallographic analyses. A nearly complete set of assignments of all the observed Raman lines in the 1700—150 cm⁻¹ range is proposed on the basis of a previous normal coordinate treatment of guanine and cytosine with a set of force constants determined by an ab initio MO method, and on the basis of a mutual comparison of the observed spectra. A number of conformation sensitive Raman lines are found here, and several rules on the structure—spectrum correlations are proposed. Raman spectral features in the 1400—1300 cm⁻¹ and 700—600 cm⁻¹ ranges seem to reflect sensitively and regularly the conformation of the guanosine residue, namely its ribose-ring puckering state at the torsion angle around its glycosidic bond. A spectral feature in the 1300—1200 cm⁻¹ range is found to be sensitive to the cytidine conformation. The position of a strong Raman line in the 900—750 cm⁻¹ region, on the other hand, seems to indicate a particular set of torsion angles along the PO5′C5′C4′C3′O3′ backbone. In the light of these proposed rules, the so-called B-form poly [d(GC)].· poly[d(GC)] in solution must have an O4′endo-anti guanosine, a C2′endo-anti cytidine, and an “alternating B” backbone as proposed by Klug [7] while its Z-form should have a C3′ endo-syn guanosine, a form of cytidine in between C2′endoC1′exo-anti cytidine, and a Z_I form backbone, as defined by Wang [41].     

Gas-phase formation of radical cations of monomers and dimers of guanosine by collision-induced dissociation of Cu(II)-guanosine complexes

An electrosprayed water/methanol solution of guanosine and Cu(NO3)2 was observed to give rise to gas-phase copper complexed ions of [CuLn]*2+, [CuL(MeOH)n]*2+, and [CuG n(NO3)]*+, as well as the ions [L]*+, [L+H]+, [G]*+, and [G+H]+ (L=guanosine, G=guanine). The Collision-Induced Dissociation (CID) of [CuL3]*2+ and [CuL(MeOH)n]*2+ (n=2, 3) generates guanosine radical cations [L]*+, while dimeric guanosine radical cations [L2]*+ are generated in the dissociation of [CuL4]*2+. Protonated guanosine [L+H]+ is one of the main products in the primary dissociation of [CuL2]*2+, while the dissociation of the higher-order [CuG2]*2+ produces the [G]*+ radical cation. The guanosine dimer radical cation, [L2]*+ presumably arises from the interaction of two guanosine molecules via proton and hydrogen bonding and is observed to dissociate into [L+H]+ and [L-H]* at low energies. We propose that the first two ligands bind strongly with Cu(II) through N7 and O6 to form a [CuL2]*2+ complex with a four-coordinated planar structure and that a third ligand binds loosely with copper to form [CuL3]*2+. Additional ligation observed in the formation of [CuLn]*2+ (n相似文献   

In situ evaluation of anticancer drug methotrexate-DNA interaction using a DNA-electrochemical biosensor and AFM characterization

An in situ evaluation of the dsDNA-methotrexate (MTX) interaction was performed by voltammetry using a DNA-electrochemical biosensor and characterized by atomic force microscopy (AFM) at a highly oriented pyrolytic graphite (HOPG) surface. Electrochemical experiments in incubated solutions showed that the interaction of MTX with dsDNA leads to modifications to the dsDNA structure in a time-dependent manner. The AFM images show reorganization of the DNA self-assembled network on the surface of the HOPG electrode upon binding methotrexate and the formation of a more densely packed and slightly thicker MTX-dsDNA lattice with a large number of aggregates embedded into the network film. The intercalation of MTX between complementary base pairs of dsDNA lead to the increase of purine oxidation peaks due to the unwinding of the dsDNA. The dsDNA-electrochemical biosensor and the purinic homo-polynucleotide single stranded sequences of guanosine and adenosine, poly[G] and poly[A]-electrochemical biosensors, were used to investigate and understand the interaction between MTX and dsDNA.     

Sensitivity to antitumor drugs and vinblastine binding to membrane in rat ascites hepatoma AH66 cells.

Rat ascites hepatoma AH66 cells have lower sensitivity to Vinca alkaloids and anthracycline antibiotics than AH66F cells, a subline of AH66 cells. AH66 cells expressed P-glycoprotein, while the protein was not detectable in AH66F cells. There are two affinity sites for [3H]vinblastine binding in the AH66 cell membrane, while AH66F cells have only one affinity site. The high affinity [3H]vinblastine binding in AH66 cells was inhibited by Adriamycin, verapamil, nicardipine, and reserpine. The high affinity site of the binding may be the multidrug transporter, P-glycoprotein. [3H]Vinblastine binding was not influenced by adenosine 3'-5'-monophosphate (AMP), adenosine triphosphate (ATP), or guanosine triphosphate (GTP). The multidrug resistance in AH66 cells may depend on P-glycoprotein which is not modulated by nucleotide.     

Assembly of Palladium(II) and Platinum(II) Metallo‐Rectangles with a Guanosine‐Substituted Terpyridine and Study of Their Interactions with Quadruplex DNA

Two novel [2+2] metallo‐assemblies based on a guanosine‐substituted terpyridine ligand ( 1 ) coordinated to palladium(II) ( 2 a ) and platinum(II) ( 2 b ) are reported. These supramolecular assemblies have been fully characterized by NMR spectroscopy, ESI mass spectrometry and elemental analyses. The palladium(II) complex ( 2 a ) has also been characterized by single crystal X‐ray diffraction studies confirming that the system is a [2+2] metallo‐rectangle in the solid state. The stabilities of these [2+2] assemblies in solution have been confirmed by DOSY studies as well as by variable temperature ¹H NMR spectroscopy. The ability of these dinuclear complexes to interact with quadruplex and duplex DNA was investigated by fluorescent intercalator displacement (FID) assays, fluorescence resonance energy transfer (FRET) melting studies, and electrospray mass spectrometry (ESI‐MS). These studies have shown that both these assemblies interact selectively with quadruplex DNA (human telomeric DNA and the G‐rich promoter region of c‐myc oncogene) over duplex DNA, and are able to induce dimerization of parallel G‐quadruplex structures.     

Factors that influence the antiproliferative activity of half sandwich Ru(II)-[9]aneS3 coordination compounds: activation kinetics and interaction with guanine derivatives

Half sandwich Ru(ii)-[9]aneS3 complexes ([9]aneS3 = 1,4,7-trithiacyclononane) are being studied for their antiproliferative activity. We investigated here the activation kinetics of three such complexes, namely [Ru([9]aneS3)(en)Cl](PF(6)) (1), [Ru([9]aneS3)(bpy)Cl](PF(6)) (2) and [Ru([9]aneS3)(pic)Cl] (3) (en = 1,2-diaminoethane, pic = picolinate), and their interaction with DNA model bases. The aim of the study was to assess how they are affected by the nature and charge of the chelating ligand. The model reactions of 1-3 with the guanine derivatives 9-methylguanine (9MeG), guanosine (Guo), and guanosine 5'-monophosphate (5'-GMP) were studied by NMR spectroscopy. All reactions lead, although with different rates and to different extents, to the formation of monofunctional adducts with the guanine derivatives N7-bonded to the Ru center. Two products, the complexes [Ru([9]aneS3)(en)(9MeG-N7)](PF(6))(2) (4) and [Ru([9]aneS3)(pic)(9MeG-N7)](PF(6)) (10), were structurally characterized also by X-ray crystallography. The structure of 4 is stabilized by strong intramolecular H-bonding between an NH of en and the carbonyl O6 of 9MeG. The kinetics of aquation and anation of complexes 2 and 3, as well as the kinetics and the mechanism of the reaction of complexes 1-3 with the biologically more relevant 5'-GMP ligand were studied by UV-Vis spectroscopy. The rate of the reaction of 1-3 with 5'-GMP depends on the nature of the chelating ligand rather than on the charge of the complex, decreasing in the order 3≈2 > 1. The measured enthalpies and entropies of activation (ΔH(≠) > 0, ΔS(≠) < 0) support an associative mechanism for the substitution process.     

无机层状复合氢氧化物中顺铂-DNA模型分子的选择性插入

药物分子的选择性包裹和控制释放是药物研究领域中具有挑战性的研究方向。本文研究表明:顺铂-DNA模型分子cis-[Pt(NH₃)₂(5′-GMP)₂](5′-GMP 5′-单磷酸鸟苷)可插入无机层状复合氢氧化物[Zn_0.68Al_0.32(OH)₂](NO₃)_0.32·mH₂O。但另一种层状复合氢氧化物[LiAl₂(OH)₆]Cl·H₂O由于其阳离子层中正电荷密度较高、阳离子层与层间阴离子之间静电作用较强,因而顺铂-DNA模型分子不能通过离子交换方式插入其层间。光谱数据证实插入层间的顺铂-DNA模型分子结构不变。这可能为铂-DNA分子的传递提供新的方法。     

顺-[Pt(NH3)2Cl2]与核苷的作用

用分光光度法研究了37℃、pH=5.5、0.1M NaClO₄介质中cis[Pt(NH₃)₂Cl₂]和DNA组成物--鸟嘌呤核苷、腺嘌呤核苷、胞嘧啶核苷及胸腺嘧啶核苷的作用。发现顺-[Pt^Ⅱ(NH₃)₂]与前三种核苷能生成组成为1:1、1:2二种络合物,与胸腺嘧啶核苷不作用。所测得一级和二级表观生成常数,以及作用初速分别有如下大小次序:Guo>Ado>Cyt》Thy;Guo>Ado>Cyt》Thy.在所得结果基础上讨论了顺-[Pt(NH₃)₂Cl₂]和癌细胞中DNA作用的可能方式。     

Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method

Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]⁺ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]⁺ interaction in the gas phase was determined from E_com50 – the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]⁺ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.     

G-quartet formation from an N2-modified guanosine derivative

[structure: see text] We report G-quartet formation from an N2-modified lipophilic guanosine nucleoside, N2-(4-n-butylphenyl)-2',3',5'-O-triacetylguanosine. We show that, in the presence of either K+ or Na+, this guanosine derivative self-assembles into a D4-symmetric octamer consisting of two stacking all-syn G-quartets in a tail-to-tail (or head-to-head) fashion and a central ion.     

"Fleximers". Design and synthesis of two novel split nucleosides

[structure: see text] A new class of shape-modified nucleosides is introduced. The purine heterobases of adenosine and guanosine have been split into their imidazole and pyrimidine components, thereby introducing flexibility while retaining the elements necessary for recognition. As a consequence, these novel "fleximers" should find use as bioprobes for investigating enzyme-coenzyme binding sites as well as nucleic acid and protein interactions. Their design and synthesis is described.     

Nitric oxide modulates tumor cell death induced by photodynamic therapy through a cGMP-dependent mechanism

Photodynamic therapy (PDT) of cancer is a very promising technique based on the formation of singlet oxygen induced by a sensitizer after irradiation with visible light. The stimulation of tumor growth by nitric oxide (NO) was reported recently, and NO was shown to have a protective effect against PDT-induced tumor death. We investigated a putative direct effect of NO on tumor cell death induced by PDT, using the human lymphoblastoid CCRF-CEM cells and bisulfonated aluminum phthalocyanine (AlPcS2) as a sensitizer. Cells were incubated with AlPcS2 in the presence or absence of NO donors ((Z)-1-[(2-aminoethyl)-N-(2-ammonioethyl)amino]diazen-1-ium-1,2-diolate, hydroxylamine and S-nitroso-N-acetylpenicillamine) or L-arginine. Under these conditions, in the absence of NO donors or L-arginine the cells died rapidly by apoptosis upon photosensitization. In the presence of NO donors or L-arginine, apoptotic cell death after photosensitization was significantly decreased. Modulation of cell death by NO was not due to S-nitrosylation of caspases and occurred at the level or upstream of caspase-9 processing. The protective effect of NO was reversed by incubating the cells with 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, an inhibitor of guanylyl cyclase, or with KT5823, an inhibitor of protein kinase G (PKG). Incubation with 8-bromo-cyclic guanosine monophosphate, a membrane permeable cyclic guanosine monophosphate analog, also decreased cell death induced by PDT. Although the protective effect of NO against apoptotic cell death in several models has been attributed to an increase in the expression of heme oxygenase-1, heat shock protein 70 or Bcl-2, this was not the case under our experimental conditions. These results show that NO decreases the extent of apoptotic cell death after PDT treatment through a PKG-dependent mechanism, upstream or at the level of caspase activation.