DNA as a programmable viscoelastic nanoelement

Neher, Richard A. and Gerland, Ulrich. (2005) DNA as a programmable viscoelastic nanoelement. Biophysical Journal, 89 (6). pp. 3846-3855.

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Official URL: http://edoc.unibas.ch/54008/

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The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Pörschke indicate the existence of a sliding process, permitting the rapid transition between different relative strand positions. Here, we use a detailed theoretical model to study the basepairing dynamics of periodic and nearly periodic DNA. As suggested by Pörschke, DNA sliding is mediated by basepairing defects (bulge loops), which can diffuse along the DNA. Moreover, a shear force f on opposite ends of the two strands yields a characteristic dynamic response: An outward average sliding velocity v approximately 1/N is induced in a double strand of length N, provided f is larger than a threshold fc. Conversely, if the strands are initially misaligned, they realign even against an external force f < fc. These dynamics effectively result in a viscoelastic behavior of DNA under shear forces, with properties that are programmable through the choice of the DNA sequence. We find that a small number of mutations in periodic sequences does not prevent DNA sliding, but introduces a time delay in the dynamic response. We clarify the mechanism for the time delay and describe it quantitatively within a phenomenological model. Based on our findings, we suggest new dynamical roles for DNA in artificial nanoscale devices. The basepairing dynamics described here is also relevant for the extension of repetitive sequences inside genomic DNA.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Biophysical Society
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:01 Nov 2019 16:02
Deposited On:27 Nov 2017 07:21

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