presence of two positive charges on the ligand undoubtedly enhances quadruplex binding. PIPER also
exhibits significant antitelomerase activity and behaves as a chaperone-like molecule, since it enhances
the folding of quadruplexes. The ligand alters the kinetics of the association reaction for dimeric quadru-
plex formation from second- to first-order and it increases the initial rate for quadruplex formation by
about 100-fold. Thus as well as binding to preformed quadruplex structures, ligands such as PIPER may
also be able to induce quadruplex formation in vivoat appropriate sequences.
Trisubstituted acridinesof the type shown in Figure 9.23 have been synthesized and exhibit very promis-
ing quadruplex affinity, selectivity and high levels of telomerase inhibition.^74 Based on an NMR structure of
the quadruplex formed from a sequence model of the human telomere, the expectation was that these mol-
ecules would end-paste in a similar manner to PIPER and 2,6-disubstituted amidoanthraquinones. Disubsti-
tuted compounds have similar affinity for duplex and quadruplex DNA ( 1 106 M^1 ) in that there is no
appreciable structure selectivity. By contrast, trisubstituted analogues bind quadruplex DNA 30 to 40 times
more strongly than to duplex DNA and telomerase inhibition correlates with quadruplex binding strength.
Thus, activity for disubstituted compounds is either very modest or nonexistent, whereas trisubstituted com-
pounds are about 100-fold more potent against telomerase activity, but without increased cellular toxicity.
Quadruplex formation may play many important biological roles. For example, promoter regions of certain
genes such as -globin genes, rat preproinsulin II gene, adenovirus serotype 2, retinoblastoma suscepti-
bility genes, the c-Myc gene, and various other oncogenes, all contain guanine-rich regions that have the
potential to form quadruplex structures. Thus G-quadruplexes may play a role in regulating gene expres-
sion, for example, inhibition of transcription. Hurley has shown that ligand-induced quadruplex formation
in c-Mycpromoter region leads to transcriptional down-regulation of that gene.^75 Conversely a G to A
mutant in the quadruplex forming region leads to 3-fold increase in the basal transcriptional activity of
the c-Mycpromoter. Thus, genomic sequences that have the propensity to form quadruplex DNA will
become major drug targets in ongoing efforts to develop structure/sequence-specific agents for the treatment
of human diseases.
Improvements in DNA and RNA synthetic techniques as well as design and synthesis of additional DNA-
interactive drugs and model compounds continue to make available systems that are providing new infor-
mation on the structure and energetics of nucleic acid complexes with small molecules and are dramatically
advancing the field of reversible nucleic acid interactions. In addition, it is clear that both DNA and RNA
are prime targets as receptors for drug development. While DNA has been the prime target for such studies,
it can be expected that RNA will play an increasing role in the next period of time.
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Reversible Small Molecule–Nucleic Acid Interactions 379