Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution

Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications.

Self-healing and Oxidation Resistance of B-Si Doped Carbon Materials Derived from Modification Coal Tar Pitch

With toluene soluble fraction of coal tar pitch, polycarbosilane and pyridine borane as raw materials, the modification coal tar pitch was synthesized by a liquid method. The B-Si-doped carbon materials were obtained by carbonization treatment at 800–1,600 °C for 1 h. The effects of carbonization temperatures on the composition, microstructure and oxidation resistance of the B-Si-doped carbon materials were investigated by XRD, SEM and TG-DSC. The results showed that the B-Si-doped carbon materials were composed of B2O3 and carbon. SiC crystal grains appeared when the carbonization temperatures were over 1,200 °C. The higher the carbonization temperatures were, the larger the SiC grain sizes of B-Si-doped carbon materials became. But oxidation rate of larger grain sizes of SiC was slow during oxidation. It was difficult to form a protective glassy film on the surface of the materials rapidly. Therefore, the B-Si-doped carbon materials obtained by carbonization at 1,200 °C showed better oxidation resistance. Oxidation resistance mechanism of B-Si-doped carbon materials was illustrated. The SiO2 produced by the oxidation of SiC and B2O3 formed protective glassy film, which had self-healing and anti-oxidation synergism.

Octahedral manganese(i) and ruthenium(ii) complexes containing 2-(methylamido)pyridine–borane as a tripod κ3N,H,H-ligand

The borane adduct of the 2-(methylamido)pyridine anion has been incorporated into octahedral metal (Mn, Ru) complexes and their bonding has been studied by theoretical methods (DFT, QTAIM).

Organic Functional Group Interconversion: (-)- β -Conhydrine (Barua) and (+)-6'-Hydroxyarenarol (Anderson)

V. T. Perchyonok and Kellie L. Tuck of Monash University found (Tetrahedron Lett. 2008, 49, 4777) that a concentrated solution of Bu4NCl and H3PO2 in water effected free radical reductions and cyclizations. Stéphane G. Ouellet of Merck Frosst demonstrated (Tetrahedron Lett. 2008, 49, 6707) that an oxazoline such as 3 could be converted to the alcohol 4 by acylation followed by reduction. Elizabeth R. Burkhardt of BASF developed (Tetrahedron Lett. 2008, 49, 5152) a protocol for scalable reductive amination using an easily metered liquid pyridine-borane complex. Mohammad Movassaghi of MIT devised (Angew. Chem. Int. Ed. 2008, 47, 8909) a strategy for conversion of an allylic carbonate 8 by way of the allylic diazene to the terminal alkene 9. Philippe Compain of the Université d’Orleans uncovered (J. Org. Chem. 2008, 73, 8647) a practical procedure for oxidizing an inexpensive aldose such as 10 to the amide 12, a valuable chiral pool starting material. Karl A. Scheidt of Northwestern University extended (Organic Lett. 2008, 10, 4331) activated MnO2 oxidation to saturated aldehydes such as 13, leading to the ester 15. Tohru Fukuyama of the University of Tokyo showed (Organic Lett. 2008, 10, 2259) that halides such as 16 could be oxidized to the oxime 18 with the reagent 17. The product oximes are readily dehydrated to the corresponding nitriles. Chutima Kuhakarn of Mahidol University devised (Synthesis 2008, 2045) a simple protocol for the oxidation of a primary amine such as 19 to the nitrile 20 . Nasser Iranpoor and Habib Firouzabadi of Shiraz University developed (J. Org. Chem. 2008, 73, 4882) the reagent 22 for Mitsunobu coupling. The stereochemical course of this reaction with simple acyclic secondary alcohols such as 21 was not reported. Salvatore D. Lepore of Florida Atlantic University optimized (Angew. Chem. Int. Ed. 2008, 47, 7511) the quisylate 24 for the displacement with retention to give the azide 25. Hideki Yorimitsu and Koichiro Oshima of Kyoto University optimized (J. Am. Chem. Soc. 2008, 130, 11276) a Co catalyst for the conversion of a secondary halide such as 26 to the terminal alkene 27 . Base-mediated elimination gave primarily the internal alkene.