Platination of full length tRNA(Ala) and truncated versions of the acceptor stem and anticodon loop

Nuclear DNA is a well characterized target for many low molecular metal-based drugs, with cisplatin and related antineoplastic compounds as typical examples. Much less is known concerning to what extent targeting of RNA may influence the activity spectrum of these types of drugs. In a preliminary communication by us (Papsai et al., Dalton Trans., 2006, 3515) we were able to show that the folded, three-dimensionally well defined structure of tRNA(Ala) readily interacts with cisplatin. In the present study we have further analyzed the binding preferences within the preferentially targeted stem region (sMh(Ala)) by modulation of the sequence around the G-U wobble base-pair and the net charge of the 3' and 5' ends. Our data show that the adduct profile is strongly influenced by the presence of the 5' end phosphate group. Further, the adduct formation reaction can be prevented by replacement of the G-U wobble base-pair with the fully complementary G-C pair. To further investigate the influence from local sequence on the platination process, a model of the anticodon region (acMh(Ala)) was also investigated. In the absence of consecutive guanine-residues in the stem- and anticodon regions, preferential platination was found to take place at the terminal AG-site in the stem region. However, after introduction of a GG-pair in the anticodon loop, platination was observed also here. At 37 degrees C, pH 6.3 and C(Pt) = 0.10 mM the rate of platination was determined to be ca. 1 x 10(-4) s(-1), with the most rapid reaction observed for interaction with the anticodon model carrying two adjacent guanines in the single-stranded loop. Together, these data show that platination of RNA is highly sequence- and structure-dependent.     

Dynamics in the DNA recognition by DAPI: exploration of the various binding modes

Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo1 using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.     

Modulation of dynamics and reactivity of water in reverse micelles of mixed surfactants

In this contribution, we attempt to correlate the change in water dynamics in a reverse micellar (RM) core caused by the modification of the interface by mixing an anionic surfactant, sodium bis(2-ethylhexyl) sulfosuccinate (AOT), and a nonionic surfactant, tetraethylene glycol monododecyl ether (Brij-30), at different proportions, and its consequent effect on the reactivity of water, measured by monitoring the solvolysis reaction of benzoyl chloride (BzCl). The dimension of the RM droplets at different mixing ratios of AOT and Brij-30 (X(Brij-30)) has been measured using dynamic light scattering (DLS) technique. The physical properties of the RM water have been determined using Fourier transform infrared spectroscopy (FTIR) and compressibility studies, which show that with increasing X(Brij-30), the water properties tend toward that of bulk-like water. The solvation dynamics, probed by coumarin 500 dye, gets faster with X(Brij-30). The rotational anisotropy studies along with a wobbling-in-cone analysis show that the probe experiences less restriction at higher X(Brij-30). The kinetics of the water-mediated solvolysis also gets faster with X(Brij-30). The increased rate of solvolysis has been correlated with the accelerated solvation dynamics, which is another consequence of surfactant headgroup-water interaction.     

A comparative study of structural, acidic and hydrophilic properties of Sn-BEA with Ti-BEA using periodic density functional theory

Periodic density functional theory has been employed to characterize the differences in the structural, Lewis acidic and hydrophilic properties of Sn-BEA and Ti-BEA. We show that the incorporation of Sn increases the Lewis acidity of BEA compared to the incorporation of Ti. Hence, the present work gives insight into the role of Sn in increasing the efficiency of the oxidation reactions. The results also justify that the percentage of Sn substituted in BEA is less than Ti. The structural analysis shows that the first coordination shell of Sn is larger than that of Ti. However, the second coordination of both sites remains the same. The water adsorption properties of these substituted zeolites are quantified. Moreover, we explain the higher Lewis acidity of Sn than the Ti site on the basis of the Fukui functions and charge population analysis.     

The effect of cold trap adsorbents on the gas chromatographic analysis of ambient VOCs under Peltier cooling conditions

In this work, the relative analytical performance of the GC-based detection method was investigated with a major focus on cold trap (CT) adsorbent materials against four aromatic volatile organic compounds (VOCs) (e. g., benzene, toluene, xylene, and styrene). A series of calibration experiments were hence conducted under cryofocusing conditions formed by the Peltier cooling system in a thermal desorber (TD) unit. During the course of this study, comparative calibration datasets were acquired for each of the three CT types: (i) CT (I) = Carbopack B + Carbopack C, (ii) CT (II) = Carbopack B + Carboxen 1000, and (iii) CT (III) = Tenax TA. All calibration datasets were obtained under subambient temperature (-10 degrees C) conditions controlled by the Peltier cooling system. The reliability of the calibration data was also assessed in an ancillary experiment with the aid of the modified injection through a thermal desorber (MITD) method. The results demonstrated that the GC detection properties of different VOCs were not altered significantly between different CT applications under Peltier conditions, although relative sensitivity could be distinguished moderately depending on the CT type.     

Two-component hydrogels comprising fatty acids and amines: structure, properties, and application as a template for the synthesis of metal nanoparticles

Stearic acid or eicosanoic acid mixed with di- or oligomeric amines in specific molar ratios form stable gels in water. The formation of such hydrogels depends on the hydrophobicity of the fatty acid, and also on the type of amine used. The gelation properties of these two-component systems were investigated using electron microscopy, FTIR spectroscopy, 1H NMR spectroscopy, differential scanning calorimetry (DSC), and both single-crystal and cast-film X-ray diffraction. Results of FTIR spectral analysis suggest salt formation during gelation. 1H NMR analysis of the gels indicates that the fatty acid chains are immobilized in the gel state and when the gel melts, these chains regain their mobility. Analysis of DSC data indicates that increase in the spacer length in the di-/oligomeric amine lowers the gel-melting temperature. Two of these gelator salts developed into crystals and structural details of such systems could be secured by single-crystal X-ray diffraction analysis. The structural information of the salts thus obtained was compared with the XRD data of the self-supporting films of those gels. Such analyses provided pertinent structural insight into the supramolecular interactions that prevail within these gelator assemblies. Analysis of the crystal structure confirmed that multilayered lamellar aggregates exist in the gel and it also showed that the three-dimensional ordering observed in the crystalline phase is retained in only one direction in the gel state. Finally, the hydrogel was used as a medium for the synthesis of silver nanoparticles. The nanoparticles were found to position themselves on the fibers and produced a long, ordered assembly of gel-nanoparticle composite.     

Second sphere interaction in fluoroanion binding: Synthesis, spectroscopic and X-ray structural study of trans-dichlorobis(ethylenediamine) cobalt(III) terafluoroborate

Trans-dichlorobis(ethylenediamine) cobalt(III) terafluoroborate was synthesised and detailed packing analysis was undertaken to delineate the topological complimentarity of [trans-Co(en)₂Cl₂]⁺ and BF₄⁻ ions by second sphere coordination. The complex was completely characterised by elemental analyses, solubility product measurement and spectroscopic studies (IR, UV–Vis, multinuclear NMR). In the crystal lattice, discrete ions [trans-Co(en)₂Cl₂]⁺ and BF₄⁻ are arranged in A–B–A–B pattern (in both a and c directions of the lattice) forming columns of anions and cations. Crystal lattice is stabilized by electrostatic forces of attraction and hydrogen bonding interactions, i.e. N–HF⁻ and N–HCl involving second sphere coordination. It appears that the topological features of [trans-Co(en)₂Cl₂]⁺ are conducive for generating second sphere interactions. This strategy may be used as a viable method for the capture of other fluoroanions.     

Novel Ag(I), Pd(II), Ni(II) complexes of N,N′-bis-(2,2-diethoxyethyl)imidazole-2-ylidene: Synthesis, structures, and their catalytic activity towards Heck reaction

Tetra-ether substituted imidazolium salts, LHX (where LH = N,N′-bis(2,2-diethoxyethyl)imidazolium cation and X = Br, BF₄, PF₆, BPh₄, NO₃ and NTf₂ anions) were derived from imidazole. Attempts to produce aldehyde functionalized imidazolium salt through acid hydrolysis of LHBr resulted an unexpected tetra-hydroxy compound L_AHBr and the dialdehyde compound L_BHBr. Reaction of LHBr with Ag₂O afforded [L₂Ag][AgBr₂] (1). Mononuclear Pd-complex trans-[L₂PdCl₂] (2) and dinuclear Pd-complex [(LPdCl₂)₂] (3) were obtained by 1:1 and 1:2 reaction of in situ generated Ag-carbene with Pd(CH₃CN)₂Cl₂. cis-[LPdPPh₃Cl₂] (4) was synthesized from reaction of PPh₃ with dinuclear complex 3. Hydrolysis of 3 under acidic conditions also generates a hydroxy derivative 3A and the aldehyde derivative 3B. Direct heating of LHBr with Ni(OAc)₂ · 4H₂O at 120 °C under vacuum generated trans-[L₂NiBr₂] (5). These complexes were characterized by NMR, mass, elemental analysis, and X-ray single crystal diffraction analysis. Pd--Pd interaction was observed in 3. All the Pd complexes exhibited excellent catalytic activity in Heck reaction.     

Ultrafast energy transfer from 3-mercaptopropionic acid-capped CdSe/ZnS QDs to dye-labelled DNA

Femtosecond-resolved fluorescence upconversion and picosecond-resolved spectroscopic measurements have been employed to confirm a highly efficient ultrafast FRET from MPA-capped CdSe/ZnS QDs to dye molecules attached to dodecamer DNA. It appears that hydrogen bonding is the associative mechanism between the MPA-capped QDs and DNA. High FRET efficiency of 92% together with the estimated donor–acceptor distance suggests that the adsorptive interactions between DNA and MPA-capped QDs result in a conformation in which DNA lies along the surface of the QD. Circular dichroism studies have been performed which reveal some perturbation in the native B-form of DNA in the nanobioconjugate.     

Simultaneous Determination of Tamsulosin and Dutasteride in Human Plasma by LC–MS–MS

A sensitive and selective liquid chromatographic tandem mass spectrometric (LC–MS–MS) method was developed for simultaneous identification and quantification of tamsulosin and dutasteride in human plasma, which was well applied to clinical study. The method was based on liquid–liquid extraction, followed by an LC procedure with a Gemini C-18, 50 mm × 2.0 mm (3 μm) column and using methanol:ammonium formate (97:3, v/v) as the mobile phase. Protonated ions formed by a turbo ionspray in positive mode were used to detect analytes and internal standard. MS–MS detection was by monitoring the fragmentation of 409.1 → 228.1 (m/z) for tamsulosin, 529.3 → 461.3 (m/z) for dutasteride and 373.2 → 305.3 (m/z) for finasteride (IS) on a triple quadrupole mass spectrometer. The lower limit of quantification for both tamsulosin and dutasteride was 1 ng mL^?1. The proposed method enables the unambiguous identification and quantification of tamsulosin and dutasteride for clinical drug monitoring.