6 Protein–nucleic acid interactions
The biological functions of both DNA and RNA are dependent on complex, and sometimes transient, three-dimensional nucleoprotein structures. It is in such structures that the enzymatic manipulation of DNA in the essential biological processes such as DNA replication, transcription and recombination occur, and it is important to understand the interactions that drive these processes. Whether it is the activity of enzymes associated with DNA, such as DNA topoisomerases, or the packaging of DNA on the histone proteins in the nucleosome, or DNA transcription with all its associated proteins such as RNA polymerase and transcription factors, the interactions of nucleic acids with proteins are particularly important to the cell. The type of interaction between proteins and DNA ranges from highly site-specific to completely non-specific. In this section, we will outline the principles of how these two types of interactions occur.