Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system

We developed intramolecular dual fluorophore-quencher base analogues for site-specific incorporation into DNA by an unnatural base pair replication system. An unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibits high fidelity in PCR amplification, and the 2-nitropyrrole moiety of Px acts as a quencher. Deoxyribonucleoside triphosphates of Px linked with a fluorophore (Cy3, Cy5 or FAM) were chemically synthesized, and the fluorescent properties and the enzymatic incorporation of the fluorophore-linked dPxTPs into DNA were examined in PCR amplification. The fluorophore-linked dPxTPs were site-specifically incorporated by PCR into DNA, opposite Ds in templates, with high selectivity. Furthermore, we found that the fluorescence of the triphosphates was partially quenched, but increased upon their incorporation into DNA. These dual fluorophore-quencher base analogues would be useful for site-specific DNA labeling and for monitoring the amplification products of target nucleic acid molecules with a specific sequence. We have demonstrated the utility of the fluorophore-linked Px substrates and the Ds-Px pairing in real-time quantitative PCR for target DNA molecule detection.     

Syntheses, characterization, and photochemical properties of amidate-bridged Pt(bpy) dimers tethered to Ru(bpy)3(2+) derivatives

Amidate-bridged diplatinum(II) entities [Pt(2)(bpy)(2)(μ-amidato)(2)](2+) (amidate = pivalamidate and/or benzamidate; bpy = 2,2'-bipyridine) were covalently linked to one or two Ru(bpy)(3)(2+)-type derivatives. An amide group was introduced at the periphery of Ru(bpy)(3)(2+) derivatives to give metalloamide precursors [Ru(bpy)(2)(BnH)](2+) (abbreviated as RuBnH, n = 1 and 2), where deprotonation of amide BnH affords the corresponding amidate Bn, B1H = 4-(4-carbamoylphenyl)-2,2'-bipyridine, and B2H = ethyl 4'-[N-(4-carbamoylphenyl)carbamoyl]-2,2'-bipyridine-4-carboxylate. From a 1:1:1 reaction of [Pt(2)(bpy)(2)(μ-OH)(2)](NO(3))(2), RuBnH, and pivalamide, trinuclear complexes [Pt(2)(bpy)(2)(μ-RuBn)(μ-pivalamidato)](4+) (abbreviated as RuBn-Pt(2)) were isolated and characterized. Tetranuclear complexes [Pt(2)(bpy)(2)(μ-RuBn)(2)](6+) (abbreviated as (RuBn)(2)-Pt(2)) were separately prepared and characterized in detail. The quenching of the triplet excited state of the Ru(bpy)(3)(2+) derivative (i.e., Ru*(bpy)(3)(2+)) upon tethering the Pt(2)(bpy)(2)(μ-amidato)(2)(2+) moiety is strongly enhanced in RuB1-Pt(2) and (RuB1)(2)-Pt(2), while it is only slightly enhanced in RuB2-Pt(2) and (RuB2)(2)-Pt(2). These are partly explained by the driving forces for the electron transfer from the Ru*(bpy)(3)(2+) moiety to the Pt(2)(bpy)(2)(μ-amidato)(2)(2+) moiety (ΔG°(ET)); the ΔG°(ET) values for RuB1-Pt(2), (RuB1)(2)-Pt(2), RuB2-Pt(2), and (RuB2)(2)-Pt(2) are estimated as -0.01, 0.00, +0.22, and +0.28 eV, respectively. The considerable difference in the photochemical properties of the B1- and B2-bridged systems were further examined based on the emission decay and transient absorption measurements, which gave results consistent with the above conclusions.     

Synthesis of polyfunctional allenes by successive copper-mediated substitutions

Readily available 1,1-dichloro-2-alkynes are versatile starting materials for the synthesis of polyfunctionalized allenes. They can be prepared from commercially available terminal alkynes in a two-step procedure. The Cu-mediated reaction of several 1,1-propargylic derivatives with functionalized alkyl, benzylic, or allylic zinc reagents proceeds exclusively with S(N)2' selectivity and allows a rapid and efficient synthesis of functionalized chloroallenes. These chloroallenes undergo a novel Cu(I) -catalyzed substitution reaction with functionalized arylmagnesium reagents with excellent S(N)2 selectivity to give trisubstituted polyfunctionalized allenes. The functional group tolerance is excellent and functionalities, such as cyano, keto, ester, phosphate, trifluoromethyl, and halogens, are well tolerated.     

Preparation,Characterization, Biological Activity and 3D Molecular Modeling of Mn(II), Co(II), Ni(II), Cu(II), Pd(II) and Ru(III) Complexes of Some Sulfadrug Schiff Bases

Mn(II), Co(II), Ni(II), Cu(II), Pd(II) and Ru(III) complexes of Schiff bases derived from the condensation of sulfaguanidine with 2,4‐dihydroxy benzaldehyde ( HL1 ), 2‐hydroxy‐1‐naphthaldehyde ( HL2 ) and salicylaldehyde ( HL3 ) have been synthesized. The structures of the prepared metal complexes were proposed based on elemental analysis, molar conductance, thermal analysis (TGA, DSC and DTG), magnetic susceptibility measurements and spectroscopic techniques (IR, UV‐Vis, and ESR). In all complexes, the ligand bonds to the metal ion through the azomethine nitrogen and α‐hydroxy oxygen atoms. The structures of Pd(II) complex 8 and Ru(III) complex 9 were found to be polynuclear. Two kinds of stereochemical geometries; distorted tetrahedral and distorted square pyramidal, have been realized for the Cu(II) complexes based on the results of UV‐Vis, magnetic susceptibility and ESR spectra whereas octahedral geometry was predicted for Co(II), Mn(II) and Ru(III) complexes. Ni(II) complexes were predicted to be square planar and tetrahedral and Pd(II) complexes were found to be square planar. The antimicrobial activity of the ligands and their metal complexes was also investigated against the gram‐positive bacteria Staphylococcus aures and Bacillus subtilis and gram‐negative bacteria, Escherichia coli and Pesudomonas aeruginosa, by using the agar dilution method. Chloramphenicol was used as standard compound. The obtained data revealed that the metal complexes are more or less, active than the parent ligand and standard. The X‐ray crystal structure of HL3 has been also reported.     

Gaining insight into the inhibition of glycoside hydrolase family 20 exo-β-N-acetylhexosaminidases using a structural approach

One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray structural analysis of a representative family 20 exo-β-N-acetylhexosaminidase in complex with various known classes of inhibitor of these types of enzymes, which highlights how different inhibitor classes can inhibit the same enzyme. This study will aid in the future development of inhibitors of not only exo-β-N-acetylhexosaminidases but also other types of glycoside hydrolases.     

Structure Elucidation of Textile Fabrics by Fourier Transform Infrared Photoacoustic Spectroscopy

A photoacoustic detection system mainly based on a Fourier transform infrared spectrometer has been constructed and some tentative evaluations of its performances have been made. Infrared photoacoustic spectra of cotton and nylon cloths have been obtained without troublesome sample preparations which are necessary in conventional infrared spectrometry. It can be said that the Fourier transform infrared photoacoustic spectroscopy is useful for the structure elucidation of organic polymers.     

Experimental determination of orientations for the 17 O electric-field-gradient and chemical shielding tensors in L-alanine

We have presented a solid-state 17 O NMR study of [13C, 17 O]-L-alanine. Using the experimental results for the 13C-17 O dipolar vector and Euler angles, the absolute orientations of 17 O chemical shielding (CS) and electric-field-gradient (EFG) tensors with respect to the molecular frame can be determined for L-alanine. The present results suggest that the intermediate EFG tensor components, VYY, lie in the carboxylate plane and parallel to the C-O bond directions, while the least shielded components, delta11, and the intermediate CS tensor components, delta22, roughly lie in the molecular plane and the direction of delta22 components are approximately 38 degrees and 25 degrees off the C-O bonds for O1 and O2, respectively. These results are in reasonable agreement with those of our quantum chemical calculations reported previously.     

Dynamic Risk Prediction via a Joint Frailty-Copula Model and IPD Meta-Analysis: Building Web Applications

Clinical risk prediction formulas for cancer patients can be improved by dynamically updating the formulas by intermediate events, such as tumor progression. The increased accessibility of individual patient data (IPD) from multiple studies has motivated the development of dynamic prediction formulas accounting for between-study heterogeneity. A joint frailty-copula model for overall survival and time to tumor progression has the potential to develop a dynamic prediction formula of death from heterogenous studies. However, the process of developing, validating, and publishing the prediction formula is complex, which has not been sufficiently described in the literature. In this article, we provide a tutorial in order to build a web-based application for dynamic risk prediction for cancer patients on the basis of the R packages joint.Cox and Shiny. We demonstrate the proposed methods using a dataset of breast cancer patients from multiple clinical studies. Following this tutorial, we demonstrate how one can publish web applications available online, which can be manipulated by any user through a smartphone or personal computer. After learning this tutorial, developers acquire the ability to build an online web application using their own datasets.