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

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 mu m(2)/s for unknotted DNA molecules and 0.014 +/- 0.001 mu m(2)/s for the DNA molecules that contain knots with an estimated knot contour length of 9 +/- 2 mu m. 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.

Automated summary

The study found that the diffusion rate of DNA molecules is significantly reduced in the presence of large knots in nanochannels, indicating that DNA-wall friction dominates the friction of knotted DNA in the extended de Gennes regime.