The G-Quadruplex: Structural Diversity and Target for Drug Design
G-Quadruplexes (G4s) have been shown to form from G-rich DNA sequences and consist of four-stranded nucleic acid structures in which guanine bases form stacked planar tetrads stabilized by hydrogen bonding and cation coordination. Biostatistical analyses have revealed more than 300.000 occurrences of putative G4-forming sequences in the human genome. In addition to the repetitive G-rich sequences found in single-stranded telomeric DNA there is a significant prevalence in promoter regions of various oncogenes like c-MYC or VEGF. Indeed, recent studies have demonstrated quadruplex formation in cells, raising important questions on G4 regulatory roles in vivo.
In addition to its physiological role, the quadruplex scaffold has been shown to also constitute the basis of many nucleic acid aptamers and may also exhibit various enzymatic activities. These properties may be exploited in many different ways. Thus, various approaches have been adopted to detect proteins, nucleic acids, metabolites, or metal ions based on the unique catalytic properties of G4-derived DNAzymes.
Design of Novel Quadruplex Conformers. The site-specific substitution of guanosine nucleotides by analogs with particular steric or conformational features, e.g. 8-bromo-guanosine, 2‘-fluoro-riboguanosine or 2‘-fluoro-arabinoguanosine, is often associated with quadruplex structural transitions. Consequently, the structure of quadruplexes may be modified and tailored to yield novel species with unique chemical and physical properties. Whereas glycosidic torsion angle preferences constitute a major driving force for G4 refolding, other factors like steric interactions or non-conventional hydrogen bonds may contribute to specific conformational changes. Understanding local interactions in more detail will enable the rational design for a particular quadruplex conformation with potentially improved enzyme activity or metabolite binding.
Development of Quadruplex-Selective Ligands. Targeting quadruplex-forming sequences with selective ligands will induce or stabilize the quadruplex structure. In the following, gene expression will be modulated, making the targeting of G-quadruplexes a promising strategy for novel anticancer treatments. For their use as therapeutic agents, drugs targeting quadruplexes should exhibit high affinity but also high selectivity toward a particular quadruplex topology. Thus, first-generation ligands have to be characterized in terms of their quadruplex interactions. A complete thermodynamic profile of binding complements structural information, identifying the dominant driving forces for drug-quadruplex interactions and allowing for a future rational drug design.