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Backing out of the nanotunnel
Date:1/10/2012

increasingly being employed to investigate the secondary structures of RNA and DNA," Gerland points out. "Passage through narrow nanopores causes the sequence to unfold, and the dynamics of translocation provide insights into the structural features of the molecules, without the need to modify them by adding a fluorescent label. The technique is relatively new, and its potential has not yet been fully explored."

In the new study, he and his collaborators used a new experimental procedure, which allowed them to quantitatively describe the passage of simply structured polynucleotide sequences through nanopores, and develop a theoretical model that accounts for their findings. This level of understanding has not been achieved previously, because complicating factors such as interactions between the protein nanopore and the polynucleotide have had a significant influence on the measurements and made it difficult to predict the behavior of the test molecules.

Thanks to a clever change in experimental design, the impact of these factors has now been minimized. The trick is to perform the measurements on molecules as they translocate through the pore in reverse. First, the polynucleotide of interest is forced through the conical orifice from one side under the influence of an electrical potential. This causes its secondary structure to unfold and, as it emerges, the molecule refolds. An anchor at the end of the polynucleotide chain prevents it from passing completely through the pore onto the other side. For the return journey the potential is reversed, so that the process of unfolding now begins at the narrow end of the pore, and at this point the analysis is initiated.

"In contrast to the situation during forward translocation, no significant interactions appear to take place during the reverse trip," says Simmel.

On the basis of their experimental measurements, the researchers went on to construct a theoretical model that enabled
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Contact: Dr. Katrhin Bilgeri
kathrin.bilgeri@lmu.de
49-892-180-6938
Ludwig-Maximilians-Universitt Mnchen
Source:Eurekalert

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