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We compute for the first time the effects of excluded volume on theprobability for double-stranded DNA to form a loop. We utilize a Monte-Carloalgorithm for generation of large ensembles of self- avoiding worm-like chains,which are used to compute the J-factor for varying lengthscales. In theentropic regime, we confirm the scaling-theory prediction of a power-law dropoff of -1.92, which is significantly stronger than the -1.5 power-law predictedby the non-self-avoiding worm-like chain model. In the elastic regime, we findthat the angle-independent end-to-end chain distribution is highly anisotropic.This anisotropy, combined with the excluded volume constraints, lead to anincrease in the J-factor of the self-avoiding worm-like chain by about half anorder of magnitude relative to its non-self-avoiding counterpart. This increasecould partially explain the anomalous results of recent cyclizationexperiments, in which short dsDNA molecules were found to have an increasedpropensity to form a loop.

Self-avoiding worm-like chain model for dsDNA loop formation