1. Troy A. Lionberger¹,²,*,

2. Davide Demurtas³,⁴,
3. Guillaume Witz³,⁵,
4. Julien Dorier³,
5. Todd Lillian²,⁶,
6. Edgar Meyhöfer¹,² and
7. Andrzej Stasiak³,*

+Author Affiliations

1. 
   
   ¹Cellular and Molecular Biology Program, ²Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA, ³Centre Intégratif de Génomique, Faculté de Biologie et de Médecine, Université de Lausanne, ⁴Centre Interdisciplinaire de Microscopie Électronique, École Polytechnique Fédérale de Lausanne, ⁵Laboratoire de Physique de la Matière Vivante, Faculté des Sciences de Base, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland and ⁶Department of Mechanical Engineering, Texas Tech University, Box 41021, Lubbock TX 79409, USA

1. *To whom correspondence should be addressed. Tel: 041 21 692 42 82; Fax: 041 21 692 41 15; Email: Andrzej.Stasiak@unil.ch
2. Correspondence may also be addressed to Troy Lionberger. Tel: 001 734 764 9421; Fax: 001 734 615 6647; Email: talionberger@gmail.com

• Received June 29, 2011.
• Revision received July 28, 2011.
• Accepted July 28, 2011.

Abstract

In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are capable of relieving mechanical stress within the template. DNA minicircles offer a robust model system to study stress-induced DNA structures. Using DNA minicircles on the order of 100 bp in size, we have been able to control the bending and torsional stresses within a looped DNA construct. Through a combination of cryo-EM image reconstructions, Bal31 sensitivity assays and Brownian dynamics simulations, we have been able to analyze the effects of biologically relevant underwinding-induced kinks in DNA on the overall shape of DNA minicircles. Our results indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small regulatory DNA loops, minimize their free energy by undergoing sequential, cooperative kinking at two sites that are located about 180° apart along the periphery of the minicircle. This novel form of structural cooperativity in DNA demonstrates that bending strain can localize hyperflexible kinks within the DNA template, which in turn reduces the energetic cost to tightly loop DNA.