Statistical-mechanical lattice models for protein-DNA binding in chromatin

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Reduction of Oxygen at a NaX-Ag Composite Electrode and Its Application to the Determination of Oxygen in Aqueous Media

A composite mixture Ag-NaX zeolite (silver concentration 16.7% w/w) is synthesized usingimpregnation and thermal decomposition. For silver impregnation, a solution of an Ag acetylacetonate complex in acetone was used. Despite the quantity of silver applied was substantially less than it would be necessary to fill the inner pore space in the zeolite completely, some part of silver formed nanocrystallites and nanoparticles giving rise to a novel composite material. The composite powder was uniformed with soot (10% w/w) and applied onto a mirror-smooth graphite surface used as an electrode matrix. The reduction of oxygen on such a surface proceeded with activity comparable to that observed on the most active planes of the silver single crystal, Ag(100)