Entropic elasticity of DNA with a permanent kink

Abstract

Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for theories of DNA elasticity which include helix-deforming proteins. Previous theoretical work on bent DNA has examined a long DNA molecule with many nonspecifically binding proteins. However, recent experiments used relatively short DNA molecules with a single, well-defined bend site. Here we develop a simple theoretical description of the effect of a single bend. We then include the description of the bend in the finite worm like chain model (FWLC) of short DNA molecules attached to beads. We predict how the DNA force-extension relation changes due to formation of a single permanent kink, at all values of the applied stretching force. Our predictions show that high-resolution single-molecule experiments could determine the bend angle induced upon protein binding.