Many biophysical studies involve diffusing particle in a potential field, especially in a harmonic field. Optical tweezers, magnetic tweezers and tethered particle motion (TPM) are some examples for such experiments. In order to extract dynamical properties from these experiments, there is a need to accurately calibrate the setup.

I will show a method, based on the known solution of Smoluchowski’s equation, for finding all of the relevant parameters (i.e. the particle’s diffusion coefficient and the spring constant of the harmonic field) without pre-calibrating the setup. In addition, I’ll present the implementation of our formalism by showing results from computer simulations and TPM experiments.

Click here to read more details in our paper.

Chromosomes are organized in distinct territories of the interphase nucleus. The rules governing chromosome territory maintenance are still not understood. We used dynamic methods to examine the organization of the genome in living cells. We developed method that allows measuring the diffusion of genomic regions in time-range of 10^-2 – 10⁴ sec. We compared the effect on diffusion motion caused by differing parameters such as genomic region, physical location inside the nucleus, transcription activation, and condensation level, as well as the effect caused by depletion of proteins that are known to interact with chromatin. We found that Lamin A protein depletion has the strongest effect on chromatin diffusion properties. Diffusion analysis of chromatin motion in Lamin A depleted cells indicates that Lamin A binding to the chromatin restricts its local freedom of motion. Furthermore, our data suggests that Lamin A-associated protein Lap2 ? down-regulates binding of Lamin A to the chromatin, resulting in down-regulation of chromatin mobility. We suggest that constrained chromatin mobility maintains chromosome territory. Thus, the novel discovery of this function of nucleoplasmic Lamin A and Lap2 ? proteins sheds light on the maintenance mechanism of chromosome territory in the interphase nucleus, which helps ensure the proper function of the genome.

HU is a highly conserved protein that is believed to play an important role in the architecture and dynamic compaction of bacterial DNA. Its ability to control DNA bending is crucial for functions such as transcription and replication. The effects of HU on the DNA structure have been studied so far mainly by single molecule methods that require us to apply stretching forces on the DNA and therefore may perturb the DNA-protein interaction. To overcome this hurdle, we study the effect of HU on the DNA structure without applying external forces by using an improved tethered particle motion method. By combining the results with DNA curvature analysis from atomic force microscopy measurements we find that the DNA consists of two different curvature distributions and the measured persistence length is determined by their interplay. As a result, the effective persistence length adopts a bimodal property that depends primarily on the HU concentration.
The results can be explained according to a recently suggested model that distinguishes single protein binding from cooperative protein binding.

We developed a method for studying DNA-protein interactions on a single-molecule level using an optical method that is based on tethered particle motion (TPM) with a gold nano-bead. The plasmonic properties of gold nano-beads tremendously extend the measurements capabilities and allows for improved spatial and temporal measurements. Using the method we measured the three dimensional end-to-end distribution of a DNA tethered to a wall. Although the lateral distribution is well known and studied, the axial distribution was never measured before. Finally, we used the system to measure the interaction of HU protein with DNA and confirmed a bi-modal that depends on the protein concentration.
The results confirm the capabilities of rather simple optical methods to detect fundamental biological interactions at the nano-level by using nano-particles and devices.

Nano-technology has deeply evolved in the last couple of years. The ability to miniturize and manufacture complex materials with extremely small dimensions allows the production of materails with interesting properties and the development of systems that where not so long ago just a fantasy.