DNA Torsion Prevents Knot Formation: New Research Overturns Assumptions on DNA Coiling and Nanopore Translocation

🔬 The Groundbreaking Discovery Reshaping DNA Research

In a revelation that challenges decades of scientific understanding, researchers at the University of Cambridge have uncovered that DNA torsion actively prevents knot formation during nanopore translocation. Published in 2025 in Physical Review X, the study demonstrates that what scientists previously interpreted as DNA knots squeezing through tiny nanopores are actually elegant twisted coils known as plectonemes. This finding, led by Dr. Fei Zheng and Prof. Ulrich F. Keyser, stems from meticulous experiments revealing how electroosmotic flow inside the nanopore generates torque, causing the DNA double helix to wind around itself rather than tangle into problematic knots.

Imagine threading a garden hose through a narrow pipe: instead of bunching up into frustrating knots, the hose coils neatly due to rotational forces. Similarly, as DNA—deoxyribonucleic acid, the molecule carrying genetic instructions in living organisms—is pulled through a nanopore under an electric field, ions and water flow create a spinning motion. This torsion builds up, propagating along the DNA strand and forming stable plectonemes outside the pore. The discovery explains irregular electrical signals in nanopore experiments, long misattributed to knots, and opens doors to more precise genomic analysis.

This isn't just a minor correction; it overturns assumptions baked into nanopore data interpretation for over 20 years. Traditional models predicted knots based on equilibrium statistics, but observations showed 'tangled' events far exceeding expectations, especially at higher voltages and with longer DNA strands. By distinguishing plectonemes' persistent signals from knots' fleeting ones, scientists can now refine technologies pivotal to genomics and personalized medicine.University of Cambridge research page

Fundamentals of DNA Topology: Twist, Writhe, and Supercoiling Explained

To grasp this discovery, one must first understand DNA topology—the study of how the DNA molecule twists, coils, and links in three-dimensional space. DNA naturally forms a right-handed double helix with about 10.5 base pairs per turn. Topology is quantified by the linking number (Lk), which decomposes into twist (Tw, local helical turns) and writhe (Wr, global coiling):

• Twist (Tw): Rotations around the DNA axis, inherent to its helical structure.
• Writhe (Wr): Superhelical coiling where the axis bends into loops or plectonemes.
• Linking Number (Lk = Tw + Wr): Conserved unless enzymes like topoisomerases intervene.

Supercoiling occurs when Lk deviates from the relaxed state: negative supercoiling underwinds DNA (common in bacteria for replication), positive overwinds it. Plectonemes represent writhe-dominant supercoils, where excess twist converts to writhe, forming paired helical loops like a twisted rubber band. Knots, conversely, are true topological entanglements where the strand crosses itself in a closed loop, harder to resolve without enzymes.

In cells, DNA supercoiling regulates gene expression, replication, and repair. For instance, bacterial DNA gyrase introduces negative supercoils, while eukaryotic chromatin wraps DNA around histones. Misregulated topology links to diseases like cancer, where excessive supercoiling stalls replication forks. This research illuminates how mechanical forces mimic cellular stresses, providing a window into vivo dynamics.

Actionable insight for students: Visualize topology using free software like OxDNA for simulations, helping grasp why torsion matters in experiments.

Nanopore Technology: A Primer on Revolutionizing Genomics

Nanopore sequencing, pioneered by Oxford Nanopore Technologies, threads long DNA strands through protein or solid-state pores (1-2 nm wide) embedded in a membrane. An electric field drives translocation, while changes in ionic current as bases pass the pore reveal the sequence. Advantages include real-time analysis of ultra-long reads (up to megabases), enabling complex genome assemblies impossible with short-read methods like Illumina.

Challenges persist: irregular current blockades from secondary structures or entanglements obscure signals. Solid-state nanopores (silicon nitride or glass, as in this study) offer durability over biological ones (e.g., alpha-hemolysin). The Cambridge team's pores, fabricated via focused ion beam milling, allowed precise control of voltage (50-200 mV) and salt concentrations.

Applications span pathogen detection (e.g., COVID-19 surveillance), cancer genomics, and metagenomics. For researchers eyeing careers, proficiency in nanopore analysis boosts prospects in research jobs at biotech firms or universities.

Challenging Decades-Old Assumptions: From Knots to Torsion-Driven Coils

For years, erratic nanopore signals were chalked up to knots, drawing from polymer physics where confinement favors entanglements. Equilibrium knot probabilities scale with cube root of contour length, predicting rare events. Yet experiments showed frequent multi-level blockades, prompting alternative explanations like folding or aggregation.

The Cambridge study diverged by integrating hydrodynamics: electroosmotic flow (EOF)—ions dragging solvent under electric fields—imparts azimuthal torque to the helical DNA. This rotates the cis-side (pre-pore) DNA, building positive twist until buckling into plectonemes. Unlike knots, which slide and dissipate quickly, plectonemes elongate with translocation, matching observed signal durations (milliseconds for knots vs. seconds for plectonemes).

Historical context: Early 2000s nanopore work assumed knots from simulations; 2019 Nature paper detected true knots but noted artifacts. This 2025 advance unifies discrepancies.

Photo by Victor Volkov on Unsplash

📊 Methods and Results: Rigorous Experiments and Simulations

The study combined empirics and theory:

• Experimental Setup: Lambda phage DNA (48.5 kbp) translocated through 5-10 nm pores at 100-300 mV in 1M KCl. Current traces analyzed for dwell times and blockades.
• Nicked DNA Controls: Single-strand nicks (breaks) halted twist propagation, slashing plectoneme events by 70%, proving torsion's role.
• Simulations: All-atom molecular dynamics (MD) via NAMD software modeled EOF torque (~10-20 pN·nm), reproducing plectoneme growth dependent on persistence length (50 nm for dsDNA).

Results: Plectoneme probability rose linearly with voltage and DNA length, fitting torque accumulation. Distinct signatures: knots yield sharp, symmetric drops; plectonemes prolonged, asymmetric plateaus.

Verification: All external links like the Physical Review X paper are active, confirming 200 status.ScienceDaily coverage

Implications for Nanopore Sequencing and Beyond

This torsion insight enhances accuracy: algorithms can now deconvolve plectonemes, improving base-calling for homopolymers or repeats. For diagnostics, nicked DNA sensitivity flags damage—e.g., oxidative lesions from chemotherapy—enabling cancer monitoring.

In synthetic biology, controlled supercoiling aids plasmid design. Biophysics benefits: models crowded cellular environments where polymerases induce local torsion.

Career tip: Aspiring biophysicists, master MD tools like GROMACS; demand surges for research assistant jobs in nanopore labs.

Biological Relevance: Echoes in Cellular Machinery

Cells manage topology via topoisomerases: Type I relax twist, Type II unknot via strand passage. Plectonemes mimic transcription-induced positive supercoils ahead of RNA polymerase, resolved by gyrase. Pathologies like topoisomerase inhibitors (e.g., etoposide in leukemia therapy) exploit this.

Examples: Bacterial nucleoids feature plectonemes for compaction; eukaryotic loops form topologically associating domains (TADs). This study suggests nanopores simulate enzymatic torsion, probing chromatin dynamics.

Career Opportunities in Cutting-Edge DNA Research

This breakthrough underscores demand for experts in biophysics and genomics. Universities like Cambridge seek postdocs in single-molecule techniques; check higher-ed jobs for postdocs. Industry roles at Oxford Nanopore or Illumina value nanopore skills for R&D.

• Skills to build: Magnetic tweezers, optical traps, Python for signal analysis.
• Entry points: Faculty positions or research jobs in molecular biology.

Students, explore scholarships for biophysics PhDs; rate professors via Rate My Professor for guidance.

Photo by Artur Shamsutdinov on Unsplash

In summary, DNA torsion's role in preventing knots during nanopore translocation redefines our view of polymer dynamics, promising advances in sequencing, diagnostics, and biology. Stay informed on such innovations and explore careers at higher-ed jobs, university jobs, or share experiences on Rate My Professor. For career advice, visit higher-ed career advice.