Ligands that bind to and stabilize
guanine-quadruplex (G4) structures
to regulate DNA replication have therapeutic potential for cancer
and neurodegenerative diseases. Because there are several G4 topologies,
ligands that bind to their specific types may have the ability to
preferentially regulate the replication of only certain genes. Here,
we demonstrated that binding ligands stalled the replication of template
DNA at G4, depending on different topologies. For example, naphthalene
diimide derivatives bound to the G-quartet of G4 with an additional
interaction between the ligand and the loop region of a hybrid G4
type from human telomeres, which efficiently repressed the replication
of the G4. Thus, these inhibitory effects were not only stability-dependent
but also topology-selective based on the manner in which G4 structures
interacted with G4 ligands. Our original method, referred to as a
quantitative study of topology-dependent replication (QSTR), was developed
to evaluate correlations between replication rate and G4 stability.
QSTR enabled the systematic categorization of ligands based on topology-dependent
binding. It also demonstrated accuracy in determining quantitatively
how G4 ligands control the intermediate state of replication and the
kinetics of G4 unwinding. Hence, the QSTR index would facilitate the
design of new drugs capable of controlling the topology-dependent
regulation of gene expression.