Forces maintaining the DNA double helix and its complexes with transcription factors

Precise calorimetric studies of DNA duplexes of various length and composition have revised several long-held beliefs about the forces holding together the double helix and its complexes with the DNA binding domains (DBDs) of transcription factors. Heating DNA results in an initial non-cooperative increase of torsional oscillations in the duplex, leading to cooperative dissociation of its strands accompanied by extensive heat absorption and a significant heat capacity increment. The enthalpy and entropy of duplex dissociation are therefore temperature dependent quantities. When compared at the same temperature the enthalpic and entropic contributions the CG base pair are less than that of the AT pair - not more as previously assumed from the extra hydrogen bond. Thus the stabilizing effect of the CG base pair comes from its smaller entropic contribution. The greater enthalpic and entropic contributions of the AT pair result from water fixed by its polar groups in the minor groove of DNA. This water is also responsible for the so-called "nearest-neighbour effects" used to explain the sequence-dependent stabilities of DNA duplexes. Removal of this water by binding DBDs to the minor groove makes this an entropy driven process, in contrast to major groove binding which is enthalpy driven. Analysis of the forces involved in maintaining DNA-DBD complexes shows that specificity of DBD binding is provided by enthalpic interactions, while the electrostatic component that results from counter-ion dispersal is entirely entropic and not sequence-specific. Although the DNA double helix is a rather rigid construction, binding of DBDs to its minor groove often results in considerable DNA bending without the expenditure of significant free energy. This suggests that the rigidity of the DNA duplex comes largely from the water fixed to AT pairs in the minor groove, the loss of which then enables sharp bending.