7 research outputs found
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures
DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes
Electrostatic Modulation of Aromatic Rings via Explicit Solvation of Substituents
Solvent
effects are implicated as playing a major role in modulating
electrostatic interactions via through-space and polarization effects,
but these phenomena are often hard to dissect. By using synthetic
molecular torsion balances and a simple explicit solvation model,
we demonstrate that the solvation of substituents substantially affects
the electrostatic potential of aromatic rings. Although polarization
effects are important, we show that a simple additive through-space
model also provides a reasonable account of the experimental data.
The results deliver insights into solvent structure and might contribute
to the development of computationally inexpensive solvent models
A General One-Step Synthesis of Alkanethiyl-Stabilized Gold Nanoparticles with Control over Core Size and Monolayer Functionality
In spite of widespread interest in the unique size-dependent
properties
and consequent applications of gold nanoparticles (AuNPs), synthetic
protocols that reliably allow for independent tuning of surface chemistry
and core size, the two critical determinants of AuNP properties, remain
limited. Often, core size is inherently affected by the ligand structure
in an unpredictable fashion. Functionalized ligands are commonly introduced
using postsynthesis exchange procedures, which can be inefficient
and operationally delicate. Here, we report a one-step protocol for
preparing monolayer-stabilized AuNPs that is compatible with a wide
range of ligand functional groups and also allows for the systematic
control of core size. In a single-phase reaction using the mild reducing
agent tert-butylamine borane, AuNPs that are compatible
with solvents spanning a wide range of polarities from toluene to
water can be produced without damaging reactive chemical functionalities
within the small-molecule surface-stabilizing ligands. We demonstrate
that the rate of reduction, which is easily controlled by adjusting
the period over which the reducing agent is added, is a simple parameter
that can be used irrespective of the ligand structure to adjust the
core size of AuNPs without broadening the size distribution. Core
sizes in the range of 2–10 nm can thus be generated. The upper
size limit appears to be determined by the nature of each specific
ligand/solvent pairing. This protocol produces high quality, functionally
sophisticated nanoparticles in a single step. By combining the ability
to vary size-related nanoparticle properties with the option to incorporate
reactive functional groups at the nanoparticle–solvent interface,
it is possible to generate chemically reactive colloidal building
blocks from which more complex nanoparticle-based devices and materials
may subsequently be constructed
Software and data for endoscopic sensing of alveolar pH
Previously unobtainable measurements of alveolar pH were obtained using an endoscope-deployable optrode. The pH sensing was achieved using functionalized gold nanoshell sensors and surface enhanced Raman spectroscopy (SERS). The optrode consisted of an asymmetric dual-core optical fiber designed for spatially separating the optical pump delivery and signal collection, in order to circumvent the unwanted Raman signal generated within the fiber. Using this approach, we demonstrate a ~100-fold increase in SERS signal-to-fiber background ratio, and demonstrate multiple site pH sensing with a measurement accuracy of ±0.07 pH units in the respiratory acini of an ex vivo ovine lung model. We also demonstrate that alveolar pH changes in response to ventilation.Choudhury, Debaditya; Tanner, Michael G.; McAughtrie, Sarah; Yu, Fei; Mills, Bethany; Choudhary, Tushar R.; Seth, Sohan; Craven, Thomas H.; Stone, James M.; Mati, Ioulia K.; Campbell, Colin J.; Bradley, Mark; Williams, Christopher K. I.; Dhaliwal, Kevin; Birks, Timothy A.; Thomson, Robert Roderick. (2016). Software and data for endoscopic sensing of alveolar pH, [software]. http://dx.doi.org/10.7488/ds/1583