Research Casts New Light on 3D Structure of DNA

Using a multidisciplinary approach, an international team of scientists has revealed in never-before-seen detail the 3D structure of biologically active DNA.

This image shows the structure of DNA calculated with the supercomputer simulations (in color) superimposed upon the electron cryo-tomography data (in white or yellow); one can see that the familiar double helix has been either simply bent into a circle or twisted into a figure-8. Image credit: Thana Sutthibutpong.

(Sci-News.com) The team, led by scientists at Baylor College of Medicine (BCM) in Houston, Texas, imaged various DNA shapes – including figure-8s – using a cutting-edge technique called electron cryo-tomography, and then examined them using supercomputer simulations.

“When Watson and Crick described the DNA double helix, they were looking at a tiny part of a real genome, only about one turn of the double helix,” said Dr Sarah Harris of the University of Leeds, UK, a co-author on a study that appeared in the journal Nature Communications Monday.

“This is about 12 DNA base pairs, which are the building blocks of DNA that form the rungs of the helical ladder.”

“Our study looks at DNA on a somewhat grander scale – several hundreds of base pairs – and even this relatively modest increase in size reveals a whole new richness in the behavior of the DNA molecule,” she added.

Dr Harris and her colleagues examined tiny DNA minicircles, now known as ‘MiniVectors,’ containing only 336 base pairs.

“Previous studies were on short fragments of linear DNA, but human DNA is constantly moving around in your body – and it coils and uncoils,” said lead co-author Prof. Lynn Zechiedrich, of the BCM.

“You can’t coil linear DNA and study it, so we had to make circles so the ends would trap the different degrees of winding.”

Each cell in the human body holds about a meter of DNA – around 10 million times longer than the tiny circles the scientists made.

They wound or unwound a single turn at a time the DNA double helix comprising their circles and asked how the winding changed what the circles looked like, using very powerful microscopes.

The scientists devised a test to make sure that the tiny twisted up DNA circles that they made in the lab were biologically active. They used purified human topoisomerase II alpha, an essential enzyme that manipulates DNA and important target of anticancer drugs.

This enzyme relieved the winding stress from all of the supercoiled minicircles, even the most coiled ones, which is its normal job in the human body.

This result means that the circles must look and act like the much longer DNA that topoisomerases encounter in human cells.

“These enzymes don’t do anything to linear DNA because it’s not coiled up,” said study co-author Dr Daniel Catanese, Jr., also of the BCM.

The scientists used the electron cryo-tomography to provide the first 3D structures of individual DNA molecules. They saw that the coiling caused many different shapes.

“Some of the circles had sharp bends, some were figure-8s, and others looked like racquets or sewing needles,” said lead author Dr Rossitza Irobalieva, also of the BCM.

“Some looked like rods because they were so coiled.”

The static images were then compared to and matched with shapes generated in supercomputer simulations. These simulated images provided a higher-resolution view of the DNA and show how its dynamic motion makes its shape constantly change to form a myriad of structures.

The electron cryo-tomography of the small DNA circles also revealed another surprise finding.

Base pairs in DNA are like a genetic alphabet, in which the letters on one side of the DNA double helix only pair with a particular letter on the other side.

While the team expected to see the opening of base pairs – that is, the separation of the paired letters in the genetic alphabet – when the DNA was under-wound, they were surprised to see this opening for the over-wound DNA.

This is because over-winding is supposed to make the DNA double helix stronger.

“This disruption of base pairs may cause flexible hinges, allowing the DNA to bend sharply, perhaps helping to explain how a meter of DNA can be jammed into a single human cell,” the scientists said.

“The next step is to start adding the other components of the cell or anticancer drugs to see how the DNA shapes change,” said co-author Dr Jonathan Fogg, of the BMC.

“We are sure that supercomputers will play an increasingly important role in drug design. We are trying to do a puzzle with millions of pieces, and they all keep changing shape,” Dr Harris concluded.

Source – Sci-News.com

Reference

Irobalieva RN, Fogg JM, Catanese DJ, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L. (2015) Structural Diversity of supercoiled DNA. Nature Comm [Epub ahead of print]. [article]