Role of sequence and conformation on the photochemistry and the photophysics of A-T DNA dimers: an experimental and computational approach

The role of base sequence and conformation on the photochemistry and photophysics of thymidylyl (3'-5')-2'-deoxyadenosine sodium salt (TpdA) and 2-deoxyadenylyl (3'-5')-thymidine ammonium salt (dApT) was studied. To this end, nanosecond transient absorption at 266 nm, steady-state irradiation at 254 nm, and quantum chemical calculations were used. The transient absorption spectra show the solvated electron broad band in the visible region for each dinucleotide. In addition, low-intensity absorption bands are observed in the UV region, which are attributed to the deprotonated and protonated neutral radicals of adenine and thymine bases. Photoionization (PI) occurs by one- and two-photon pathways; the latter accounting for approximately 70% of the net PI yield. A diffusion-limited rate constant of 2.0 x 10(10) M(-1) s(-1) was obtained for the reaction of the neutral molecule with the photoejected electron in both sequences. The photodestruction yield, measured from the chromophore loss at 260 nm, decreases in the presence of well-known electron scavengers. This suggests the participation of base radical anions as one of the photodegradation pathways, which is higher in TpdA than in dApT. The intermediacy of a radical ion pair (charge separated state) between the adjacent adenine and thymine bases is proposed in the formation of the [2 + 2] cycloadduct intermediate. The [2 + 2] cycloadduct intermediate is known to be the precursor of the thymine-adenine eight-member ring photoproduct (TA*). Conformational constrains in the radical ion pair are suggested to explain the absence of the TA* photoproduct in dApT. This hypothesis is supported by semiempirical calculations performed on all relevant reactive intermediates proposed to participate in the mechanism of formation of TA*. Altogether, the results show that sequence and conformation profoundly influence the photochemistry and the photophysics of these DNA model systems.     

Stability of emulsions of water in mineral oils containing asphaltenes

Emulsions of water in mineral oils are stable if the oil phase contains asphaltenes which are near the condition of incipient flocculation. This condition is determined by the composition of the oil phase and by the nature of the asphaltenes. High aromaticity of the oil phase and the presence of deflocculants prevent flocculation of asphaltenes; the deflocculants may be interfacially active agents or asphaltene-like compounds with better solubility in the oil phase. Conditions of incipient flocculation of asphaltenes correlate very well with a considerable increase of rheological resistance of the interface between the oil phase and distilled water, determined according to the torsion oscillation method. Stabilization of the water-in-oil emulsions is therefore caused by the build-up of a coherent layer of asphaltenes in the water-oil interface in these cases. Deflocculants of asphaltenes in the oil phase destroy their stabilizing effect; however, the deflocculants themselves may stabilize the water-in-oil emulsions by adsorption on the water-oil interface and then the correlation between the condition of asphaltenes and emulsion stability does not hold, nor is the interfacial viscosity perceptibly increased. Under borderline conditions of emulsion stability a few percent of sodium chloride in the water phase counteracts the build-up of a stabilizing layer of asphaltenes in the water-oil interface and so do higher p_H values of a buffered water phase. At low p_H-values emulsion stability does not correlate with interfacial resistance. It can be concluded that asphaltenes stabilize water-in-oil emulsions if they accumulate on the water-oil interface. This interfacial layer may show a coherence, which is an indication of the presence of asphaltenes rather than a condition for stability of the emulsions.     

Novel design of a pentacyclic scaffold as structural mimic of saframycin A

The design, synthesis and evaluation of a pentacyclic scaffold, CWO-324 to mimic saframycin A is described. CWO-324 is readily synthesized in five steps from 1,4-diacetyl-piperazine-2,5-dione and 2,5-dimethoxybenzaldehyde. CWO-324 was found to scission DNA, binds to bases 69-83(5′-GCAGTCAGG CACCGT-3′) of Hind III/Rsa I from plasmid pBR322 DNA in a foot-printing study and possesses anti-tumor activity.     

Photoelectrode characteristics of an organic bilayer in water phase containing a redox molecule

We have recently reported that the organic bilayer of 3,4,9,10-perylenetetracarboxyl-bisbenzimidazole (PTCBI, n-type semiconductor) and 29H,31H-phthalocyanine (H₂Pc, p-type semiconductor), which is a part of a photovoltaic cell, acts as a photoanode in the water phase (Abe et al., ChemPhysChem 5:716, [2004]); in that case, the generation of the photocurrent involving an irreversible thiol oxidation at the H₂Pc/water interface took place to be coupled with hole conduction through the H₂Pc layer, based on the photophysical character of the bilayer. In the present work, the photoelectrode characteristics of the bilayer were investigated in the water phase containing a redox molecule , where the photo-induced oxidation and reduction for the couple were found to take place at the bilayer. The photoanodic current involving the oxidation efficiently occurred at the interface of H₂Pc/water, similar to the previous example. In the view of the voltammograms obtained, it was noted that there are pin-holes in the H₂Pc layer of the bilayer, leading to a cathodic reaction with at the PTCBI surface especially in the dark; that is, the band bending at the PTCBI/water interface can essentially be reduced by applying a negative potential [e.g., < ∼ 0 V (vs Ag/AgCl)] to the PTCBI, when the cathodic reaction may take place through the conduction band of the PTCBI. Moreover, under that applied potential condition of irradiation, the photogenerated electron carrier part can move to the PTCBI surface, thus enhancing the reduction of .     

Comparative binding of antitumor drugs to DNA containing the telomere repeat sequence

Telomeres are the ends of the linear chromosomes of eukaryotes and consist of tandem GT-rich repeats in telomere sequence i.e. 500-3000 repeats of 5'-TTAGGG-3' in human somatic cells, which are shortened gradually with age. The G-rich overhang of telomere sequence can adopt different intramolecular fold-backs and tetra-stranded DNA structures, in vitro, which inhibit telomerase activity. In this report, DNA binding agents to telomere sequence were studied novel therapeutic possibility to destabilize telomeric DNA sequences. Oligonucleotides containing the guanine repeats in human telomere sequence were synthesized and used for screening potential antitumor drugs. Telomeric DNA sequence was characterized using spectral measurements and CD spectroscopy. CD spectrum indicated that the double-stranded telomeric DNA is in a right-handed conformation. Polyacrylamide gel electrophoresis was performed for binding behaviors of antitumor compounds with telomeric DNA sequence. Drugs interacted with DNA sequence caused changes in the electrophoretic mobility and band intensity of the gels. Depending on the binding mode of the anticancer drugs, telomeric DNA sequence was differently recognized and the efficiency of cleavage of DNA varies in the bleomycin-treated samples under different conditions. DNA cleavage occurred at about 1% by the increments of 1 micromM bleomycin-Fe(III). These results imply that the stability of human telomere sequence is important in conjunction with the cancer treatment and aging process.     

Second generation of a polypyridine ligand to mimic enzymes containing non-heme iron centers

A new tetrapyridyl ligand (BDPEA) and the corresponding di-iron(III) μ-oxo complex were synthesized. The iron complex structure, determined by X-ray crystallography, exhibited the dinuclear core [Fe₂^III(BDPEA)₂(μ-O)(NO₃)₂](NO₃)₂ (1). With monopersulfate as oxidant, this complex catalyzed the conversion of 2,4,6-trichlorophenol and catechol, with a better activity and an enhanced life-time compared to the previously reported complex [Fe^III(BDPMA)](NO₃)₃ (2) (BDPMA: bis[di(2-pyridyl)methyl]amine) which contained two fragile benzylic C–H bonds on the tetrapyridyl ligand.     

Stability of chemical sequence in a periodic polymeric nematogen

The stability of a polymeric nematogen's chemical sequence was studied by differential scanning calorimetry, optical microscopy, and ¹³C-NMR; the nematogen studied was a thermotropic polyester and had a periodic chemical structure. Model compounds were used to investigate transesterfication in the melt at different temperatures with the addition of phenol or benzoic acid as analogues of polymer end groups. Ester interchange reactions at high temperature were found to be partly suppressed when acidic end groups of the periodic nematogen were capped. However, sequence reorganization was completely suppressed in capped nematogens when temperatures remained below the isotropization transition of the nematogen investigated. Rapid disordering of the periodic nematogen was observed above the nematic-isotropic transition, suggesting that both chemical and physical factors play a role in sequence redistribution of periodic nematogens. © 1994 John Wiley & Sons, Inc.     

Diffusion mechanism of water vapour in a zeolitic tuff rich in clinoptilolite

The adsorption kinetics of H₂O in a clinoptilolite rich zeolitic tuff was experimentally investigated at 18°C. In the identification of the diffusion mechanism the isothermal adsorption model equation was used. It was found out that the intraparticle mass transfer becomes more dominant over the heat transfer with increase in particle size and the adsorptive dose pressure. Although initially intraparticle mass transfer was the controlling resistance later external heat transfer also contributes to the transfer mechanism.     

Rare-earth quinolinates: infrared-emitting molecular materials with a rich structural chemistry

Near-infrared-emitting rare-earth chelates based on 8-hydroxyquinoline have appeared frequently in recent literature, because they are promising candidates for active components in near-infrared-luminescent optical devices, such as optical amplifiers, organic light-emitting diodes, .... Unfortunately, the absence of a full structural investigation of these rare-earth quinolinates is hampering the further development of rare-earth quinolinate based materials, because the luminescence output cannot be related to the structural properties. After an elaborate structural elucidation of the rare-earth quinolinate chemistry we can conclude that basically three types of structures can be formed, depending on the reaction conditions: tris complexes, corresponding to a 1:3 metal-to-ligand ratio, tetrakis complexes, corresponding to a 1:4 metal-to-ligand ratio, and trimeric complexes, with a 3:8 metal-to-ligand ratio. The intensity of the emitted near-infrared luminescence of the erbium(III) complexes is highest for the tetrakis complexes of the dihalogenated 8-hydroxyquinolinates.     

Synthesis and DNA triplex formation of an oligonucleotide containing an urocanamide

An urocanamide nucleoside designed and previously tested as its protected ribose derivative in aprotic solvents for binding a cytosine-guanine (CG) Watson-Crick base pair was successfully incorporated into a triplex forming oligonucleotide. Binding affinity and specificity of this nonnatural nucleoside were studied in a triple helix with duplex targets containing all four possible Watson-Crick base pairs opposite the nucleoside analog in the third strand. UV melting experiments indicate the formation of a well-defined triplex with specific binding of the urocanamide analog to a CG inversion of the homopurine-homopyrimidine target. However, binding affinities in the triplex are weak and much lower when compared to the canonical base triads.     

Stability prediction of nafamostat mesilate in an intravenous admixture containing sodium bisulfite

The hydrolysis of nafamostat mesilate (NM) in aqueous solution was found to be accelerated by sodium bisulfite (SBS) using high-performance liquid chromatographic assay. The hydrolysis of NM catalyzed by SBS was pseudo-first-order and was considered to be a reaction between nafamostat cation (N+) and sulfite ion. The effects of SBS concentration and temperature on the hydrolysis of NM in buffer solution were examined. From the findings obtained, we estimated the compatible pH range of the intravenous admixture (mixed infusion) of NM after a constant storage time at a constant SBS concentration and temperature employing a simulated pH-profile for the mixed infusion. In order to evaluate the compatibility of the prescribed mixed infusion, the method of pH estimation for the mixed infusion was also investigated using the pH titration curve of each preparation.     

Synthesis of cyclic oligopeptides containing an Arg-Gly-Asp (RGD) sequence

The synthesis of cyclic RGD peptides with 8-10 residues cyclized by an amide bond and the relationship between their structure and activity (i.e. circular dichroism spectrum and inhibition of platelet aggregation) are reported. The linear peptides were synthesized by the solution method and their cyclization was performed in high dilution using DPPA.     

Scaffolded amino acids as a close structural mimic of type-3 copper binding sites

We report the use of triazacyclophane (TAC)-scaffolded amino acids as a structural mimic for 3-histidine metal-binding sites in metalloproteins, especially for the mimicry of type-3 copper binding sites as are present in hemocyanin, tyrosinase and catechol oxidase.     

Express analysis of the structural properties of water clusters containing more than 12 water molecules and impurities

An express analysis technique for the determination of the structural properties of water clusters with impurities and the number of contained water molecules more than 12 is developed. The technique is based on the derivation of three matrices for a water cluster, which makes it possible to write down the unique code characterizing its structure. The technique significantly decreases the computation time (approximately 10⁴ times) in comparison with the procedure developed previously [1], and consequently, allows the analysis of the structural properties of aqueous systems with a large number of molecules on usual PCs. In order to illustrate the technique the code for the typical configuration of the (H₂O)₁₃ cluster is determined within the water model at a temperature of 268 K and a density of 0.99930 g/cm³.     

Surface-initiated growth of poly d(A-T) by Taq DNA polymerase

In this paper, we report surface-initiated d(A-T) polymerization by Taq DNA polymerase as a method for constructing DNA-tethered surfaces using an enzyme. The enzymatic polymerization was conducted successfully via two steps: tethering of oligo d(A-T)s onto the surface presenting carboxylic acids by amide coupling and surface-initiated polymerization using Taq DNA polymerase. In this enzymatic polymerization process, the design and construction of carboxylic acid-presenting surfaces were found to be an important factor: DNA growth did not occur on the gold surface coated only with the self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid (MHDA), but effectively proceeded on the surfaces presenting mixed SAMs of MHDA and 1-pentadecanethiol. The coupling of oligo d(A-T)s and the subsequent DNA polymerization reaction were characterized by polarized infrared external reflectance spectroscopy, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy.     

Observation of an octameric water cluster containing a book-shaped hexamer in a 4f-3d complex

An octameric water cluster consisting of a book-shaped water hexamer and two dangling water molecules has been observed in a 4f-3d ionic pair complex [Y(dpdo)2(H2O)4][Co(CN)6].4H2O.     

KNI-102, a novel tripeptide HIV protease inhibitor containing allophenylnorstatine as a transition-state mimic.

HIV-1 protease inhibitors containing allophenylnorstatine [Apns; (2S,3S)-3-amino-2-hydroxy-4-phenylbutyric acid]-Pro (syn diastereomer) as a transition-state mimic were established to be potent and highly selective. Z-Asn-Apns-Pro-NHBut (KNI-102) is the only tripeptide exhibiting substantial anti-HIV activity and may be of minimum size for potent, selective inhibition of HIV protease. Ready availability due to its simple chemical structure and stability should make it valuable for studies of the development of metabolically stable anti-AIDS drugs.     

Stability of Se species in plant extracts rich in phenolic substances

Since there is growing awareness of the strong dependence of the antioxidative function of selenium (Se) upon its chemical form, the stability of Se species during sample preparation is an important factor in obtaining qualitative and quantitative results. Many plant samples are rich in phenolic compounds (antioxidants), but data about their effect on specific Se species in extracts of plant samples are scarce. Therefore, the aim of this study was to investigate the effect of the most common phenolic substances in plant parts, namely tannin and the flavonoid rutin, on the concentration and/or transformation of several Se species (SeMet, SeCys₂, SeMeSeCys, Se(VI) and Se(IV)) during sample preparation (24 h incubation at 37 °C) and storage (4 days at 4 °C). Moreover, the effect observed was then studied in a real sample, buckwheat, because this plant is known as a rich source of phenolics, especially tannin and rutin. Se speciation was carried out by on-line coupling of ion-exchange HPLC-ICP-MS after water and enzymatic (protease) hydrolysis. The results showed that the ratio between the two antioxidants has an important role. When the antioxidants were present together, the response for Se(IV) was observed to start to decrease only at a ratio of rutin to tannin of 1:100 (w/w), indicating the ratio between antioxidants in buckwheat seeds. After water extraction, only 40% and after enzymatic extraction 80% of Se(IV) remained, but no other Se compound was detected with the system used. Furthermore, the extracts were not stable during storage at 4 °C. Signals for other Se species were stable. The results obtained for buckwheat seeds showed a decrease in Se(IV) response during sample preparation and storage, comparable to the one obtained with the experiments performed in vitro. However, Se species in extracts of other buckwheat parts (leaves, stems and sprouts) were stable. These results indicate that reactions in the extraction process and during storage may affect Se speciation and may result in misidentifications and inaccurate values.