The energy of changing a DNA conformation is affected by many factors. For instance, the DNA can be
curved by selectively neutralizing charges on one surface, which happens if one surface of the DNA inter-
acts with a basic surface of a recognition protein. An important contribution to DNA conformation comes
from the energy required to change the base stacking, since stacking and hydrogen bonding of the bases are
key determinants of DNA structure.
The energy of DNA deformation contributes to indirect readout and, for a typical DNA–protein complex
interacting over five or six bases, is likely to be in the order of 5–20 kJ mol^1. In the case of the nucleo-
some, the calculated energy for DNA bending is 126 kJ mol^1 for 124 base pairs.^22 Indirect readout is thus
important for fine-tuning specificity. The different base steps have different stacking energies, with TpA
having the least stacking energy and GpC the greatest of the ten possible base steps. Correspondingly,
the most easily distorted base step is the TpA step, and this step commonly occurs in examples of indirect
read-out. Conformational variability occurs more frequently for steps in the order pyrimidine–purine
Protein–Nucleic Acid Interactions 401
Figure 10.10 A representative example of a non-specific protein–DNA complex. The BamHI restriction endonuclease,
showing the free state, bound to non-specific DNA and bound to specific DNA