Single and double box HMGB proteins differentially destabilize nucleosomes.

Nucleosome disruption plays a key role in many nuclear processes including transcription, DNA repair and recombination. Here we combine atomic force microscopy (AFM) and optical tweezers (OT) experiments to show that high mobility group B (HMGB) proteins strongly disrupt nucleosomes, revealing a new mechanism for regulation of chromatin accessibility. We find that both the double box yeast Hmo1 and the single box yeast Nhp6A display strong binding preferences for nucleosomes over linker DNA, and both HMGB proteins destabilize and unwind DNA from the H2A-H2B dimers.

Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid.

The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model.

Communication: nanoscale ion fluctuations in Nafion polymer electrolyte.

Ion conduction mechanisms and the nanostructure of ion conduction networks remain poorly understood in polymer electrolytes which are used as proton-exchange-membranes (PEM) in fuel cell applications. Here we study nanoscale surface-potential fluctuations produced by Brownian ion dynamics in thin films of low-hydration Nafion™, the prototype PEM. Images and power spectra of the fluctuations are used to derive the local conductivity-relaxation spectrum, in order to compare with bulk behavior and hopping-conductivity models.

Basic N-terminus of yeast Nhp6A regulates the mechanism of its DNA flexibility enhancement.

HMGB (high-mobility group box) proteins are members of a class of small proteins that are ubiquitous in eukaryotic cells and nonspecifically bind to DNA, inducing large-angle DNA bends, enhancing the flexibility of DNA, and likely facilitating numerous important biological interactions. To determine the nature of this behavior for different HMGB proteins, we used atomic force microscopy to quantitatively characterize the bend angle distributions of DNA complexes with human HMGB2(Box A), yeast Nhp6A, and two chimeric mutants of these proteins. While all of the HMGB proteins bend DNA to preferred angles, Nhp6A promoted the formation of higher-order oligomer structures and induced a significantly broader distribution of angles, suggesting that the mechanism of Nhp6A is like a flexible hinge more than that of HMGB2(Box A).

Mechanism of DNA flexibility enhancement by HMGB proteins.

The mechanism by which sequence non-specific DNA-binding proteins enhance DNA flexibility is studied by examining complexes of double-stranded DNA with the high mobility group type B proteins HMGB2 (Box A) and HMGB1 (Box A+B) using atomic force microscopy. DNA end-to-end distances and local DNA bend angle distributions are analyzed for protein complexes deposited on a mica surface. For HMGB2 (Box A) binding we find a mean induced DNA bend angle of 78 degrees, with a standard error of 1.

Local dielectric spectroscopy of near-surface glassy polymer dynamics.

A noncontact scanning probe microscopy method was used to probe local near-surface dielectric susceptibility and dielectric relaxation in polyvinyl acetate near the glass transition. Dielectric spectra were measured from 10(-4) to 10(2) Hz as a function of temperature. The measurements probed a 20 nm thick layer below the free surface of a bulk film.

Imaging nanoscale spatio-temporal thermal fluctuations.

Spatial and temporal fluctuations of the electric polarization were imaged in polymer thin films near the glass transition using electric force microscopy. Below the glass transition the fluctuations are quasi-static, and spatial fluctuations were found to quantitatively agree with predictions for thermal fluctuations. Temporal fluctuations appear near the glass transition.

Local polarization fluctuations in an aging glass.

Polarization fluctuations were measured in nanoscale volumes of a polymer glass during aging following a temperature quench through the glass transition. Statistical properties of the noise were studied in equilibrium and during aging. The noise spectral density had a larger temporal variance during aging; i.

Direct observation of molecular cooperativity near the glass transition.

The increasingly sluggish response of a supercooled liquid as it nears its glass transition (for example, refrigerated honey) is prototypical of glassy dynamics found in proteins, neural networks and superconductors. The notion that molecules rearrange cooperatively has long been postulated to explain diverging relaxation times and broadened (non-exponential) response functions near the glass transition. Recently, cooperativity was observed and analysed in colloid glasses and in simulations of binary liquids well above the glass transition.