Elastic Rod Model of a DNA Loop in the <span class="aps-inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><mi mathvariant="italic">Lac</mi></math></span> Operon

Alexander Balaeff; L. Mahadevan; Klaus Schulten

doi:10.1103/PhysRevLett.83.4900

Elastic Rod Model of a DNA Loop in the $Lac$ Operon

Alexander Balaeff, L. Mahadevan, and Klaus Schulten

Phys. Rev. Lett. 83, 4900 – Published 6 December 1999

Abstract

We use the theory of elasticity to compute the shape of the DNA loop bridging the gap in the crystal structure of the lac repressor-DNA complex. The Kirchhoff system of equations with boundary conditions derived from the crystal structure is solved using a continuation method. This approach can be applied effectively to find coarse-grained conformational minima of DNA loops.

Received 22 June 1998

DOI:https://doi.org/10.1103/PhysRevLett.83.4900

Authors & Affiliations

Alexander Balaeff^1,2, L. Mahadevan³, and Klaus Schulten^1,2,4

¹Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
²Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
³Department of Mechanical Engineering, MIT, Cambridge, Massachusetts 02139
⁴Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801