  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 Poerschke indicate the existence of a sliding process,
permitting the rapid transition between different relative strand positions
[Biophys. Chem. 2 (1974) 83]. Here, we use a detailed theoretical model to
study the basepairing dynamics of periodic and nearly periodic DNA. As
suggested by Poerschke, 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 less than
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.
