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Researchers have directly imaged two already-formed DNA double helices pairing side by side in the presence of divalent ions. High-resolution atomic force microscopy (AFM) revealed grooves on neighboring helices aligned against one another; atomistic simulations support a mechanism in which ions bridge their minor grooves. The result supports a model proposed more than 20 years ago, but it is not a movie of DNA zipping in real time—and it does not show the process happening in living cells.
What “DNA zipping” means in this study
The zipper is not the familiar formation of one DNA double helix from two strands. The researchers studied two DNA duplexes—each already a double helix—coming together and aligning along their lengths. In the proposed arrangement, grooves on one helix face grooves on the other.
The helical-alignment model behind this idea was proposed more than 20 years ago by Alexey Kornyshev and collaborators, according to the University of York. The new work adds direct structural images of paired DNA under controlled laboratory conditions.
How the researchers observed the pairing
AFM showed the grooves, not motion
The team used high-resolution atomic force microscopy to image purified DNA duplexes in the presence of divalent ions. The reported images resolve the major and minor grooves on adjacent molecules and show that strongly paired duplexes often align groove to groove. They are static observations, not a real-time recording of molecules zipping together. As Sheffield biophysicist Alice Pyne explained to ScienceAlert, static imaging made it possible to resolve and measure the individual grooves.
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Simulations suggested how the helices stay together
Alongside imaging, the researchers ran atomistic molecular dynamics simulations. These calculations support an interpretation in which positively charged divalent ions form bridges between the minor grooves of neighboring DNA duplexes, helping hold the molecules together. The images establish the groove-to-groove arrangement; the simulations provide evidence for a possible molecular explanation of that arrangement.
What the study confirms—and what it does not
The peer-reviewed study, “Imaging and mechanism of DNA–DNA recognition mediated by divalent ions,” reports direct visualization of DNA pairing in the presence of divalent ions and presents ionic bridging as a mechanism consistent with the observed alignment. Study co-lead author Agnes Noy told ScienceAlert that the images were the first visualization of the long-hypothesized idea. The authors describe the findings as a molecular framework for the helical-alignment model.
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The work does not establish that the same pairing occurs in living cells, where proteins and other cellular components also shape DNA organization. Nor does it prove that this mechanism causes genetic recombination or cancer. The University of York presents those biological connections as questions for future investigation, not conclusions demonstrated by these experiments.
Why sequence and ion type matter
The simulations indicate that DNA sequence can influence the stability and specificity of contacts, and that these effects vary with the ion. In nickel-ion simulations, the ScienceAlert report singles out the sequence GTAC as associated with particularly stable contacts. That is a result within the modeled system, not evidence that GTAC is a genomic hotspot: the study did not map such sites across genomes.
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Nickel ions were used for optimal spatial resolution of individual grooves in the AFM imaging; larger-area scans also examined pairing with magnesium and calcium, according to ScienceAlert. The results therefore should not be read as showing that all divalent ions, sequences, or biological conditions produce identical interactions.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.What to take from the finding
- Direct observation: AFM images show purified DNA double helices aligned groove to groove under controlled conditions.
- Mechanistic support: Atomistic simulations support ion bridges between minor grooves as an explanation for the pairing.
- Scope: The evidence supports a long-standing structural model; it does not demonstrate the mechanism in cells or establish a role in cancer or recombination.
The peer-reviewed article by Thomas E. Catley, Victor Velasco-Berrelleza, Daniel E. Rollins, Alice L. B. Pyne, and Agnes Noy appeared in Nucleic Acids Research 54(16), article gkag817. The institutional record lists online publication on 25 August 2026 and journal publication on 9 September 2026. Read the primary article for the methods and conclusions, or consult the White Rose Research Online record for its publication details.
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- Package includes five setsthe package list includes 5 x set of dna teaching model, providing multiple units for classroom rotation, group activities, or shared learning environments
- Package includes five setsthe package list includes 5 x set of dna teaching model, providing multiple units for classroom rotation, group activities, or shared learning environments
- Package includes five setsthe package list includes 5 x set of dna teaching model, providing multiple units for classroom rotation, group activities, or shared learning environments
- Package includes five setsthe package list includes 5 x set of dna teaching model, providing multiple units for classroom rotation, group activities, or shared learning environments
- Package includes five setsthe package list includes 5 x set of dna teaching model, providing multiple units for classroom rotation, group activities, or shared learning environments
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- √Principle: In a double-stranded DNA molecule, A=T, G=C. That is: A + G = T + C or A + C = T + G;
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- √Completed model measures 33cm [13"] high
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- √Note: Recommended for ages 14+
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