Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules

A new fluorogenic cyanine dye was synthesized and found to have low fluorescence quantum yield in fluid solution and in the presence of double-stranded DNA but 80-fold enhanced fluorescence in viscous glycerol solution. An RNA aptamer selected for binding to the new dye exhibits K(d) = 87 nM and 60-fold fluorescence enhancement. The dye-aptamer pair is a fluoromodule that can be incorporated into fluorescent sensors and labels.     

Thermolysis of ammonium nitrate/potential donor of active chlorine compositions

The thermal stability of the ammonium nitrate (AN)/sodium salt of 1,3-dichlor-2,4,6-trioxo-1,3,5-triazacyclohexane (DC) composition has been studied. The factors of influence on the rates of reactions in the composition, namely, a water content, composition wetting methods, a dispersion of composition components, sample mass values, have been examined. The water presence in the composition reduces its thermal stability. The mechanism includes the partial dissociation of AN to HNO₃ and NH₃ and the hydrolysis of DC with the formation of some unstable Cl-containing compounds (chloramines, nitrogen chloride). The reaction of ammonium cation with active chlorine has been found to give rise to the explosion of the AN/DC composition. Such a situation is typical for other ammonium salt/DC compositions.     

Intramolecular sensitization of photocleavage of the photolabile 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group: photoproducts and photokinetics of the release of nucleosides

Novel photolabile protecting groups based on the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for deprotection of the NPPOC group proceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves beta elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.     

An amperometric biosensor based on multiwalled carbon nanotube-poly(pyrrole)-horseradish peroxidase nanobiocomposite film for determination of phenol derivatives

An amperometric biosensor based on horseradish peroxidase (HRP) and carbon nanotube (CNT)/polypyrrole (PPy) nanobiocomposite film on a gold surface has been developed. The HRP was incorporated into the CNT/PPy nanocomposite matrix in one-step electropolymerization process without the aid of cross-linking agent. Amperometric response was measured as a function of concentration of phenol derivatives, at a fixed bias voltage of -50 mV. Optimization of the experimental parameters was performed with regard to pH and concentration of hydrogen peroxide. The linear range, sensitivity and detection limit of the biosensor were investigated for eighteen phenol derivatives. The sensitivity in the linear range increased in this order: 4-methoxyphenol>2-aminophenol>guaiacol=m-cresol>2-chlorophenol=4-chlorophenol=hydroquinone=pyrocatechol>2,6-dimethoxyphenol>3-chlorophenol>p-cresol>p-benzoquinone=4-acetamidophenol>catechol>phenol=pyrogallol=2,4-dimethylphenol. CNTs was shown to enhance the electron transfer as a mediator and capable to carry higher bioactivity owing to its intensified surface area. The biosensor exhibited low detection limits with a short response time (2s) for the tested phenolics compared to the reported working electrodes. It retained 70% of its initial activity after using for 700 measurements in 1 month.     

Preparation of ribavirin analogues by copper- and ruthenium-catalyzed azide-alkyne 1,3-dipolar cycloaddition

In this study, we described the synthesis of 1,4- and 1,5-disubstituted-1,2,3-triazolo-nucleosides from various alkynes with 1′-azido-2′,3′,5′-tri-O-acetylribose using either copper-catalyzed azide-alkyne cycloaddition (CuAAC) or ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC), respectively. Optimized RuAAC conditions were realized with the commercially available [Cp^∗RuCl(PPh₃)₂] under microwave heating, which allows a significant acceleration of the reaction times (from 6 h to 5 min). This reaction can work under water-containing system. RuAAC and CuAAC are useful tools for the synthesis of 1,2,3-triazolyl-nucleosides small libraries.     

Kinetics of the β-picoline oxidation to nicotinic acid over vanadia-titania catalyst. 2. Effect of dioxygen and β-picoline

The effect of the dioxygen and β-picoline concentrations on the oxidation of β-picoline to nicotinic acid was studied at 270°C over a 20% V₂O₅-80% TiO₂ (wt. %) catalyst. The study was performed in a differential reactor at constant concentrations of water and nicotinic acid. A considerable excess of dioxygen was shown to be necessary for the formation of nicotinic acid. It was found that the rates of β-picoline transformation into nicotinic acid, pyridine-3-carbaldehyde, pyridine-3-nitrile, pyridine and carbon oxides as well as selectivities to products and the catalyst state depend strongly on the ratio of dioxygen to β-picoline concentrations. The minimum admissible ratio of these concentrations under industrial conditions was determined.     

Tetranitromethane as an efficient reagent for the conversion of epoxides into β-hydroxy nitrates

A convenient regioselective method for the preparation of β-hydroxy nitrates based on the ring opening reaction of epoxides by tetranitromethane in the presence of triethylamine is described. A series of substituted β-hydroxy nitrates were obtained in high yields under mild conditions.     

Resolving the sign ambiguity in the singular value decomposition

Many modern data analysis methods involve computing a matrix singular value decomposition (SVD) or eigenvalue decomposition (EVD). Principal component analysis is the time‐honored example, but more recent applications include latent semantic indexing (LSI), hypertext induced topic selection (HITS), clustering, classification, etc. Though the SVD and EVD are well established and can be computed via state‐of‐the‐art algorithms, it is not commonly mentioned that there is an intrinsic sign indeterminacy that can significantly impact the conclusions and interpretations drawn from their results. Here we provide a solution to the sign ambiguity problem and show how it leads to more sensible solutions. Copyright © 2008 John Wiley & Sons, Ltd.     

Erratum: Resolving the sign ambiguity in the singular value decomposition

J. Chemometrics 22 (2): 135–140. DOI: 10.1002/cem.1122 It has come to our attention that an error arose during correction of this article. In Figure 3, Step 3 should as appear as follows:

     

Synthesis of novel 8-(het)aryl-6H-pyrano[4′,3′:4,5]thieno[3,2-b]pyridines by 6-endo-dig cyclization of Sonogashira products and halolactonizations with Cu salts/NXS. Preliminary antitumor evaluation

Novel 8-(het)aryl-6H-pyrano[4′,3′:4,5]thieno[3,2-b]pyridines were prepared in good to high yields by a tandem one-pot procedure of Sonogashira coupling and 6-endo-dig lactonization from 3-bromothieno[3,2-b]pyridine-2-carboxylic acid and (het)arylalkynes. Sonogashira coupling products were also prepared from the corresponding methyl ester giving in the same reaction the corresponding 6-endo-dig compounds as minor products. The Sonogashira phenyl ester product gave cyclization with electrophiles only in low to moderate yields. Nevertheless, halolactonizations using Cu(I) or (II) salts/N-halosuccinimides (NXS) from either the phenyl ester or the carboxylic acid derivatives occurred in good to high yields. The growth inhibition potential of the compounds was evaluated using human tumor cell lines, HCT-15 (colorectal adenocarcinoma) and NCI-H460 (non-small cell lung cancer) and studies of apoptosis induction were performed for the three most promising compounds in HCT-15?cells. Two of them caused almost 40% of cell death by apoptosis when tested at their 1.5?×?GI₅₀ concentrations. The tricyclic lactone with a F atom in the meta position showed to be the most promising one.