Looping charged elastic rods: applications to protein-induced DNA loop formation |
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Authors: | A G Cherstvy |
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Institution: | 1.Theorie-2, Institut für Festk?rperforschung,Forschungszentrum Jülich,Jülich,Germany;2.Max-Planck-Institut für Physik komplexer Systeme,Dresden,Germany |
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Abstract: | We analyze looping of thin charged elastic filaments under applied torques and end forces, using the solution of linear elasticity
theory equations. In application to DNA, we account for its polyelectrolyte character and charge renormalization, calculating
electrostatic energies stored in the loops. We argue that the standard theory of electrostatic persistence is only valid when
the loop’s radius of curvature and close-contact distance are much larger than the Debye screening length. We predict that
larger twist rates are required to trigger looping of charged rods as compared with neutral ones. We then analyze loop shapes
formed on charged filaments of finite length, mimicking DNA looping by proteins with two DNA-binding domains. We find optimal
loop shapes at different salt amounts, minimizing the sum of DNA elastic, DNA electrostatic, and protein elastic energies.
We implement a simple model where intercharge repulsions do not affect the loop shape directly but can choose the energy-optimized
shape from the allowed loop types. At low salt concentrations more open loops are favored due to enhanced repulsion of DNA
charges, consistent with the results of computer simulations on formation of DNA loops by lac repressor. Then, we model the
precise geometry of DNA binding by the lac tetramer and explore loop shapes, varying the confined DNA length and protein opening
angle. The characteristics of complexes obtained, such as the total loop energy, stretching forces required to maintain its
shape, and the reduction of electrostatic energy with increment of salt, are in good agreement with the outcomes of more elaborate
numerical calculations for lac-repressor-induced DNA looping. |
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