Molecular force balance measurements reveal that dsDNA unbinds under force in rate dependent pathways
Christian H Albrecht 1*, Gregor Neuert 2, Robert A Lugmaier 3 and Hermann E Gaub 3
1 Ludwig-Maximilians-University Munich
2 Massachusetts Institute of Technology
3 Ludwig-Maximilians-University
* To whom correspondence should be addressed. E-mail: christian.hermann.albrecht{at}physik.uni-muenchen.de.
Submitted on November 8, 2007
Revised on December 7, 2007
Accepted on 24 January 2008
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Abstract |
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Strand separation of double stranded DNA (dsDNA) is a crucial step for essential cellular processes like recombination and transcription. By means of a molecular force balance we have analyzed the impact of different pulling directions and different force loading rates on the unbinding process of short dsDNA. At loading rates above 9·105 pN/s we found a marked difference in rupture probability for pulling the duplex in 3'-3'-direction compared to 5'-5'-direction indicating different unbinding pathways. We propose a mechanism where unbinding at low loading rates, is dominated by non-directional thermal fluctuations, whereas at high loading rates mechanical properties of the DNA become more important and reveal the asymmetry of the phosphoribose backbone. A model is proposed that explains the difference of 3'-3' and 5'-5' unbinding as a kinetic process, where the loading rate exceeds the relaxation time of DNA melting bubbles.
Key Words:
DNA, DNA fluctuations, RICM, differential force measurements, fluorescence, molecular force balance
