The dependence of DNA supercoiling on solution electrostatics

• Published in: Acta biomaterialia Vol. 8; no. 6; pp. 2133 - 2143
• Main Authors: Argudo, David, Purohit, Prashant K.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.07.2012
• Subjects: Biological material; chemistry; DNA; DNA plectonemes; DNA, Superhelical; DNA, Superhelical - chemistry; electrostatic interactions; Electrostatics; energy; Entropy; Models, Theoretical; Multivalent counterions; Nucleic Acid Conformation; Solutions; Static Electricity; Thermal fluctuations; torque; Thermal fluctuations; Multivalent counterions; DNA plectonemes; Electrostatics; Biological material
• ISSN: 1742-7061; 1878-7568; 1878-7568
• DOI: 10.1016/j.actbio.2012.01.030

We develop an elastic–isotropic rod model for twisted DNA in the plectonemic regime. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuations. We apply our model to single-molecule experiments on a DNA molecule attached to a substrate at one end, while subjected to a tensile force and twisted by a given number of turns at the other end. The free energy of the DNA molecule is minimized subject to the imposed end rotations. We compute values of the torsional stress, radius, helical angle and key features of the rotation–extension curves. We also include in our model the end loop energetic contributions and obtain estimates for the jumps in the external torque and extension of the DNA molecule seen in experiments. We find that, while the general trends seen in experiments are captured simply by rod mechanics, the details can be accounted for only with the proper choice of electrostatic and entropic interactions. We perform calculations with different ionic concentrations and show that our model yields excellent fits to mechanical data from a large number of experiments. Our methods also allow us to consider scenarios where we have multiple plectonemes or a series of loops forming in the DNA instead of plectonemes. For a given choice of electrostatic and entropic interactions, we find there is a range of forces in which the two regimes can coexist due to thermal motion.