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Pause Point Spectra in DNA Constant-Force Unzipping

J. D. Weeks ^*, J. B. Lucks , Y. Kafri ^*, C. Danilowicz ^*, D. R. Nelson ^* and M. Prentiss ^*

^* Department of Physics and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138

Correspondence: Address reprint requests to Julius B. Lucks, E-mail: lucks{at}fas.harvard.edu.

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 presented, which generates theoretical pause point spectra through Monte Carlo simulation of the unzipping process. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 basepairs for unzipping the bacteriophage -genome. The model only requires the sequence, temperature, and a set of empirical basepair binding and stacking energy parameters, and the good agreement with experiment suggests that pause point locations are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the bacteriophage X174 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.

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