form intramolecular folds with regions of duplex, internal loops, bulges and hairpins, for example, in ribo-
somes, tRNA, or genomic viral RNA (Chapter 7). Such non-standard duplex folds in RNA offer a varied array
of molecular architectures that can be exploited as drug targets, for example, those found in pathogenic RNA
viruses such as HIV-1.
9.3 Counter-Ion Condensation and Polyelectrolyte Theory
Nucleic acids are highly charged polyanions, and thus polyelectrolyte effects have a major impact on their
biological behaviour. For example, the polyanionic nature of nucleic acids directly affects the binding of
charged drugs and proteins and the denaturation and folding of nucleic acids as well as the condensation
and packaging of DNA and RNA in cells.
A nucleoside monophosphate has two ionizable hydroxyl groups of pKa1 and ca.6.8 (Figure 2.5).
These pKavalues are only slightly dependent on the location of the phosphate on the nucleoside or which
of the bases is involved. At pH 7.0 and above, a terminal phosphate group has two negative charges while
an internucleoside phosphate diester has one.
Monovalent cations bind to nucleic acids in a somewhat unusual manner that is unique to highly
charged linear polyelectrolytes. In the early 1970s Gerald Manning described such binding as counter-ion
condensation:1–3territorial binding of ions that are constrained to stay within a few angstroms of the DNA
surface, yet are free to move along the helix. Hence cations associate with nucleic acids largely as a function
of polymer charge density. To be stable, DNA must associate with counter-ions from solution. Additional
counter-ions are associated with remaining charges on the polyanion through Debye–Hückel interactions.
The initial interaction of counter-ions with nucleic acids is referred to as condensation because the cations
generally form a cloud around the charge density of the nucleic acid and are not bound at specific sites.
The ions retain their inner sphere water of hydration and they move up and down the phosphate backbone.
Secondary hydration layers of both the ion and the nucleic acid are affected by this interaction. With B-type
duplex DNA, counter-ion condensation theory predicts an average of 0.76 monovalent counter-ions condensed
per phosphate group, rising to a total of 0.88 counter-ions per phosphate group including Debye–Hückel type
interactions.
The effect of counter-ion condensation is to reduce the effective charge on the nucleic acid. This in turn
has a profound effect on solution properties, binding interactions, and stability of nucleic acids. A proportion
of the overall free energy for binding intercalators and groove-binders can be derived from the entropically
favourable release of condensed counter-ionsupon binding. At constant temperature, the entropic effect
resulting from counter-ion release can also lead to nucleic acid denaturation as well as to an apparent
Reversible Small Molecule–Nucleic Acid Interactions 343
Figure 9.1 Schematic representations of the three primary binding modes for ligand–duplex DNA binding. The
ligand is shown in red and the DNA chains are in black: (a) Outside-edge binding. (b) Intercalation.
(c) Groove binding