Strong cooperativity and inhibitory effects in DNA multi-looping processes

We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance of another. The underlying loop selection mechanism is analyzed by means of a Hamiltonian model from which the looping free energy and the corresponding repression level can be computed. We show significant differences between the probability of single and multiple loop formation. The consequences that these collective effects might have on gene regulation processes are outlined.