New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility.

Publisher Summary This chapter discusses the unusual DNA structures with known sequence dependencies such as bends, and the relatively new concept of sequence-directed structural softness or flexibility, and correlates these with protein structural motifs wherever possible. It shows that analyses of consensus binding sequences in DNA can provide important clues both for identifying possible roles of localized DNA structures (or microstructures) in protein-DNA interactions and for interpreting these roles in structure-function terms. An important consequence is that most biological processes are modulated at the molecular level by the interactions of regulatory proteins with themselves or other proteins, and with their characteristic operator DNA. A corollary is that the trajectory of the DNA is precisely defined, particularly in large, multi-subunit nucleoprotein complexes. Because both of these factors are highly site specific, they can confer a corresponding level of site specificity to the processes they control, which include transcriptional regulation, the action of hormone receptors, and certain types of site-specific recombination, including the precise insertion of viral DNA into host genomes.