grooveand forms van der Waals contacts with the atoms of DNA that constitute the sugar–phosphate walls
of the groove. These contacts hold the ligand pyrrole rings approximately parallel to the walls of the
groove and since there is helical twist in the groove, the two pyrrole rings are twisted by about 33° with
respect to one another. The two cationic termini of netropsin are also in the central minor groove and they
are associated with N-3 atoms of the outer adenine bases of the central four A T base pairs. Steric interactions
between pyrrole methyl groups and the DNA bases prevent deep penetration of the drug into the groove.
The result is that some of the hydrogen bonds between the drug and DNA are quite long (3.3–3.8 Å) compared
to standard values (less than 3 Å). The binding of netropsin causes a slight widening of the minor groove
and a bending of the helical axis away from the binding site.
The binding of distamycin to DNA has many features that are similar to that of netropsin. A 2.2 Å reso-
lution X-ray crystal structure of the 1:1 distamycin/A3T3 complex^32 (Figure 9.14a) shows a snug fit of the
crescent-shaped ligand into the A T minor groove.
NMR studies of the same distamycin–DNA interaction from David Wemmer reveal an interesting add-
itional binding mode for distamycin^33 (Figure 9.14b). Sequences that contain more than four successive
A T base pairs in the minor groove, such as A3T3, can accommodate two distamycin moleculesin the cen-
tral AT-tract. Sequences that contain only four A T base pairs favour the 1:1 complex. Hence with a run of
six A T base pairs, the 2:1 complex is favoured. The NMR data suggest that the distamycin molecules are
stacked on each other with their charged groups arranged in opposite (antiparallel) directions. The fact that
netropsin binds as a single molecule per binding site is probably because it is a dication and thus side-by-
side 2:1 binding is inhibited due to drug–drug electrostatic repulsion.
Both distamycins in the dimer complex lie deep within the minor groove and form hydrogen bonds with
adenine N-3 and thymine O-2, in the same way as in the 1:1 complex. An interesting feature of the dimer
Reversible Small Molecule–Nucleic Acid Interactions 363
Figure 9.14 (a) X-ray structure of the distamycin-d(CGCAAATTTGCG) 2 complex (NDB: GDL003; PDB: 2DND).
(b) Exactly the same complex solved using NMR, Note the different groove widths in the two structures
(Coordinates supplied by David E. Wemmer in a personal communication to I. Haq and T. C. Jenkins)