DNA based molecular motors

Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.     

Total Synthesis of Resveratrone and iso-Resveratrone

The first total synthesis of resveratrone and iso-resveratrone based on an epoxide olefination approach is described. The pivotal reaction proceeds by insertion of the lithiated epoxide into a boronic ester and subsequent syn-elimination. Resveratrone has been described to have remarkable photophysical properties, including two-photon absorption. Therefore, an azide derivative has been prepared to allow for use as a biological label.     

Correcting saturation effects of the arterial input function in dynamic susceptibility contrast-enhanced MRI: a Monte Carlo simulation

To prevent systematic errors in quantitative brain perfusion studies using dynamic susceptibility contrast-enhanced magnetic resonance imaging (DSC-MRI), a reliable determination of the arterial input function (AIF) is essential. We propose a novel algorithm for correcting distortions of the AIF caused by saturation of the peak amplitude and discuss its relevance for longitudinal studies. The algorithm is based on the assumption that the AIF can be separated into a reliable part at low contrast agent concentrations and an unreliable part at high concentrations. This unreliable part is reconstructed, applying a theoretical framework based on a transport-diffusion theory and using the bolus-shape in the tissue. A validation of the correction scheme is tested by a Monte Carlo simulation. The input of the simulation was a wide range of perfusion, and the main aim was to compare this input to the determined perfusion parameters. Another input of the simulation was an AIF template derived from in vivo measurements. The distortions of this template was modeled via a Rician distribution for image intensities. As for a real DSC-MRI experiment, the simulation returned the AIF and the tracer concentration-dependent signal in the tissue. The novel correction scheme was tested by deriving perfusion parameters from the simulated data for the corrected and the uncorrected case. For this analysis, a common truncated singular value decomposition approach was applied. We find that the saturation effect caused by Rician-distributed noise leads to an overestimation of regional cerebral blood flow and regional cerebral blood volume, as compared to the input parameter. The aberration can be amplified by a decreasing signal-to-noise ratio (SNR) or an increasing tracer concentration. We also find that the overestimation can be successfully eliminated by the proposed saturation-correction scheme. In summary, the correction scheme will allow DSC-MRI to be expanded towards higher tracer concentrations and lower SNR and will help to increase the measurement to measurement reproducibility for longitudinal studies.     

Insights into LiAlH4 Catalyzed Imine Hydrogenation

Commercial LiAlH₄ can be used in catalytic quantities in the hydrogenation of imines to amines with H₂. Combined experimental and theoretical investigations give deeper insight in the mechanism and identifies the most likely catalytic cycle. Activity is lost when Li in LiAlH₄ is exchanged for Na or K. Exchanging Al for B or Ga also led to dramatically reduced activities. This indicates a heterobimetallic mechanism in which cooperation between Li and Al is crucial. Potential intermediates on the catalytic pathway have been isolated from reactions of MAlH₄ (M=Li, Na, K) and different imines. Depending on the imine, double, triple or quadruple imine insertion has been observed. Prolonged reaction of LiAlH₄ with PhC(H)=NtBu led to a side-reaction and gave the double insertion product LiAlH₂[N]₂ ([N]=N(tBu)CH₂Ph) which at higher temperature reacts further by ortho-metallation of the Ph ring. A DFT study led to a number of conclusions. The most likely catalyst for hydrogenation of PhC(H)=NtBu with LiAlH₄ is LiAlH₂[N]₂. Insertion of a third imine via a heterobimetallic transition state has a barrier of +23.2 kcal mol⁻¹ (ΔH). The rate-determining step is hydrogenolysis of LiAlH[N]₃ with H₂ with a barrier of +29.2 kcal mol⁻¹. In agreement with experiment, replacing Li for Na (or K) and Al for B (or Ga) led to higher calculated barriers. Also, the AlH₄⁻ anion showed very high barriers. Calculations support the experimentally observed effects of the imine substituents at C and N: the lowest barriers are calculated for imines with aryl-substituents at C and alkyl-substituents at N.     

B(C6F5)3‐Catalyzed Hydrogenation of Oxime Ethers without Cleavage of the NO Bond

The hydrogenation of oximes and oxime ethers is usually hampered by N? O bond cleavage, hence affording amines rather than hydroxylamines. The boron Lewis acid B(C₆F₅)₃ is found to catalyze the chemoselective hydrogenation of oxime ethers at elevated or even room temperature under 100 bar dihydrogen pressure. The use of the triisopropylsilyl group as a protecting group allows for facile liberation of the free hydroxylamines.