Discontinuities at the DNA supercoiling transition

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 80, Issue 4, 2009, Pages

  Daniels, Bryan C ^a   Forth, Scott ^a   Sheinin, Maxim Y ^a   Wang, Michelle D ^a,b   Sethna, James P ^a  

^a School of Operations Research and Industrial Engineering   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABRUPT TRANSITION; APPLIED FORCES; CO-EXISTING STATE; DNA SUPERCOILING; ELASTIC ROD; EXPERIMENTAL EVIDENCE; PHENOMENOLOGICAL THEORY; SINGLE MOLECULE; SUPERCOILING;

DNA; NUCLEIC ACIDS;

GENES;

EID: 70350534421     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.80.040901     Document Type: Article

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18. As described in Ref. (see also supplemental material), C is renormalized to a smaller value by bending fluctuations. We use C calculated from the torque measured in the experiment, which gives its renormalized value.
19. See EPAPS Document No. E-PLEEE8-80-R06910 for supplemental material. For more information on EPAPS, see http://www.aip.org/pubservs/epaps.html.
20. The language of phase coexistence is approximate in that the finite barrier to nucleation in one-dimensional systems precludes a true (sharp) phase transition.
21. We have also explored increasing the entropic repulsion by a constant factor of up to 3. Though this does bring the torques closer to the experiment, the only other significant change is a decrease in F0 (data not shown)-specifically, this does not change the discussed discrepancies between the simulation and experiment.
22. Though the 4.2 kbp z0 data alone would be arguably consistent with the model predictions, the 2.2 kbp data highlights the discrepancy at small applied forces.