Probing DNA conformational changes with high temporal resolution by Tethered Particle Motion

TL;DR

This paper enhances the Tethered Particle Motion technique by analyzing its temporal resolution through theory, simulations, and experiments, revealing how particle size and DNA length influence relaxation time and enabling millisecond-scale measurements.

Contribution

We provide a dynamical calibration of TPM, showing how relaxation time depends on DNA length and particle size, and identify conditions for optimal high-resolution measurements.

Findings

Relaxation time increases with DNA length and particle radius.

Particles of 20 nm or less do not significantly slow DNA dynamics.

TPM can achieve a temporal resolution as short as 20 ms.

Abstract

The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150~nm). Notably we demonstrate that, for a particle of radius 20~nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20~ms.