NMR, and ITC have all shown that TMPyP4 does indeed stabilize both parallel and antiparallel quadru-
plex DNA. In addition, this compound has been shown to inhibit telomerase activity, but the exact mode
of interaction of TMPyP4 with DNA is uncertain. Photocleavage assays suggest that the porphyrin “end-
pastes” by stacking externally to the G-tetrad at the end of a model quadruplex based on the human telomere
sequence. By contrast, calorimetric and spectroscopic measurements of stoichiometry as well as molecular
modelling indicate that the porphyrin intercalates between adjacent G-tetrads. Very recent ITC experiments
show that there is an initial, high-affinity, entropic binding event that probably is end-pasting. Following
the initial tight binding event, secondary binding probably occurs by intercalation. Some 150 porphyrin
analogues have been screened in a cell-free telomerase assay as well as an assay that monitors arrest of DNA
synthesis. The results show that binding strength of these porphyrin analogues to quadruplex DNA is
dependent on overall charge, side chain length and presence of hydrogen bonding groups.^57
Another promising group of polycyclic quadruplex-interactive ligands is based on a perylene moiety,
for example, the dicationic compound PIPER (N,N - bis[2-(1-piperidino)-ethyl]-3,4,9,10-perylenete-
tracarboxylic diimide) (Figure 9.23). PIPER binds specifically to quadruplex DNA and there is only low-
level binding to duplex DNA. In slightly alkali conditions, where PIPER aggregates, the selectivity of the
ligand for quadruplex over duplex is about 10^3. However at pH 7, PIPER is less selective and binds 10-fold
better to quadruplex than to duplex DNA. The NMR structure for a complex of PIPER and quadruplex DNA
shows that PIPER end-pastes, i.e.it stacks externally on to terminal G-tetrads. By doing so it can form a
2:1 quadruplex/PIPER complex, where the ligand forms a sandwich between two quadruplex molecules.^73
The ligand only has minimal -overlap with two of the guanine residues in the terminal G-tetrad but the
378 Chapter 9
Figure 9.23 Chemical structures of quadruplex-binding small molecules