  Problems of search and recognition appear over different scales in biological
systems. In this review we focus on the challenges posed by interactions
between proteins, in particular transcription factors, and DNA and possible
mechanisms which allow for a fast and selective target location. Initially we
argue that DNA-binding proteins can be classified, broadly, into three distinct
classes which we illustrate using experimental data. Each class calls for a
different search process and we discuss the possible application of different
search mechanisms proposed over the years to each class. The main thrust of
this review is a new mechanism which is based on barrier discrimination. We
introduce the model and analyze in detail its consequences. It is shown that
this mechanism applies to all classes of transcription factors and can lead to
a fast and specific search. Moreover, it is shown that the mechanism has
interesting transient features which allow for stability at the target despite
rapid binding and unbinding of the transcription factor from the target.
