Heat conductivity of DNA double helix

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure

Xenobiotic-induced activation of human aryl hydrocarbon receptor target genes in Drosophila is mediated by the epigenetic chromatin modifiers

Aryl hydrocarbon receptor (AHR) is the key transcription factor that controls animal development and various adaptive processes. The AHR\u27s target genes are involved in biodegradation of endogenous and exogenous toxins, regulation of immune response, organogenesis, and neurogenesis. Ligand binding is important for the activation of the AHR signaling pathway. Invertebrate AHR homologs are activated by endogenous ligands whereas vertebrate AHR can be activated by both endogenous and exogenous ligands (xenobiotics). Several studies using mammalian cultured cells have demonstrated that transcription of the AHR target genes can be activated by exogenous AHR ligands, but little is known about the effects of AHR in a living organism. Here, we examined the effects of human AHR and its ligands using transgenic Drosophila lines with an inducible human AhR gene. We found that exogenous AHR ligands can increase as well as decrease the transcription levels of the AHR target genes, including genes that control proliferation, motility, polarization, and programmed cell death. This suggests that AHR activation may affect the expression of gene networks that could be critical for cancer progression and metastasis. Importantly, we found that AHR target genes are also controlled by the enzymes that modify chromatin structure, in particular components of the epigenetic Polycomb Repressive complexes 1 and 2. Since exogenous AHR ligands (alternatively - xenobiotics) and small molecule inhibitors of epigenetic modifiers are often used as pharmaceutical anticancer drugs, our findings may have significant implications in designing new combinations of therapeutic treatments for oncological diseases. © Akishina et al

Adsorption of Silicon-Containing Dendrimers: Effects of Chemical Composition, Structure, and Generation Number

We studied the conformational behavior of silicon-containing dendrimers during their adsorption onto a flat impenetrable surface by molecular dynamics (MD) simulations. Four homologous series of dendrimers from the 4th up to the 7th generations were modeled, namely, two types of carbosilane dendrimers differing by the functionality of the core Si atom and two types of siloxane dendrimers with different lengths of the spacers. Comparative analysis of the fractions of adsorbed atoms belonging to various structural layers within dendrimers as well as density profiles allowed us to elucidate not only some general trends but also the effects determined by dendrimer specificity. In particular, it was found that in contrast to the carbosilane dendrimers interacting with the adsorbing surface mainly by their peripheral layers, the siloxane dendrimers with the longer –O–Si(CH3)2–O spacers expose atoms from their interior to the surface spreading out on it. These findings are important for the design of functional materials on the basis of silicon-containing dendrimers

A Comparative Study of Intramolecular Mobility of Single Siloxane and Carbosilane Dendrimers via Molecular Dynamics Simulations

A comparative analysis of intramolecular dynamics of four types of isolated dendrimers from the fourth to the seventh generations belonging to the siloxane and carbosilane families, differing in spacer length, core functionality, and the type of chemical bonds, has been performed via atomic molecular dynamics simulations. The average radial and angular positions of all Si branching atoms of various topological layers within the dendrimer interior, as well as their variations, have been calculated, and the distributions of the relaxation times of their radial and angular motions have been found. It has been shown that the dendrons of all the dendrimers elongate from the center and decrease in a solid angle with an increasing generation number. The characteristic relaxation times of both angular and radial motions of Si atoms are of the order of a few nanoseconds, and they increase with an increasing generation number and decrease with temperature, with the angular relaxation times being larger than the radial ones. The relaxation times in the carbosilanes are larger than those in the siloxanes. The rotational angle dynamics of the carbosilane dendrimers show that the chain bending is mainly realized via trans-gauche transitions in the Si branching bonds