DNA Coiling Prevents Knots

DNA forms coils when passing through nanopores,
rather than forming messy knots: a finding that could
influence future advances in genomics and biosensing.

 

Not Knots: How the Hidden Order in DNA Coils
Overturns Decades of Biological Assumptions

by Dr. Sarah Buckland-Reynolds

Deoxyribonucleic Acid (DNA) has been the subject of fascination for scientists ever since its structure was first discovered in 1953 by James Watson and Francis Crick. That breakthrough revealed the famous double helix, a twisting ladder-like molecule that encodes the instructions for life itself. Since then, DNA has remained central to biology, genetics, medicine, and even technology, widely described as the “molecule of life” because it carries the genetic blueprint of every living organism.

Among the topics of fascination was the changing behaviour of DNA when interfaced with nanopore technology, which is used for sequencing and diagnostics. For decades, the observation of irregular electrical signals when DNA passed through nanopores led to the longstanding view that this process forms ‘knots’, much like a shoelace snagging when pulled through a narrow hole.

A new research paper overturns decades of assumptions about DNA knot formation.

Torsion-Driven Plectoneme Formation During Nanopore Translocation of DNA Polymers (Zheng et al., Physical Review X, 12 Aug 2025).  The related press release from Cambridge University, “Scientists Were Wrong for Decades About DNA Knots, reproduced in Science Daily on February 2026, further underscores how new evidence can force a substantial rethinking of molecular dynamics.

This discovery goes far beyond a technical correction; rather, it highlights that DNA is not a fragile polymer that tangles randomly when stressed, but its resilience and efficiency undermine the notion of being blindly evolved. This DNA coil discovery adds to the list of publications exposing how evolutionary worldviews, with their tendency to assume inefficiency and randomness, can mislead science for decades.

DNA Structure Unravels Design Once Again: Coils vs. Knots

The Cambridge team, led by researcher Fei Zheng, built on decades of research assessing the dynamics of polymer translocation through nanopores, reflecting the central role that DNA transport through nanoscale pores plays in shaping many biological processes, including bacterial gene exchange and viral infection.

The traditional view in polymer physics, grounded in statistical mechanics, predicts that long polymers are likely to form knots when passing through a narrow opening. However, Zheng et al., combining detailed experiments with computer simulations, revealed a completely different mechanism for DNA translocation, showing that DNA defies the predicted behaviour of regular polymers. Instead of forming knots, electrically driven water flow exerts torque on the DNA strand, causing it to rotate. This torque propagates along the molecule, forming coils instead of knots. In the words of lead author Dr. Fei Zheng, he explained in the press release:

“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.”

These coil structures (called ‘plectonemes’) leave distinctive electrical fingerprints that have several functional advantages over the pre-supposed knot structures, including:

• Superior structural organization: Plectonemes, being coiled superstructures, help compact DNA into manageable forms. Without such coiling, the long DNA molecule would be unwieldy and prone to damage.
• Regulation of accessibility: By twisting and coiling, plectonemes influence which regions of DNA are exposed to enzymes and transcription machinery. This means they play a role in gene regulation, turning certain genes “on” or “off” depending on how the DNA is folded.
• Mechanical resilience and stress absorption: Plectonemes help maintain the balance between DNA flexibility and stability by distributing mechanical stress along the DNA strand. Rather than breaking under tension, the molecule can absorb torsional strain by forming these coils, thereby protecting its structural integrity. Their ability to grow and persist under sustained torque enables DNA to withstand dynamic cellular processes without fragmentation.
• Signal persistence improving diagnostic potential: Unlike knots, which vanish quickly, plectonemes linger and leave distinctive electrical fingerprints. This persistence allows researchers to detect them and use them as markers of DNA’s physical state to detect DNA damage or structural variations.
• Cellular stress response: In living cells, enzymes such as topoisomerases and polymerases generate torsional stress. Plectonemes are part of how DNA accommodates and responds to this stress, ensuring replication and transcription proceed smoothly.

By contrast, knots would not be an ideal design for DNA. Knots tighten under tension, concentrating stress, and increasing the likelihood of strand damage. They can obstruct replication and transcription machinery and impede enzymes such as polymerases and helicases, thereby disrupting essential processes including replication and repair.

Alignment with Irreducible Complexity

The functionality of plectonemes provides a prime example of irreducible complexity, as it depends on multiple interdependent processes. Because DNA coiling naturally occurs in various biological processes, including gene regulation and chromosomal folding, examining whether intermediate stages of plectoneme formation could arise through gradual intermediate steps that retain functional value. This issue is directly relevant to debates about the origin of complex molecular features. For plectonemes to be functional, it requires the following conditions:

• Intact DNA capable of transmitting twist
• Liquid that moves around the pore to produce torque
• Pulling forces that drive translocation

A partial system lacking any of these components would result in the failure of plectoneme formation. Zheng and colleagues demonstrated this experimentally by introducing “nicks” or blocks in the DNA strands to prevent the twist from spreading along the molecule. As the researchers noted:

“These interruptions prevented twist from spreading along the molecule and sharply reduced the formation of plectonemes.”

Steps blocking the propagation of these structures resulted in destruction of the coiling process, which has many adverse implications for DNA health. For example, if propagation is blocked, the stress builds locally, increasing the risk of strand breakage. Blocked plectonemes would also result in disrupted regulatory interactions, leading to misregulation of gene expression and other types of instability.

The coordinated requirements for effective plectoneme formation resemble what has been described as irreducible complexity: the system’s function depends on multiple interacting components whose disruption compromises the whole. Such interdependent systems cannot be explained by gradual evolutionary steps because partial versions are nonfunctional.

Evolutionary Theory in Knots Again…Exposing Faulty Assumptions

If the functionality of coiling versus knotting is so profound in living systems, how did this evade scientific enquiry for decades? One reason could be the underlying worldview of evolution. From an evolutionary perspective of origins, there is an expectation of randomness. Evolutionary frameworks would interpret biological systems as products of chance, prone to inefficiency and disorder, with knots fitting neatly into that narrative. The work of Zheng et al. underscores the importance of testing those assumptions directly rather than relying on theoretical extrapolation.

The distinction between DNA coils and knots therefore adds to a growing list of long-held assumptions. From an intelligent design perspective, this pattern is consistent with previous cases in which features once dismissed as evolutionary leftovers were later shown to have function. Examples include so-called “junk DNA,” which was once assumed to be useless genetic baggage, and “vestigial” organs, which were long viewed as evolutionary relics but have since been found to possess functional significance.

In each case, evolutionary assumptions of inefficiency blinded researchers to underlying function. Intelligent design, by contrast, anticipates that biological systems are purposeful, even when that purpose is not immediately understood.

Potential Innovations from the Discovery

Alongside their scientific find, Zheng et al. (2025) further recognized that this discovery of plectonemes opens several new frontiers in innovation. Among those listed include:

• Nanotechnology: Harnessing DNA’s torque transmission could inspire new molecular machines.
• Genomic Models: Understanding plectonemes refines models of chromosome organization and gene regulation.
• Improved Diagnostics: Since DNA breaks interfere with twist propagation, nanopores could detect subtle damage linked to disease.

Innovative applications are a clear indication of intelligent design worth copying for inventive purposes.

DNA and the Glory of God

The overturning of the DNA knot theory is yet another reminder that evolutionary assumptions of inefficiency can mislead science for decades. From “junk DNA” to vestigial organs and now to DNA coils, history shows that evolutionary assumptions dismissed as accidents often prove essential.

Beyond its biological implications, Zheng et al.’s study provides yet another amazing testimony to the wisdom of our Creator’s engineering of life. Consistent with Scriptural affirmation, we see that DNA reveals both intricacy and purpose. As Psalm 104:24 declares: “O Lord, how manifold your works! In wisdom have you made them all.”  Colossians 1:17 further proclaims: “He is before all things, and in him all things hold together.” DNA’s ability to transmit torsional stress and maintain structural integrity echoes this truth. The molecule that holds genetic information together reflects the deeper reality of Christ holding creation together.

This discovery reminds us that even at the microscopic level of life, God has built in remarkable resilience; resilience that can and one that can yield beneficial applications for society through scientific innovation. May we join the Psalmist in declaring: “I praise you, for I am fearfully and wonderfully made,” as even our DNA bears witness to the wonder of God’s design.

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Dr. Sarah Buckland-Reynolds is a Christian, Jamaican, Environmental Science researcher, and journal associate editor. She holds the degree of Doctor of Philosophy in Geography from the University of the West Indies (UWI), Mona with high commendation, and a postgraduate specialization in Geomatics at the Universidad del Valle, Cali, Colombia. The quality of her research activity in Environmental Science has been recognized by various awards including the 2024 Editor’s Award from the American Meteorological Society for her reviewing service in the Weather, Climate and Society Journal, the 2023 L’Oreal/UNESCO Women in Science Caribbean Award, the 2023 ICETEX International Experts Exchange Award for study in Colombia. and with her PhD research in drought management also being shortlisted in the top 10 globally for the 2023 Allianz Climate Risk Award by Munich Re Insurance, Germany. Motivated by her faith in God and zeal to positively influence society, Dr. Buckland-Reynolds is also the founder and Principal Director of Chosen to G.L.O.W. Ministries, a Jamaican charitable organization which seeks to amplify the Christian voice in the public sphere and equip more youths to know how to defend their faith.