two or more six-membered rings that form a platform of approximately the same size as a DNA base pair.
Intercalators are an important type of DNA binding agent, not least because some of these compounds
have been used as drugs.
Simple intercalators, such as ethidium, propidiumand proflavin, contain only the intercalating chro-
mophore and they are often cationic at neutral pH. The archetypal simple DNA intercalatoris ethidium
bromide, which binds to two adjacent G C base pairs (Figure 9.5). However, many ligands that bind by this
mode are not “simple” intercalators but rather their intercalating moiety is decorated by a variety of chem-
ical substituents, sugar rings or peptide groups. These additional, often non-planar, functional groups have
a major role in the exact sequence specificity, thermodynamic stability and structural orientation of the
bound ligand. This is because the ancillary groups occupy the DNA grooves, where they form favourable
noncovalent interactions, such as van der Waals, hydrophobic and hydrogen bonding to the bases that pro-
trude into the grooves. Whilst intercalation itself leads to only a slight preference for 5 -pyrimidine-purine-3
dinucleotides, because of stacking requirements, more complex intercalators with various functional groups
attached to the intercalating chromophore can give rise to direct sequence readout and hence sequence
selectivity. Some intercalating molecules bind by nonclassical mechanisms that involve threading through
the DNA base stack prior to intercalation (Section 9.6.6).
Over the past 40 years, numerous studies in intercalator–DNA systems have greatly increased our under-
standing of the intercalation process. When a ligand intercalates into the DNA stack,the bases must be
348 Chapter 9
Figure 9.3 The hexagonal hydration motif observed in A-tract DNA at high resolution. This view is across the minor
groove, roughly along the normal of the central hexagons. Solvent sites are indicated by red spheres,
with solid lines designating molecular contacts. Distances greater than 3.4 Å are specified by dashed
lines. Watson–Crick hydrogen bonds are indicated by dotted lines. The site of confirmed cation occupancy
is indicated by a plus sign
(Figure prepared and kindly provided by Loren D. Williams)