Supercoiled DNA Is far more
Dynamic
than the “Watson-Crick” Double Helix
than the “Watson-Crick” Double Helix
Researchers have
imaged in unprecedented detail the three-dimensional structure of supercoiled
DNA, revealing that its shape is much more dynamic than the well-known double
helix.
Various DNA shapes, including figure-8s, were imaged using a
powerful microscopy technique by researchers at the Baylor College of Medicine
in the US , and then examined
using supercomputer simulations run at the University of Leeds
As reported online today in the journal Nature
Communications, the simulations also show the dynamic nature of DNA, which
constantly wiggles and morphs into different shapes – a far cry from the
commonly held idea of a rigid and static double helix structure.
Improving our understanding of what DNA looks like when it
is in the cell will help us to design better medicines, such as new antibiotics
or more effective cancer chemotherapies.
Dr Sarah Harris from the School
of Physics and Astronomy at the University of Leeds
The double helix shape has a firm place in the public's collective
consciousness. It is referenced in popular culture and often features in art
and design. But the shape of DNA isn’t always that simple.
Dr Harris said: “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. 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.”
There are actually about 3 billion base pairs that make up
the complete set of DNA instructions in humans. This is about a metre of DNA.
This enormous string of molecular information has to be precisely organised by
coiling it up tightly so that it can be squeezed into the nucleus of cells.
To study the structure of DNA when it is crammed into cells,
the researchers needed to replicate this coiling of DNA.
Dr Lynn Zechiedrich, the corresponding author for the study
from the Baylor College of Medicine, said: “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.”
To investigate how the winding changed what the circles
looked like, the researchers wound and then unwound the tiny DNA circles – 10
million times shorter in length than the DNA contained within our cells – a
single turn at a time.
The researchers devised a test to make sure that the tiny
twisted up DNA circles that they made in the laboratory acted in the same way
as the full-length DNA strands within our cells, when it is referred to as
‘biologically active’.
They used an enzyme called ‘human topoisomerase II alpha’
that manipulates the twist of DNA. The test showed that the enzyme relieved the
winding stress from all of the supercoiled circles, even the most coiled ones,
which is its normal job in the human body. This result means that the DNA in
the circles must look and act like the much longer DNA that the enzyme
encounters in human cells.
Dr Rossitza Irobalieva, the co-lead author on the
publication, who conducted the work while she was at Baylor, used
‘cryo-electron tomography’ – a powerful microscopy technique that involves
freezing biologically active material – to provide the first three-dimensional
images of individual circular DNA molecules. She saw that coiling the tiny DNA
circles caused them to form a zoo of beautiful and unexpected shapes.
“Some of the circles had sharp bends, some were figure-8s,
and others looked like handcuffs or racquets or even sewing needles. Some
looked like rods because they were so coiled,” said Dr Irobalieva.
The static images produced by the cryo-electron tomography
were then compared to and matched with shapes generated in supercomputer
simulations that were run at the University
of Leeds
The cryo-electron tomography of the tiny 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 researchers 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.
The researchers hypothesise that 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.
Dr Harris concludes: “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.”
[Link (which itself has another link to a 13 second long
video of moving, supercoiled DNA from computer simulation—this has to be seen to be
properly understood):]
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