Within living cells, many different proteins play important functional roles by binding to DNA. Some proteins bind to DNA but not in a sequence-specific manner. For example, histones are proteins important in the formation of chromosome structure. The positively charged histone proteins bind to the negatively charged phosphate groups in DNA. In addition, several other proteins interact with DNA but do not require a specific nucleotide sequence to carry out their function. For example, DNA polymerase, which catalyzes the synthesis of new DNA strands, does not bind to DNA in a sequencedependent way. By comparison, many other proteins do interact with nucleic acids in a sequence-dependent fashion. This means that a specific sequence of bases can provide a structure that is recognized by a particular protein. Throughout this textbook, the functions of many of these proteins will be described. Some examples include transcription factors that affect the rate of transcription and proteins that bind to origins of replication in bacteria. With regard to the threedimensional structure of DNA, where would you expect DNA-binding proteins to bind if they recognize a specific base sequence? What about DNA-binding proteins that do not recognize a base sequence?