Molecular forces: The surprising stretching behavior of DNA

Date:
August 5, 2020
Source:
Vienna University of Technology
Summary:
Experiments with DNA molecules show that their mechanical
properties are completely different from what those of macroscopic
objects - and this has important consequences for biology and
medicine. Scientists has now succeeded in explaining these
properties in detail by combining ideas from civil engineering
and physics.



FULL STORY ==========================================================================
When large forces, for example in bridge construction, act on a heavy
beam, the beam will be slightly deformed. Calculating the relationship
between forces, internal stresses and deformations is one of the
standard tasks in civil engineering. But what happens when you apply
these considerations to tiny objects -- for example, to a single DNA
double helix?

========================================================================== Experiments with DNA molecules show that their mechanical properties
are completely different from what those of macroscopic objects -- and
this has important consequences for biology and medicine. Scientists
at TU Wien (Vienna) has now succeeded in explaining these properties in
detail by combining ideas from civil engineering and physics.

Unexpected behaviour at the molecular level At first glance, you might
think of the DNA double helix as a tiny little spring that you can
simply stretch and compress just like you would an ordinary spring. But
it is not quite that simple: "If you stretch a piece of DNA, you would
actually expect the number of turns to decrease. But in certain cases
the opposite is true: "When the helix gets longer, it sometimes twists
even more," says civil engineer Johannes Kalliauer from the Institute of Mechanics of Materials and Structures at TU Wien. "Apart from that, DNA molecules are much more ductile than the materials we usually deal with
in civil engineering: They can become 70% longer under tensile stress."
These strange mechanical properties of DNA are of great importance for
biology and medicine: "When the genetic information is read from the
DNA molecule in a living cell, the details of the geometry can determine whether a reading error occurs, which in the worst case can even cause
cancer," says Johannes Kalliauer. "Until now, molecular biology has
had to be satisfied with empirical methods to explain the relationship
between forces and the geometry of DNA." In his dissertation, Johannes Kalliauer got to the bottom of this issue -- and he did so in the form of
a rather unusual combination of subjects: His work was supervised on the
one hand by the civil engineer Prof. Christian Hellmich, and on the other
hand by Prof. Gerhard Kahl from the Institute of Theoretical Physics.

"We used molecular dynamics methods to reproduce the DNA molecule on
an atomic scale on the computer," explains Kalliauer. "You determine
how the DNA helices are compressed, stretched or twisted -- and then you calculate the forces that occur and the final position of the atoms." Such calculations are very complex and only possible with the help of large supercomputers -- Johannes Kalliauer used the Vienna Scientific Cluster
(VSC) for this purpose.

That way, the strange experimental findings could be explaned -- such
as the counterintuitive result that in certain cases the DNA twists even
more when stretched. "It's hard to imagine on a large scale, but at the
atomic level it all makes sense," says Johannes Kalliauer.

Strange intermediate world Within the atomic models of theoretical
physics, interatomic forces and distances can be determined. Using certain rules developed by the team based on principles from civil engineering,
the relevant force quantities required to describe the DNA strand
as a whole can then be determined -- similar to the way the statics
of a beam in civil engineering can be described using some important cross-sectional properties.

"We are working in an interesting intermediate world here, between
the microscopic and the macroscopic," says Johannes Kalliauer. "The
special thing about this research project is that you really need
both perspectives and you have to combine them." This combination of significantly different size scales plays a central role at the Institute
for Mechanics of Materials and Structures time and again. After all,
the material properties that we feel every day on a large scale are
always determined by behaviour at the micro level. The current work,
which has now been published in the "Journal of the Mechanics and Physics
of Solids," is intended to show on the one hand how to combine the large
and the small in a scientifically exact way, and on the other hand to
help to better understand the behaviour of DNA -- right down to the
explanation of hereditary diseases.


========================================================================== Story Source: Materials provided
by Vienna_University_of_Technology. Original written by Florian
Aigner. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Johannes Kalliauer, Gerhard Kahl, Stefan Scheiner, Christian
Hellmich. A
new approach to the mechanics of DNA: Atoms-to-beam homogenization.

Journal of the Mechanics and Physics of Solids, 2020; 143: 104040
DOI: 10.1016/j.jmps.2020.104040 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/08/200805102012.htm

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