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The DNA tug-o’-war –

Exploiting molecular forces to control the form of nanostructures

Munich, 03/19/2010

The ability to manipulate structures that have dimensions in the nanometer range (one millionth of a millimetre) in a controlled manner is at the heart of modern nanotechnology. Perhaps surprisingly, DNA is one of the most versatile tools available for use in this realm of the minuscule. DNA is found in linear and closed-circular forms in cells, and as such they can serve as component for the assembly of nanostructures of technological interest. The conformations adopted by DNA molecules depend on their intrinsic characteristics and the forces that act upon them. LMU researchers led by the biophysicist Professor Erwin Frey, in cooperation with colleagues based at the EPFL in Switzerland, have quantified the effects of these different factors on the shapes of DNA rings on surface. “We have been able to arrive at a quantitative description of DNA rings, so that we can now translate basic molecular characteristics like chain diameter and rigidity directly into nanoscopic parameters such as the form and the area occupied by polymer rings”, says Frey. “We hope that this detailed understanding of polymer behaviour will enable us to develop new sorts of nanostructures.” (Nanoletters online, 17 March 2010)

DNA is unique in its ability to serve as a scaffold upon which copies of itself can be assembled. As in biology, the molecule’s significance for nanotechnology derives from this capacity to act as a molecular template. However, the building blocks of interest in nanotechnology will often differ from those that make up the DNA in vivo. DNA is a polymer, a molecule made up of subunits, linked together in a chain. Like other biological polymers, DNA does not automatically lend itself to application for the development of nanostructures, and appropriate tuning of its properties requires a thorough understanding of the forces that determine the spatial conformations available to DNA molecules.

In geometrical terms, the simplest polymer form is the linear filament with two free ends. Closed rings represent the next step up in the scale of complexity. What form a semi-flexible polymer adopts is determined by the interplay between its intrinsic molecular attributes and the precise combination of forces that act upon it. Entropic forces favour disordered structures, and on their own these will cause a linear polymer to curl up into a random coil -- an effect that is opposed by the polymer’s stiffness, which limits its ability to bend. Furthermore, two polymer segments cannot occupy the same region of space simultaneously due to steric hindrance. This gives rise to the so-called excluded-volume effect. “We set out to define how the intrinsic physical attributes of the ring molecules influence the conformations they can adopt”, reports Frey. “These parameters are important because they will determine the effective form of the templates we can obtain.“ Frey’s team collaborated with Professor Giovanni Dietler’s group at the Laboratory for the Physics of Living Matter (EPFL) in Lausanne, who are specialists in the experimental preparation of effectively two-dimensional, semi-rigid DNA rings.

In their experiments, the researchers varied the length of the DNA strands in order to alter the magnitude of the elastic and entropic forces acting on them. Theoretical simulations (using ideal or “phantom” polymers that are allowed to overlap) then permitted them to estimate the size of the excluded-volume effect. “It turned out that when the rigidity of the molecule is low, entropic forces dominate and the rings curl up into cigar-shaped forms”, says Frey. “Greater intrinsic stiffness causes them to un-fold into extended ellipses. Our quantitative description of the conformations available to DNA rings enables us to derive nanoscopic parameters such as the form and volume of space occupied by polymer rings from fundamental factors such molecular rigidity. This should lead to further advances in the technological development of designed nanostructures.“ (suwe)

The project was accomplished within the Cluster of Excellence Nanosystems Initiative Munich“ (NIM) and was supported by the LMUinnovativ Initiative.

“Excluded volume effects on semiflexible ring polymers”,
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler, and Erwin Frey,
Nanoletters online, 17 March 2010

Professor Dr. Erwin Frey
Arnold-Sommerfeld-Center für Theoretische Physik und das “Center for NanoScience” (CeNS) der LMU München
Phone: +49 (0) 89 / 2180 – 4537
Fax: +49 (0) 89 / 2180 - 4538

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