ABSTRACT
In this chapter, the authors examine the special structural features of DNA-binding proteins and explore how these features enable a DNA-binding protein to attach to the genome, focusing in particular on the way in which a sequence-specific binding protein recognizes its attachment sites. They begin by studying the methods used to elucidate the structures of DNA-binding proteins and to identify their binding positions on a DNA molecule. Many prokaryotic and eukaryotic DNA-binding proteins utilize an HTH motif. In bacteria, HTH motifs are present in some of the best-studied regulatory proteins, which switch on and off the expression of individual genes. An example is the lactose repressor, which regulates expression of the lactose operon in Escherichia coli. RNA-binding proteins also have specific motifs that form attachments with RNA molecules, most of these acting in a sequence-independent manner.
