Chromatin hierarchical branching visualized at the nanoscale by electron microscopy.

Chromatin is spatially organized in a hierarchical manner by virtue of single nucleosomes condensing into higher order chromatin structures, conferring various mechanical properties and biochemical signals. These higher order chromatin structures regulate genomic function by organization of the heterochromatin and euchromatin landscape. Less is known about its transition state from higher order heterochromatin to the lower order nucleosome form, and there is no information on its physical properties.

The transition structure of chromatin fibers at the nanoscale probed by cryogenic electron tomography.

The naked DNA inside the nucleus interacts with proteins and RNAs forming a higher order chromatin structure to spatially and temporally control transcription in eukaryotic cells. The 30 nm chromatin fiber is one of the most important determinants of the regulation of eukaryotic transcription. However, the transition of chromatin from the 30 nm inactive higher order structure to the actively transcribed lower order nucleosomal arrays is unclear, which limits our understanding of eukaryotic transcription.

Ultrasensitive detection of microbial cells using magnetic focus enhanced lateral flow sensors.

We report on an improved lateral flow immunoassay (LFIA) sensor with a magnetic focus for ultrasensitive naked-eye detection of pathogenic microorganisms at a near single cell limit without any pre-enrichment steps, by allowing the magnetic probes to focus the labelled pathogens to the target zone of the LF strip.

Rapid and unbiased extraction of chromatin associated RNAs from purified native chromatin.

An ultra fast and unbiased method that uses salicylic acid coated magnetic nanoparticles (SAMNPs) and magnetophoretic chromatography is developed to extract chromatin associated RNAs (CARs). The SAMNPs were first used for enriching cells from the cell culture media and further used for capturing chromatin after cells were lysed. The formed SAMNPs-chromatin complexes were transferred to a viscous polyethylene glycol (PEG) solution stored in a 200-μl pipette tip.

Trichloroethylene sensing in water based on SERS with multifunctional Au/TiO2 core-shell nanocomposites.

Herein we report on a rapid and highly sensitive scheme to detect trichloroethylene (TCE), an environmental contaminant, by surface enhanced Raman scattering (SERS) with multifunctional Au/TiO2 core-shell nanocomposites as SERS substrates. A facile approach to fabricate TiO2 shell around gold core nanocomposites is proposed as sensors for TCE detection by SERS. During detection, TCE was first oxidized due to the photocatalytic activity of the TiO2 shell and the increase in SERS intensity due to the product of TCE photooxidation can be used to determine the concentration of TCE.

A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin.

Native chromatin contains valuable genetic, epigenetic and structural information. Though DNA and nucleosome structures are well defined, less is known about the higher-order chromatin structure. Traditional chromatin extraction methods involve fixation, fragmentation and centrifugation, which might distort the higher-order structural information of native chromatin.

One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles.

Salicylic acid-coated magnetic nanoparticles were prepared via a modified one-step synthesis and used for a one-stop extraction of genomic DNA from mammalian cells. The synthesized magnetic particles were used for magnetic separation of cells from the media by nonspecific binding of the particles as well as extraction of genomic DNA from the lysate. The quantity and quality were confirmed by agarose gel electrophoresis and polymerase chain reaction.

PCR-ready human DNA extraction from urine samples using magnetic nanoparticles.

Urine-derived human genomic DNA (gDNA) has wide application in a variety of disciplines including clinical medicine, sports, and forensic science. We describe a novel method for gDNA extraction from urine samples using carboxylated magnetic nanoparticles (CMNPs) as solid-phase adsorbents. Sedimentation associated with freezing of urine samples significantly reduces cell capture by CMNPs.

Bacteria capture, lysate clearance, and plasmid DNA extraction using pH-sensitive multifunctional magnetic nanoparticles.

A multifunctional magnetic nanoparticle (MNP)-assisted bioseparation method was developed to isolate plasmid DNA (pDNA) from Escherichia coli culture. Using the pH-sensitive carboxyl-modified magnetic nanoparticles, both cell capture and the subsequent removal of genomic DNA/protein complex after lysis can be achieved simply by magnetic separation. Furthermore, the yield and purity of pDNA extracted by MNPs are comparable to those obtained using organic solvents or commercial kits.

Molecular dynamics study of polymer conformation as a function of concentration and solvent quality.

A coarse-grained model for molecular dynamics simulations of polymer solutions with variable solvent quality is proposed. This model allows solvent quality to be varied over the whole range from very poor to very good solvent conditions by varying a single parameter. The model has several advantages.

Role of nonadditive forces on the structure and properties of liquid water.

The role of nonadditive interactions on the structure and dielectric properties of water is investigated at different temperatures using molecular dynamics. A new intermolecular potential is developed which contains an ab initio description of two-body additive interactions plus nonadditive contributions from both three-body interactions and polarization. Polarization is the main nonadditive influence, resulting in improved agreement with experiment for the radial distribution function, dielectric constant, and dipole moment.

A molecular dynamics study of nitric oxide in water: diffusion and structure.

We present molecular dynamics simulations of the diffusion coefficients and structure of water-nitric oxide mixtures at ambient (298 K) and in vivo (310 K) conditions. A two-site rigid-body molecular model with partial charges and a Lennard-Jones potential on both sites is proposed for nitric oxide and used in conjunction with the extended simple point-charge model for liquid water in our simulations. The diffusion coefficients obtained from the simulations are in good agreement with experimental data.