Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
Journal article, 2015

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.

Author

Mohammadreza Alizadehheidari

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry, Physical Chemistry

Erik Werner

University of Gothenburg

C. Noble

Lund University

M. Reiter-Schad

Lund University

Lena Nyberg

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry, Physical Chemistry

Joachim Fritzsche

Chalmers, Applied Physics, Chemical Physics

Bernhard Mehlig

University of Gothenburg

J. O. Tegenfeldt

Lund University

Tobias Ambjörnsson

Lund University

Fredrik Persson

Uppsala University

Fredrik Westerlund

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry, Physical Chemistry

Macromolecules

00249297 (ISSN) 15205835 (eISSN)

Vol. 48 3 871-878

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Subject Categories

Physical Sciences

DOI

10.1021/ma5022067

More information

Latest update

3/2/2018 9