The role of organic linkers in directing DNA self-assembly and significantly stabilizing DNA duplexes

We show a simple method to control both the stability and the self-assembly behavior of DNA structures. By connecting two adjacent duplexes with small synthetic linkers, factors such as linker rigidity and DNA strand orientation can increase the thermal denaturation temperature of 17 base-pair duplexes by up to 10 °C, and significantly increase the cooperativity of melting of the two duplexes. The same DNA sequence can thus be tuned to melt at vastly different temperatures by selecting the linker structure and DNA-to-linker connectivity. In addition, a small rigid m-triphenylene linker directly affects the self-assembly product distribution. With this linker, changes in the orientation of the linked strands (e.g., 5'3' vs 3'3') can lead to dramatic changes in the self-assembly behavior, from the formation of cyclic dimer and tetramer to higher-order oligomers. These variations can be readily predicted using a simple strand-end alignment model.     

Detecting drug promiscuity using gaussian ensemble screening

Polypharmacology describes the binding of a ligand to multiple protein targets (a promiscuous ligand) or multiple diverse ligands binding to a given target (a promiscuous target). Pharmaceutical companies are discovering increasing numbers of both promiscuous drugs and drug targets. Hence, polypharmacology is now recognized as an important aspect of drug design. Here, we describe a new and fast way to predict polypharmacological relationships between drug classes quantitatively, which we call Gaussian Ensemble Screening (GES). This approach represents a cluster of molecules with similar spherical harmonic surface shapes as a Gaussian distribution with respect to a selected center molecule. Calculating the Gaussian overlap between pairs of such clusters allows the similarity between drug classes to be calculated analytically without requiring thousands of bootstrap comparisons, as in current promiscuity prediction approaches. We find that such cluster similarity scores also follow a Gaussian distribution. Hence, a cluster similarity score may be transformed into a probability value, or "p-value", in order to quantify the relationships between drug classes. We present results obtained when using the GES approach to predict relationships between drug classes in a subset of the MDL Drug Data Report (MDDR) database. Our results indicate that GES is a useful way to study polypharmacology relationships, and it could provide a novel way to propose new targets for drug repositioning.     

Analysis of the essential oil of Teucrium polium ssp. capitatum from the Balkan Peninsula

The chemical composition of the essential oil of the aerial parts of Teucrium polium ssp. capitatum collected during the flowering period from rocky places and dry pastures, (Serbia, Nis, Kamenica), and dunes along the sea-side, (Bulgaria, Burgas, Primorsko) has been studied by GC and GC/MS. The identified compounds, 45 for the oil from Serbia and 44 for that from Bulgaria, amounted to 97.3% and 96.4% of the oils, respectively. The dominant constituents of the Serbian oil were sesquiterpenes {59.6%, the most abundant components being germacrene D (31.8%), trans-caryophyllene (8.8%) and bicyclogermacrene (6.2%)}, while monoterpenes accounted for 37.5% {the most abundant components being linalool (14.0%) and beta-pinene (10.7%)}. The essential oil from Bulgaria was characterized by a high percentage of monoterpenes, amounting to 62.9% {the most abundant components being beta-pinene (26.8%), alpha-pinene (9.3%) and limonene (6.4%)}, while sesquiterpenes accounted for 33.5% (the most abundant component was germacrene D 17.7%)}.     

Elimination of motion and pulsation artifacts using BLADE sequences in knee MR imaging

The purpose of this study is to evaluate the ability of proton density (PD)-BLADE sequences in reducing or even eliminating motion and pulsatile flow artifacts in knee magnetic resonance imaging examinations. Eighty consecutive patients, who had been routinely scanned for knee examination, participated in the study. The following pairs of sequences with and without BLADE were compared: (a) PD turbo spin echo (TSE) sagittal (SAG) fat saturation (FS) in 35 patients, (b) PD TSE coronal (COR) FS in 19 patients, (c) T2 TSE axial in 13 patients and (d) PD TSE SAG in 13 patients. Both qualitative and quantitative analyses were performed based on the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures of normal anatomic structures. The qualitative analysis was performed by experienced radiologists. Also, the presence of image motion and pulsation artifacts was evaluated. Based on the results of the SNR, CRN and ReCon for the different sequences and anatomical structures, the BLADE sequences were significantly superior in 19 cases, whereas the corresponding conventional sequences were significantly superior in only 6 cases. BLADE sequences eliminated motion artifacts in all the cases. However, motion artifacts were shown in (a) six PD TSE SAG FS, (b) three PD TSE COR FS, (c) three PD TSE SAG and (d) two T2 TSE axial conventional sequences. In our results, it was found that, in PD FS sequences (sagittal and coronal), the differences between the BLADE and conventional sequences regarding the elimination of motion and pulsatile flow artifacts were statistically significant. In all the comparisons, the PD FS BLADE sequences (coronal and sagittal) were significantly superior to the corresponding conventional sequences regarding the classification of their image quality. In conclusion, this technique appears to be capable to potentially eliminate motion and pulsatile flow artifacts in MR images.     

New route for the synthesis of benzimidazoles by a one-pot multistep process with mono and bifunctional solid catalysts

One-pot multistep reactions involving a new environmentally friendly catalytic procedure have been developed for the synthesis of benzimidazoles. Benzimidazole derivatives with biological and pharmaceutical interest have been prepared by a one-pot four step process with a solid catalyst containing basic and oxidation sites. The four steps refer to: (a) oxidation of the alcohol; (b) cyclocondensation of the aldehyde formed with ortho-phenylenediamines, (c) oxidation of the carbon-nitrogen bond, (d) N-alkylation reaction. The process is illustrated by the synthesis of 1,2-disubstituted benzimidazole derivative with antiviral activity.     

Theoretical study on structural and mechanistic aspects of synthesis of a 3-aminopyrazole derivative

The structure of 5-hydroxy-3,5-dimethyl-1-S-methylisothiocarbamoyl-2-pyrazolinium iodide (HDMCPI), a cyclic intermediate for a 3-aminopyrazole derivative, was determined by means of X-ray analysis and spectroscopic techniques. In a treatment of HDMCPI in alkaline aqueous solution, 4-acetyl-3(5)-amino-5(3)-methylpyrazole (AAMP) was unexpectedly yielded. The reaction of HDMCPI was monitored by ¹H and ¹³C NMR spectroscopy. It was shown that keto-imine tautomer appears as the only tautomeric form. Density functional theory explained the spontaneous formation of keto-imine tautomer, whose existence is the main condition for generating a carbanion in alkaline medium. The carbanion further undergoes cyclization and elimination of MeSH, thus yielding AAMP. In the reaction of acetylacetone with thiosemicarbazide instead of S-methylisothiosemicarbazide, there were no traces of AAMP. This result can be attributed to the absence of keto-imine form in the tautomeric equilibrium, which would provide the formation of a carbanion for a nucleophilic attack and further cyclization.