Analysis Of Steric Effects Research Articles

Analysis of steric effects in DamID profiling of transcription factor target genes

DNA adenine methyltransferase identification (DamID) is an enzymatic technology for detecting DNA regions targeted by chromatin-associated proteins. Proteins are fused to bacterial DNA adenine methyltransferase (Dam) and expressed in cultured cells or whole organisms. Here, we used DamID to detect DNA regions bound by the cardiac-restricted transcription factors (TFs) NKX2-5 and SRF, and ubiquitously-expressed co-factors ELK1 and ELK4. We compared targets bound by these TFs as N- and C-terminal fusions with Dam, for both wild type (WT) NKX2-5 and mutant proteins mimicking those found in congenital heart disease. Overall, DamID is highly robust: while the orientation of WT Dam fusions can affect the size of the target sets, their signatures remained largely reproducible. Furthermore, a severe NKX2-5 mutant lacking the homeodomain showed strong steric effects negatively impacting target discovery. The extent of steric effect is likely to be dependent on the protein in question and the orientation of Dam fusion.

Radical-chain addition of benzenethiol to allenes. Analysis of steric effects and reversibility

Radical-chain addition of benzenethiol to allenes. Analysis of steric effects and reversibility

Principles of the analysis of steric effects and the selectivity of complex-formation

Principles of the analysis of steric effects and the selectivity of complex-formation

Absolute configuration of allenes, conversion of molecular dissymmetry into centrodissymmetry by heterogeneous catalytic hydrogenation

Palladium-catalysed hydrogenation of 4-methylhexa-2,3-dienoic acid and its methyl ester has been studied, by product analysis, over the complete range of hydrogen absorption. 4-Methyl[1-14C]hex-cis-2-enoic and 4-methyl[1-14C]hex-3-enoic acid and methyl ester have been employed in co-hydrogenations with the allene, which show that the substantial amount of 4-methylhex-trans-2-enoic acid (or ester) formed in the first stage arises neither directly from the allene, nor by isomerisation of the 3-enoic acid, but by stereomutation of 4-methylhex-cis-2-enoic acid on the catalyst. The conversion of molecular dissymmetry into centrodissymmetry by catalytic hydrogenation can therefore be used to determine the absolute configuration of allenes.(–)-Methyl 4-methylhexa-2,3-dienoate gave (–)-(R)-methyl 4-methylhexanoate on catalytic semi- and full-hydrogenation and, from analysis of steric effects in the transition state for adsorption, the (–)-allene ester has the R-configuration. Semihydrogenation of the (+)-allenic acid, followed by esterification, gave methyl (+)-4-methylhex-2-enoate, oxidised and esterified to (+)-(S)-methyl 2-methylbutyrate: this provides a variant of the method. The assumption of cis-addition of hydrogen from the catalyst surface is formally proved by hydrogenation of (+)-methyl 4-phenyl-penta-2,3-dienoate of established S-configuration.