Researchers at the University of Cambridge have revealed that DNA forms twisted coils rather than knots when passing through tiny nanopores, challenging a long-held assumption in genetics. This discovery, driven by electroosmotic flow, could refine DNA sensing technologies and improve detection of genetic damage. The findings appear in Physical Review X.
For decades, scientists interpreted irregular electrical signals in nanopore experiments as evidence of DNA knots, much like a tangled shoelace snagging in a narrow hole. This view guided the analysis of genetic data, assuming that any uneven translocation indicated knotted strands.
A new study from the University of Cambridge, in collaboration with international teams, demonstrates that these signals often stem from plectonemes—twisted coils resembling a coiled phone cord—instead of true knots. As DNA threads through the nanopore, ionic flow inside generates torque, spinning the strand and forming these persistent twists outside the pore.
"Our experiments showed that as DNA is pulled through the nanopore, the ionic flow inside twists the strand, accumulating torque and winding it into plectonemes, not just knots," said lead author Dr. Fei Zheng from the Cavendish Laboratory. "This 'hidden' twisting structure has a distinctive, long-lasting fingerprint in the electrical signal, unlike the more transient signature of knots."
The team conducted tests using glass and silicon nitride nanopores under varying voltages and conditions. They observed frequent 'tangled' events, especially with longer DNA strands and higher voltages, which knot theory could not fully account for. Computer simulations confirmed that electroosmotic flow—water movement induced by electric fields—propagates twist along the DNA, enabling plectoneme formation.
Further evidence came from experiments with 'nicked' DNA, where interruptions in the strand prevented twist propagation and drastically reduced plectonemes. This underscores the role of intact DNA in transmitting torque.
"What's really powerful here is that we can now tell apart knots and plectonemes in the nanopore signal based on how long they last," noted Prof. Ulrich F. Keyser, a co-author from the Cavendish Laboratory. "Knots pass through quickly, just like a quick bump, whereas plectonemes linger and create extended signals."
These insights extend to biology, where DNA twisting influences genome stability during enzymatic processes. In technology, distinguishing plectonemes from knots promises more precise nanopore sensors for genomics, biosensing, and early detection of DNA damage linked to diseases.
