Diffusion of Knotted DNA Molecules in Nanochannels in the Extended de Gennes Regime

Abstract

We study the diffusion of T4 GT7 deoxyribonucleic acid (DNA) molecules confined in nanochannels with an effective size of 307 nm before and after knot formation. The measured DNA chain diffusivity is 0.0243 ± 0.0009 μm²/s for unknotted DNA molecules and 0.014 ± 0.001 μm²/s for the DNA molecules that contain knots with an estimated knot contour length of 9 ± 2 μm. The reduced diffusivity in the presence of large knots indicates that the DNA–wall friction, rather than the shortening of the nondraining molecule, dominates the friction of knotted DNA in the extended de Gennes regime of nanochannel confinement.