A model of sequence-dependent protein diffusion along DNA.
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. Hydrogen bonds formed at the target site are used as the main sequence-dependent interaction between protein and DNA. The resulting dynamical properties and the possibility of an experimental verification are discussed in details. We show that, while at large times the process reaches a linear diffusion regime, it initially displays a sub-diffusive behavior. The sub-diffusive regime can last sufficiently long to be of biological interest.
Dipartimento di Fisica "E.R. Caianiell" and INFM, Università di Salerno, Baronissi (SA), Italy  ; Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, case courrier 121, 4 Place Jussieu, 75252 Paris cedex 05, France.
Maria
M
Barbi
Christophe
C
Place
Vladislav
V
Popkov
Mario
M
Salerno
DNA-protein interaction; anomalous diffusion; dynamical models; sliding; target site