Achiral dye/surfactant heteroaggregates for chiral sensing of phosphocholines

An investigation, based on absorption and circular dichroism spectroscopy, was carried out on assemblies formed in water upon the interaction of heteroaggregates, composed of dyes (Congo Red or Evans Blue) and cetyltrimethylammonium bromide (CTAB), with four enantiopure phopshocholines (DMPC, DPPC, DOPC, and POPC) characterized by the same po- lar head and different hydrophobic tails. The results show that the nature of the lipid as well as the concentration ratios influence sensitively the absorption and chiroptical properties of the su- pramolecular structure. Intriguingly, the transfer of chirality from the lipid to the assembly may be triggered or not, depending on the nature of the lipid hydrophobic chain. These findings con- firm the fundamental role of hydrophobic interactions in the transcription of chirality from mol- ecules to complex architectures

環境管理計画への市民参加とその規定因としてのエンパワーメント

<p>DMPC/2/siRNA treatment of Jurkat T cells, 48 hours from the beginning of transfection.</p

Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR

Specificity in protein-DNA recognition arises from the synergy of several factors that stem from the structural and chemical signatures encoded within the targeted DNA molecule. Here, we deciphered the nature of the interactions driving DNA recognition and binding by the bacterial transcription factor PdxR, a member of the MocR family responsible for the regulation of pyridoxal 5 &amp; PRIME;-phosphate (PLP) biosynthesis. Single particle cryo-EM performed on the PLP-PdxR bound to its target DNA enabled the isolation of three conformers of the complex, which may be considered as snapshots of the binding process. Moreover, the resolution of an apo-PdxR crystallographic structure provided a detailed description of the transition of the effector domain to the holo-PdxR form triggered by the binding of the PLP effector molecule. Binding analyses of mutated DNA sequences using both wild type and PdxR variants revealed a central role of electrostatic interactions and of the intrinsic asymmetric bending of the DNA in allosterically guiding the holo-PdxR-DNA recognition process, from the first encounter through the fully bound state. Our results detail the structure and dynamics of the PdxR-DNA complex, clarifying the mechanism governing the DNA-binding mode of the holo-PdxR and the regulation features of the MocR family of transcription factors

Structural analysis of 30-nm chromatin fiber architecture

The folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientational constraints of the nucleosome units that provide the geometrical conditions of helical conformations. Recently, the elucidation of the x-ray crystal structure of a nucleosome tetramer array and the interpretation of electron microscopy images of reconstituted nucleosome arrays suggested two different architectures of the chromatin fiber. We approached the problem by integrating the experimental findings with geometrical, conformational and topological restraints, under the hypothesis of the minimum distortion of the nucleosome and linker DNA structures. Weshow that the excluded volume at linker crossing and the torsional energy limit the possible close packing of the nucleosomes in the chromatin fiber. In particular, the torsional energy of the chromatin fiber appears crucial in determining the kind of nucleosome packing for short nucleosome repeat lengths as in telomeres and yeast chromatin

A Statistical Thermodynamic Approach for Predicting The Sequence-Dependent Nucleosome Positioning along Genomes

The distribution of nucleosomes, the fundamental repeating units of chromatin, along the eukaryotic genome rules replication, transcription, repair, and regulation processes through modulation of DNA accessibility. Genome-wide maps provide much information about the factors that direct nucleosome positioning. However, the experimental nucleosome maps do not permit to conclude unambiguously that the DNA sequence of the eukaryotic genomes encodes nucleosome positioning and organization. A possible way to disclose this important issue is to develop theoretical models capable of predicting nucleosome positioning in terms of the DNA sequence. Toward this goal, we propose a physical model for predicting nucleosome thermodynamic stability in terms of DNA sequence. The model, based on a statistical mechanical approach, allows the calculation of the canonical ensemble free energy involved in the formation of each nucleosome along a DNA tract. The theoretical nucleosome distribution along genomes was compared with the experimental positioning maps of yeast genome. The results are comparable with those obtained with pure statistical models based on identifying some recurrent sequence features obtained from the statistical analysis of a very large pool of nucleosomal DNA sequences. However, our model based on the physical properties of the DNA such as curvature and flexibility appears universal and applicable to any genomes without rearrangements