partially neutralize the DNA charges and therefore contribute to duplex stability. These counter-ions are
displaced when the complex forms and so they affect the free energy of binding.
Classic examples of protein/DNA complexes (Figure 10.2) illustrate how a dimeric protein engages with
its DNA target. Both the protein and the DNA have twofold symmetry, often referred to as a palindrome
on the DNA, and each monomer inserts an -helix into the DNA major groove. Side chains from these
helices (not shown here) make equivalent hydrogen-bonding interactions with the bases in the two symmetry-
related DNA sites.
Protein–Nucleic Acid Interactions 385
Figure 10.2 Representative helical motifs and their docking into the grooves of DNA. (a) The helix-turn-helix motif
of the Drosophila engrailed protein (PDB: 1YSA). (b) Basic helix of the leucine zipper motif (PDB:
1YSA). (c) Glucocorticoid hormone receptor (PDB: 1GLU)
Figure 10.1 Space-filling representations of duplex nucleic acids. (a) The idealized A-form of DNA (PDB: 348D).
(b) An RNA–DNA heteroduplex from the crystal structure of yeast RNA polymerase II (see Section
10.7.2) (PDB: 1I6H). (c) The idealized B-form DNA (PDB: 1ILC). (d) A segment of the DNA from
the experimental structure of the nucleosome particle, illustrating its in-plane curvature (PDB: 1A0I).
The sugar–phosphate backbone of each duplex is coloured red and blue, respectively, and the
corresponding bases are pink and cyan. In the RNA–DNA duplex (b), the RNA backbone is red and
the DNA backbone is blue. The arrows indicate the principal grooves