DNA as a programmable viscoelastic nanoelement.

ABSTRACT: 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

SUBMITTER: Neher RA 

PROVIDER: S-EPMC1366951 | biostudies-literature | 2005 Dec

REPOSITORIES: biostudies-literature