Effects of DNA-distorting proteins on DNA elastic response

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Abstract
Many DNA-binding proteins distort the double helix, and therefore can be studied using single-molecule experiments to investigate how they modify double-helix polymer elasticity. We study this problem theoretically using discrete wormlike-chain models to describe the mechanics of protein-DNA composites. We consider the cases of nonspecific and specific (sequence-targeted) binding. We find that, in general, proteins which bend DNA can be described in terms of a reduction of bending persistence length as long as the binding strength is relatively weak (well below the dissociation point). For strong binding, the force response depends strongly on the bending stiffness of the DNA-protein complex. Since most DNA-bending proteins will cause local DNA untwisting, we also show how the constraint of DNA linking number modifies the observed elastic response. We also show how essentially the same model may be used to describe the binding of proteins and drugs which stiffen and stretch the double helix.