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Gene expression and regulation rely on an apparently finely tuned set ofreactions between some proteins and DNA. Such DNA-binding proteins have to findspecific sequences on very long DNA molecules and they mostly do so in absenceof any active process. It has been rapidly recognized that to achieve this taskthese proteins should be efficient at both searching (i.e. sampling fastrelevant parts of DNA) and finding (i.e. recognizing the specific site). Atwo-mode search and variants of it have been suggested since the 70s to explaineither a fast search or an efficient recognition. Combining these twoproperties at a phenomenological level is however more difficult as they appearto have antagonist roles. To overcome this difficulty, one may simply need todrop the dihcotomic view inherent to the two-mode search and look morethoroughly at the set of interactions between DNA-binding proteins and a givenDNA segment either specific or non-specific. This chapter demonstrates that, indoing so in a very generic way, one may indeed find a potential reconciliationbetween a fast search and an efficient recognition. Although a lot remains tobe done, this could be the time for a change of paradigm

Protein-DNA electrostatics: toward a new paradigm for protein sliding