16 February 2021

First videos to show the helix of ‘dancing DNA’ developed by scientists

Videos allowing us to see for the first time how small circles of DNA adopt dance-like movements inside a cell have been developed by researchers at universities in Yorkshire.

  • Researchers from the Universities of Sheffield, Leeds and York have captured the highest resolution images of a single molecule of DNA ever taken 
  • Images combined with supercomputer simulations have made it possible to see the position of every single atom in the DNA and how it twists and writhes
  • Study reveals that as the DNA dances, it adopts exotic twisted and writhed shapes
  • Being able to observe DNA in such detail could help to accelerate the development of new gene therapies

Videos allowing us to see for the first time how small circles of DNA adopt dance-like movements inside a cell have been developed by researchers at universities in Yorkshire.

The footage, developed by a team of scientists from the Universities of Sheffield, Leeds and York, are based on the highest resolution images of a single molecule of DNA ever captured. They show in unprecedented detail how the stresses and strains that are placed on DNA when it is crammed inside cells can change its shape.

Previously scientists were only able to see DNA by using microscopes that are limited to taking static images. But now the Yorkshire team has combined advanced atomic force microscopy with supercomputer simulations to create videos of twisted molecules of DNA.

The images are so detailed it is possible to see the iconic double helical structure of DNA, but when combined with the simulations, the researchers were able to see the position of every single atom in the DNA and how it twists and writhes. 

Every human cell contains two metres of DNA. In order for this DNA to fit inside our cells, it has evolved to twist, turn and coil. That means that loopy DNA is everywhere in the genome, forming twisted structures which show more dynamic behaviour than their relaxed counterparts.

The team looked at DNA minicircles, which are special because the molecule is joined at both ends to form a loop. This loop enabled the researchers to give the DNA minicircles an extra added twist, making the DNA dance more vigorously. 

When the researchers imaged relaxed DNA, without any twists, they saw that it did very little. However, when they gave the DNA an added twist, it suddenly became far more dynamic and could be seen to adopt some very exotic shapes. These exotic dance-moves were found to be the key to finding binding partners for the DNA, as when they adopt a wider range of shapes, then a greater variety of other molecules find it attractive.  

Previous research from Stanford, which detected DNA minicircles in cells, suggests they are potential indicators of health and ageing and may act as early markers for disease.

As the DNA minicircles can twist and bend, they can also become very compact. Being able to study DNA in such detail could accelerate the development of new gene therapies by utilising how twisted and compacted DNA circles can squeeze their way into cells. 

Dr Alice Pyne, Lecturer in Polymers & Soft Matter at the University of Sheffield, who captured the footage, said: “Seeing is believing, but with something as small as DNA, seeing the helical structure of the entire DNA molecule was extremely challenging. 

The videos we have developed enable us to observe DNA twisting in a level of detail that has never been seen before.”

Dr. Agnes Noy, EPSRC Early Career Fellow and Lecturer at the University of York, who did the theoretical modelling in the study, said: "The computer simulations and microscopy images agree so well that they boost the resolution of experiments and enable us to track how each atom of the double helix of DNA dances."

Professor Lynn Zechiedrich from Baylor College of Medicine in Houston Texas, USA, who made the DNA minicircles used in the study said, “Dr. Pyne and her co-worker’s new AFM structures of our supercoiled minicircles are extremely exciting because they show, with remarkable detail, how wrinkled, bubbled, kinked, denatured, and strangely shaped they are which we hope to be able to control someday.”

Dr Sarah Harris, Associate Professor in the School of Physics and Astronomy at the University of Leeds, who supervised the research, said: “The laws of physics apply just as well to the tiny looped DNA as to sub-atomic particles and galaxies. We can use supercomputers to understand the physics of twisted DNA. This should help researchers such as Professor Zechiedrich design bespoke minicircles for future therapies.”

The study, Combining high-resolution atomic force microscopy with molecular dynamics simulations shows that DNA supercoiling induces kinks and defects that enhance flexibility and recognition, is published in Nature Communications. To access the paper, visit: https://rdcu.be/cfgtI

The research was also conducted as part of a collaboration with the John Innes Centre, Bruker, UCL, University of Liverpool and Birkbeck, University of London.

The images and video simulations can be viewed and downloaded from: https://drive.google.com/drive/folders/1V9LW9qnnOFr1bKZSnSErnbh5SDGjiQcc

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