Most strategies aimed at triplex stabilization have centred on intercalators, which can also bind to
duplex DNA as well as to triplexes. For example, the prototypical duplex-binding ligand ethidium inter-
calates into triplexes. Indeed, it binds more strongly to triplexes composed of T A–T base triplets than it
does to the corresponding duplex. Conversely, ethidium binds more strongly to G C duplexes than it does
to C G–C triplex, probably because of the positive charge on the cytosine. Other intercalators have been
developed that increase triplex stability substantially.
One of the original triplex specific ligands is benzo[e]pyridoindole(BePI, Figure 9.20) developed by
Claude Hélène. Subsequently, many structurally related analogues of BePI were also made, (for example
benzoindoloquinoline, benzopyridoquinoxaline, benzoquinoquinoxaline).^56 Triplex-selective intercalators
that contain fused or unfused heterocyles have also been synthesized by a number of other groups, such as
naphthyquinoline(Wilson), anthraquinones(Jenkins) and acridine derivatives (Stevens) (Figure
9.20). Most ligands in this class have an extended planar aromatic ring system of optimal size to fit
the extended molecular surface area presented by a base triplet (compared to a base pair). Therefore, there
are maximal –stacking interactions between the ligand and the base triplets that constitute the binding
site. Most of the ligands have at least one cationic charge on the chromophore. Hence there is the
possibility of favourable electrostatic interactions with increased negative charge density in the triplex
DNA. Many of these ligands also possess pendant side chains that terminate in a protonatable amino
group. This provides extra stability through electrostatic interactions with the sugar–phosphate backbone
of the DNA.
9.10.2 Quadruplex DNA and its Interactions with Small Molecules
It is well known that four guanine bases can self-associate to form cyclic, planar tetramers of Hoogsteen
hydrogen-bonded structures known as G-tetrads(Section 2.3.7). When two or more successive guanine
residues are incorporated into a nucleic acid sequence, the DNA can fold into either an inter- or intra-
molecular, four-stranded quadruplex– or tetraplex– structure in which successive G-tetrads are stacked
on top of each other (Figure 9.21).
The stability of quadruplex DNA is highly dependent on the type and concentration of counter-ion pre-
sent. Most quadruplexes are stable in solutions containing between 100 and 200 mM Naor K. It is believed
that these monovalent cations coordinate to the eight carbonyl oxygen atoms from two stacked G-tetrads
that protrude into the central core of the folded structure. A number of different quadruplex conformations
can form in vitro depending on strand molecularity and orientation. When a sequence of DNA has a sin-
gle run of successive guanine bases, four separate strands can combine to form a parallel tetramolecular
quadruplex structure. If a sequence of DNA has two separate runs of guanines separated by three or four
T or A bases, the single strand can fold back to form a guanine-hairpin. Two such hairpins can then self-
associate to form a stable quadruplex. Finally, single-stranded sequences containing four separate runs of
guanines, again separated by intervening T or A residues, can fold intramolecularly to form an antiparal-
lel quadruplex (Figure 9.21d). Several review articles are available that discuss G-quadruplexes and their
potential as drug targets.57–61
Much interest in quadruplex DNA stems from its potential role in telomere biology. Telomeresare spe-
cialized protein–DNA complexes at the 3 -termini of linear eukaryotic chromosomes (Section 6.4.5). A
particularly remarkable feature of telomeric DNA is that its sequence is conserved across a large range of
eukaryotes. The overall consensus sequence is d(T1–3(T/A)G 3 – 4 ). These sequence motifs are tandemly
repeated for up to many thousands of base pairs. The G-rich strand extends beyond the duplex region to
form a single-stranded overhang that is a few hundred nucleotides long. This widely conserved G-rich
sequence in a wide range of species implies some conserved biological role.^62
Telomeres have key functional importance in the regulation of cellular longevity and apoptosis (Section
6.6.5).^63 Human cells typically start out with telomeres that are about 15 kb in length and they are composed
of repeating units of 5 -TTAGGG. Because DNA polymerase does not fully replicate the lagging strand, 100
base pairs of DNA are lost from chromosome termini after each round of cell replication. This process limits
Reversible Small Molecule–Nucleic Acid Interactions 375