DNA as a Programmable Viscoelastic Nanoelement

• Published in: Biophysical journal 2005-12, Vol.89 (6), p.3846-3855
• Main Authors: Neher, Richard A., Gerland, Ulrich
• Format: Article
• Language: English
• Subjects: Base Pairing; Biophysical Theory and Modeling; Computer Simulation; Computers, Molecular; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - ultrastructure; DNA polymerase; Elasticity; Information Storage and Retrieval - methods; Models, Chemical; Molecular biology; Nanostructures - analysis; Nanostructures - chemistry; Nanostructures - ultrastructure; Nanotechnology; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA - methods; Stress, Mechanical; Studies; Viscosity
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.105.068866

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 ∼ 1/ N is induced in a double strand of length N, provided f is larger than a threshold f c. Conversely, if the strands are initially misaligned, they realign even against an external force f < f c. 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.