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

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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.

Original languageEnglish (US)
Pages (from-to)4211-4218
Number of pages8
Issue number9
StatePublished - May 11 2021

Bibliographical note

Funding 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.

Publisher Copyright:
© 2021 American Chemical Society.


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