Abstract
Many positively charged molecules are known to loop and condense DNA. These positively charged condensing agents bind to the negatively charged DNA and are thought to use electrostatic interactions to bend the DNA. Here, we propose a general theory for this charge-assisted looping process, develop a computational model to support the theory, and test the model against experimental data. To computationally model charge-assisted looping, we first discretize the DNA into a piecewise linear curve. Then, we apply the worm-like chain model to the curve to simulate thermal fluctuations of the DNA.
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