Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor–binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support

Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime

The four most popular water models in molecular dynamics were studied in large-scale simulations of Brownian motion of colloidal particles in optical tweezers and then compared with experimental measurements in the same time scale. We present the most direct comparison of colloidal polystyrene particle diffusion in molecular dynamics simulations and experimental data on the same time scales in the ballistic regime. The four most popular water models, all of which take into account electrostatic interactions, are tested and compared based on yielded results and resources required. Three different conditions were simulated: a freely moving particle and one in a potential force field with two different strengths based on 1 pN/nm and 10 pN/nm. In all cases, the diameter of the colloidal particle was 50 nm. The acquired data were compared with experimental measurements performed using optical tweezers with position capture rates as high as 125 MHz. The experiments were performed in pure water on polystyrene particles with a 1 μm diameter in special microchannel cells

Electrospun poly(3-hexylthiophene)/poly(ethylene oxide)/graphene oxide composite nanofibers: Effects of graphene oxide reduction

In this article, we report on the production by electrospinning of P3HT/PEO, P3HT/PEO/GO, and P3HT/PEO/rGO nanofibers in which the filler is homogeneously dispersed and parallel oriented along the fibers axis. The effect of nanofillers' presence inside nanofibers and GO reduction was studied, in order to reveal the influence of the new hierarchical structure on the electrical conductivity and mechanical properties. An in-depth characterization of the purity and regioregularity of the starting P3HT as well as the morphology and chemical structure of GO and rGO was carried out. The morphology of the electrospun nanofibers was examined by both scanning and transmission electron microscopy. The fibrous nanocomposites are also characterized by differential scanning calorimetry to investigate their chemical structure and polymer chains arrangements. Finally, the electrical conductivity of the electrospun fibers and the elastic modulus of the single fibers are evaluated using a four-point probe method and atomic force microscopy nanoindentation, respectively. The electrospun materials crystallinity as well as the elastic modulus increase with the addition of the nanofillers while the electrical conductivity is positively influenced by the GO reduction

An example of U-shaped hydrogel nanofilament in the oscillatory flow, <i>d</i> = 181 nm, <i>L</i> = 32 μm, <i>V</i>_<i>max</i> = 282 μm/s, <i>U</i>_<i>r</i> <i>=</i> 10⁻³.

<p>(a)–lateral migration path of the nanofilament into the channel axis, center of mass position at each zero-crossing of the flow oscillation (n * π, n = 1,2,3.); (b)–relative longitudinal slip velocity <i>U</i>_<i>s</i> of the filament observed for each maxima of the oscillating flow (n * π/2, n = 1,3,5.). Remarkable out of phase pattern due to the filament deformations.</p

Hydrogel Nanofilaments via Core-Shell Electrospinning.

Recent biomedical hydrogels applications require the development of nanostructures with controlled diameter and adjustable mechanical properties. Here we present a technique for the production of flexible nanofilaments to be used as drug carriers or in microfluidics, with deformability and elasticity resembling those of long DNA chains. The fabrication method is based on the core-shell electrospinning technique with core solution polymerisation post electrospinning. Produced from the nanofibers highly deformable hydrogel nanofilaments are characterised by their Brownian motion and bending dynamics. The evaluated mechanical properties are compared with AFM nanoindentation tests

Selected characteristics of hydrogel nanofilaments analyzed in the present experiment compared with the bead-spring WLC model [18–20] and the experiment with polymer fibers [18].

<p><i>Sp</i>, <i>Pe</i>, <i>K</i>, <i>A</i>, <i>U</i>_<i>r</i>, <i>U</i>_<i>s</i> of hydrogel nanofilaments are reported as range of values and as mean ± standard deviation.</p

Lateral migration of electrospun hydrogel nanofilaments in an oscillatory flow

<div><p>The recent progress in bioengineering has created great interest in the dynamics and manipulation of long, deformable macromolecules interacting with fluid flow. We report experimental data on the cross-flow migration, bending, and buckling of extremely deformable hydrogel nanofilaments conveyed by an oscillatory flow into a microchannel. The changes in migration velocity and filament orientation are related to the flow velocity and the filament’s initial position, deformation, and length. The observed migration dynamics of hydrogel filaments qualitatively confirms the validity of the previously developed worm-like bead-chain hydrodynamic model. The experimental data collected may help to verify the role of hydrodynamic interactions in molecular simulations of long molecular chains dynamics.</p></div

Statistics of cross-stream migration.

<p>(a)—distribution of hydrogel nanofilaments across the microchannel between centerline (0) and wall (1) at initial (<i>grey bars</i>) and final (<i>dashed contour lines</i>) oscillatory cycle; (b)—relative filament slip velocity <i>Us</i> for the three groups; (c)—relative change of the inclination angle for each group of nanofilaments: final orientation (<i>dashed-patterned bars</i>) normalized to the initial orientation (<i>grey bars</i>).</p

Lateral migration for hydrogel nanofilaments.

<p>(a)—toward the channel center (<i>d = 105 nm</i>, <i>L = 41</i> μ<i>m</i>, <i>V</i>_<i>max</i> <i>= 250</i> μ<i>m/s</i>, <i>relative migration velocity U</i>_<i>r</i> <i>= 0</i>.<i>85 10</i>^<i>−3</i>; (b)—toward the wall (<i>d = 134 nm</i>, <i>L = 54</i> μ<i>m</i>, <i>V</i>_<i>max</i> <i>= 132</i> μ<i>m/s</i>, <i>U</i>_<i>r</i> <i>= 0</i>.<i>6 10</i>^<i>−3</i>.</p