We model the dynamics of a single, fluorescence-dyed DNA molecule in a nanochannel. When a single dsDNA molecule is placed in a nanochannel, its extension along the channel is up to 50% of its contour length, depending on the dimensions of the channel. This linear extension offers the possibility to study, e.g., the binding of site-specific proteins or the sequence-dependent melting of DNA, with the latter giving a coarse-grained representation of the sequence [W. Reisner et al., “Single Molecule Denaturation Mapping of DNA in Nanofluidic Channels.” Resubmitted to Nature Nanotechnology (2009)]. The resolution achieved with this approach has two limiting factors: The diffraction limit, which for isolated probes can be circumvented with FIONA, and thermal density fluctuations of the DNA in the channel. Density fluctuations make distances measured along the channel correspond to distances measured along the molecule in an unknown non-linear and random, time-dependent manner. This last problem can be circumvented if the non-linear correspondence between coordinates can be extracted from images at any point in time. To this end, we model the thermal motion of the molecule using linear elasticity theory combined with Boltzmann statistics. The thermal dynamics of the resulting model is consistent with movies of DNA displaying thermal density fluctuations.
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