9.1 Introduction
Most biological processes are reliant upon molecular recognition and the reversible interactions of one set
of molecules with another. This is particularly the case where nucleic acids are concerned, since chromosome
packaging and structural integrity as well as gene expression and DNA replication depend on numerous
protein–DNA interactions as well as, in a more subtle way, interactions with ions and water. Because
nucleic acids play a central role in critical cellular processes, such as cell division and protein expression,
they are very attractive targets for small molecule therapeutics. A desirable goal is that malfunctions in cell
replication or gene expression might be overcome by modulating nucleic acid activity through use of
sequence- or structure-specific drugs. Such compounds would have a direct and beneficial role in the treatment
of major diseases such as cancer.
Molecular recognition is a fundamental and underlying concept in chemistry and short, well-defined
nucleic acid sequences that bind to small ligands are ideal model systems for gaining understanding of the
basic principles of recognition. Nucleic acids, especially DNA, are less extensively folded and structurally
less complex than proteins, and this makes them attractive target molecules for general biophysical studies.
The equilibrium binding of small molecules to nucleic acids has been an active area of research for over
40 years. This Chapter aims to focus on basic concepts and major issues by use of selected examples. Many
of the biophysical and structural methods used in studying ligand binding to nucleic acids are outlined in
Chapter 11.
In general there are more biophysical studies of interactions of drugs with DNA than with RNA. This is
because DNA is a more attractive target for anticancer drugs and DNA has been much easier to synthesize
chemically to obtain model systems. Therefore, this chapter focuses primarily on small molecule–DNA bind-
ing and reference should be made to specialized literature for discussions on ligand–RNA interactions.
High-resolution structures are necessary to reveal the overall three-dimensional shape of a complex, the
conformations adopted by the two reacting species, as well as some of the molecular interactions in the
final complex. But resolving the structure of a complex is insufficient to understand its formation. Various
small molecule–nucleic acid complexes can have very similar structures, yet may have radically different
underlying driving forces. To gain a fuller understanding, it is also necessary to have thermodynamic and
kinetic information. In this chapter, the structures of various complexes are summarised and then rational-
ized in terms of binding thermodynamics or kinetics, where such information is available. This will sup-
port a better appreciation of the exquisite nature of small molecule–nucleic acid interactions.
9.2 Binding Modes and Sites of Interaction
There are three principal ways in which low molecular weight ligands can interact with double-stranded
DNA (Figure 9.1).
Outside-edge binding: This involves ligand binding (e.g.Na, Mg^2 or polyamines, Section 9.4) to the out-
side of the helix through non-specific, primarily electrostatic interactions with the sugar–phosphate backbone.
Intercalation: A planar (or near planar) aromatic ring system (e.g.daunomycin, Section 9.6) inserts in
between two adjacent base pairs, perpendicular to the helical axis.
Groove binding: A bound ligand (e.g.netropsin, Section 9.7) makes direct molecular contacts with
functional groups on the edges of the bases that protrude into either the major or minor grooves.
Compounds that have the potential to be clinically useful are normally either intercalators or groove-
binders. However, outside-edge, electrostatic interactions are also important, not least because the associ-
ation of positively charged counterions with the DNA polyanion has a large effect on DNA conformation
and stability.
The structure-specific recognition of higher-order nucleic acids, such as three-stranded triplexes or four-
stranded quadruplex DNA molecules (Section 9.10.2) is a developing field. Drug binding to these structures
can also be classified according to the above three groups. In addition, RNA–DNA heteroduplexes that
usually adopt the A-conformation (Section 2.2) are also attractive drug targets. Single-stranded RNA can
342 Chapter 9