  Under constant applied force, the separation of double-stranded DNA into two
single strands is known to proceed through a series of pauses and jumps. Given
experimental traces of constant-force unzipping, we present a method whereby
the locations of pause points can be extracted in the form of a pause point
spectrum. A simple theoretical model of DNA constant-force unzipping is
demonstrated to produce good agreement with the experimental pause point
spectrum of lambda phage DNA. The locations of peaks in the experimental and
theoretical pause point spectra are found to be nearly coincident below 6000
bp. The model only requires the sequence, temperature and a set of empirical
base pair binding and stacking energy parameters, and the good agreement with
experiment suggests that pause points are primarily determined by the DNA
sequence. The model is also used to predict pause point spectra for the
BacterioPhage PhiX174 genome. The algorithm for extracting the pause point
spectrum might also be useful for studying related systems which exhibit
pausing behavior such as molecular motors.
