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.
Bibliographical noteFunding Information:
This work was supported by NSF (CBET-2016879). Device fabrication was conducted in the Minnesota Nano Center, which is supported by the National Science Foundation through the National Nano Coordinated Infrastructure Network (NNCI) under Award Number ECCS-2025124.
© 2021 American Chemical Society.