Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2004-06-10
Biophysical Journal, 88, 2752-2765, (2005).
Physics
Condensed Matter
Soft Condensed Matter
15 pages, 12 figures
Scientific paper
10.1529/biophysj.104.047340
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.
Danilowicz Claudia
Kafri Yariv
Lucks Julius B.
Nelson David R.
Prentiss Mara
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