Probing DNA conformational changes with high temporal resolution by tethered particle motion.
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.
Université de Toulouse, UPS, Laboratoire de Physique Théorique (IRSAMC), F-31062 Toulouse, France. CNRS, F-31062 Toulouse, France.
Manoel
M
Manghi
Catherine
C
Tardin
Julien
J
Baglio
Philippe
P
Rousseau
Laurence
L
Salomé
Nicolas
N
Destainville
D002138:Calibration; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D015335:Molecular Probes; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation
D015335:Molecular Probes; D004247:DNA