DNA Knot Malleability in Single-Digit Nanopores.
Knots in long DNA molecules are prevalent in biological systems and serve as a model system for investigating static and dynamic properties of biopolymers. We explore the dynamics of knots in double-stranded DNA in a new regime of nanometer-scale confinement, large forces, and short time scales, using solid-state nanopores. We show that DNA knots undergo isomorphic translocation through a nanopore, retaining their equilibrium morphology by swiftly compressing in a lateral direction to fit the constriction. We observe no evidence of knot tightening or jamming, even for single-digit nanopores. We explain the observations as the malleability of DNA, characterized by sharp buckling of the DNA in nanopores, driven by the transient disruption of base pairing. Our molecular dynamics simulations support the model. These results are relevant not only for the understanding of DNA packing and manipulation in living cells but also for the polymer physics of DNA and the development of nanopore-based sequencing technologies.
['Sharma|Rajesh Kumar|RK|', 'Agrawal|Ishita|I|', 'Dai|Liang|L|0000-0002-4672-6283', 'Doyle|Patrick|P|0000-0003-2147-9172', 'Garaj|Slaven|S|0000-0001-5529-4040']
D020029:Base Pairing D004247:DNA D004277:DNA, Single-Stranded D056004:Molecular Dynamics Simulation D058608:Nanopores D011108:Polymers D017422:Sequence Analysis, DNA
DNA knots Solid-state nanopores polymers DNA sequencing knot dynamics