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Pause point spectra in DNA constant-force unzipping.
J D Weeks1, J B Lucks, Y Kafri
1Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
Biophysical Journal
|February 8, 2005
Summary
Researchers developed a method to identify DNA unzipping pause points using experimental data. A theoretical model shows pause locations depend mainly on DNA sequence, aiding studies of DNA and molecular motors.
Area of Science:
- Biophysics
- Molecular Biology
- Genomics
Background:
- Double-stranded DNA (dsDNA) separation under constant force involves pauses and jumps.
- Experimental data provides traces of dsDNA constant-force unzipping.
Purpose of the Study:
- To present a method for extracting pause point locations from experimental DNA unzipping traces.
- To develop a theoretical model for DNA constant-force unzipping and predict pause point spectra.
Main Methods:
- Extraction of pause point locations into a pause point spectrum from experimental data.
- Monte Carlo simulation of DNA unzipping to generate theoretical pause point spectra.
- Comparison of experimental and theoretical pause point spectra.
Main Results:
- A method to extract pause point spectra from experimental DNA unzipping traces was developed.
- A theoretical model accurately predicted pause point spectra for bacteriophage lambda-genome unzipping.
- Pause point locations below 6000 basepairs were found to be sequence-dependent.
Conclusions:
- The developed model and method accurately identify DNA unzipping pause points.
- DNA sequence is a primary determinant of pause point locations during constant-force unzipping.
- The pause point spectrum extraction algorithm may benefit research on molecular motors and other pausing systems.