Crystallographic studies have also shown that minor groove widthis instrumental in dictating hydration pat-
terns.The duplex d(CCAACGTTGG) 2 has a narrow minor groove that is about 4.2 Å wide and it has a spine
of hydration similar to that originally observed in the Dickerson–Drew sequence. The helix d(CCAA-
GATTGG) 2 sequence has a wider, 7.2 Å minor groove within which two side-by-side ribbons of water mol-
ecules are found. Interestingly, the sequence d(CCAGGCCTGG) 2 has a minor groove of intermediate width,
which is occupied only very sparsely by ordered water molecules and which does not possess either of the two
other hydration patterns. It has been suggested that the A T minor groove spine of hydration is important in
stabilization of B-DNA against the B→A conformational transition. High A T content DNA is associated
with narrow minor grooves and resistance to the B→A transition, which has led to the assertion that the spine
of hydration is more effective at stabilization of B-DNA than the two parallel ribbons of waters (Section 2.2.4).
9.5.1 Cation Binding in the Minor Groove
The seminal work of Dickerson and Drew has been central to the current view that DNA is conformationally
polymorphic. While many DNA structures have been solved to a resolution of 2.0–3.0 Å, Loren Williams has
achieved a resolution of 1.4 Å, thus allowing a more accurate analysis of the dodecamer structure and reveal-
ing some new insights into DNA hydration.11–13His principal conclusion is that the primary spine of hydra-
tion is composed partly of sodium ions. In other words, there is partial occupancy of primary sites of solvation
in the minor groove by both water and sodium cations. There is also a secondary, regular and highly
ordered spine of water molecules on top of the primary spinethat does not interact directly with the DNA.
This DNA structure is seen to be more conformationally ordered and not as heterogeneous as thought earlier.
However, in practice, partial occupancy (known as a sodium–water hybrid) is difficult to distinguish from
a water molecule alone, especially if sodium occupancy is less than 50%. This is because sodium ions and
water molecules have the same number of electrons and therefore yield electron density peaks of similar size.
In addition, both water and sodium ions have a wide variation in their coordination geometries. To confirmthe
hybrid–solvent model proposed for the high-resolution Dickerson–Drew dodecamer, Williams carried out
potassium substitution experiments^12 to take advantage of the fact that a potassium ion can readily be distin-
guished from water because of its larger number of electrons. These studies have confirmed that monovalent
cations penetrate the primary layer of the spine of hydration and are also present in the secondary hydration
layer. The spine of hydration forms only the bottom two layers of a four-layer arrangement of solvent
and cations in the A T minor groove, which are organised to form a repeating motif of fused hexagons
(Figure 9.3).
This work has implications for binding of other small molecules to DNA minor grooves. A substantial
favourable entropic contribution to binding free energy may arise from positioning positively charged,
minor groove-binding ligands or cationic ancillary functional groups of intercalators (e.g.the amino sugar
of daunomycin) into A T minor grooves that contain sodium or potassium ions bound in specific sites.
Favourable entropic effects will arise when monovalent metal cations are expelled from the minor groove
by cationic ligands.
9.6 DNA Intercalation
9.6.1 The Classical Model
Leonard Lerman first proposed the intercalation modelfor ligand binding to DNA in the early 1960s.14,15
Working with aminoacridines and proflavin, he postulated that DNA unwinds slightly to open a space into
which the flat polycyclic aromatic chromophorescan be inserted between adjacent base pairs. This mode of
binding has now been established for a large number of planar heteroaromatic or polycyclic aromatic ring
structures (Figure 9.4).
A common structural feature of all intercalatorsis that they possess an extended, electron-deficient,
planar aromatic ring system that is often referred to as a chromophore. Such compounds typically have
Reversible Small Molecule–Nucleic Acid Interactions 347