arXiv subjects

Simon F. Tolic-Norrelykke

Publications and source records attributed to Simon F. Tolic-Norrelykke.

3 recordsLinked to original sources

arXiv2006

Calibration of optical tweezers with positional detection in the back-focal-plane

We explain and demonstrate a new method of force- and position-calibration for optical tweezers with back-focal-plane photo detection. The method combines power spectral measurements of thermal motion and the response to a sinusoidal motion of a translation stage. It consequently does not use the drag coefficient of the trapped ob ject as an input. Thus, neither the viscosity, nor the size of the trapped ob ject, nor its distance to nearby surfaces need to be known. The method requires only a low level of instrumentation and can be applied in situ in all spatial dimensions. It is both accurate and precise: true values are returned, with small error-bars. We tested this experimentally, near and far from surfaces. Both position- and force-calibration were accurate to within 3%. To calibrate, we moved the sample with a piezo-electric translation stage, but the laser beam could be moved instead, e.g. by acousto-optic deflectors. Near surfaces, this precision requires an improved formula for the hydrodynamical interaction between an infinite plane and a micro-sphere in non-constant motion parallel to it. We give such a formula.

physics.bio-ph↗

arXiv2006

Brownian Motion after Einstein: Some new applications and new experiments

The first half of this chapter describes the development in mathematical models of Brownian motion after Einstein's seminal papers and current applications to optical tweezers. This instrument of choice among single-molecule biophysicists is also an instrument of precision that requires an understanding of Brownian motion beyond Einstein's. This is illustrated with some applications, current and potential, and it is shown how addition of a controlled forced motion on the nano-scale of the tweezed object's thermal motion can improve the calibration of the instrument in general, and make it possible also in complex surroundings. The second half of the present chapter, starting with Sect. 9, describes the co-evolution of biological motility models with models of Brownian motion, including very recent results for how to derive cell-type-specific motility models from experimental cell trajectories.

physics.bio-ph↗

arXiv2006

Stepwise bending of DNA by a single TATA-box Binding Protein

The TATA-box Binding Protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called ``TATA-boxes'' in the DNA. We present results from the study of individual Saccharomyces cerevisia TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear binding pathway. Biological implications of the intermediate states are discussed.

physics.bio-ph↗