Three Dimensional Tethered Particle Motion for DNA-Protein Interactions Studies

Abstract

We developed a unique optical system for studying the interaction of proteins with DNA based on tethered particle motion (TPM). The method uses gold nano-beads and total internal reflection (TIR) illumination and allows recording the DNA dynamics in three dimensions (3D). We studied the 3D end-to-end distribution of a tethered DNA. We measured the axial distribution that was never measured before [1] and confirmed the theoretical solution but emphasize the invalidity of the Gaussian random walk approximation for short DNA strands. We also measured the interaction of HU protein with DNA and confirmed its bi-modal effect on DNA as a function of the HU concentration [2]. To the best of our knowledge, this is the first time that TPM is used for actual DNA-protein interaction studies (except for looping). 1. Lindner, M., G. Nir, S. Medalion, H.R.C. Dietrich, Y. Rabin, and Y. Garini, Force-free measurements of the conformations of DNA molecules tethered to a wall. Physical Review E, 83, 011916-1-7 (2011). 2. Nir, G., M. Lindner, H.R.C. Dietrich, O. Girshevitz, C.E. Vorgias, and Y. Garini, HU protein induces incoherent DNA persistence length. Biophysical Journal, 100, 784–790 (2011).