Characterization of G-quadruplexes in nucleic acids

Abstract

The inclination of GMP or guanine-rich oligonucleotides to self assemble in to G-quadruplexes has been recognized for over 40 years (Gellert et al., 1962). G-rich sequences get associated in the presence of univalent cations like Na+, K+ etc, through Hoogsteen hydrogen bonding to form stacks of G-quartets (Keniry, 2000). Variations in the molecularity, topology, strand orientation (parallel/anti-parallel), and glycosidic conformation of the G-quadruplex DNA provide a diverse array of structures. Several reports indicating putative quadruplex forming sites in a number of significant regions in the human genome have intensified research in this field (Huppert et al., 2008; Huppert, 2008; Huppert and Balasubramanian, 2005; Huppert and Balasubramanian, 2007). Evidence for the formation of G4 DNA in vivo has been shown by electron microscopy (Duquette et al., 2004). One of the most extensively studied G-rich regions, capable of forming quadruplex, is the telomeric ends of chromosomes (Balagurumoorthy et al., 1992; Balagurumoorthy and Brahmachari, 1994). Quadruplex formation in telomeric region is known to inhibit the activity of the enzyme telomerase (Gomez et al., 2003; Zahler et al., 1991). Research in this area has further been propelled by the discovery of large number of quadruplex stabilizing agents (Cairns et al., 2002; Hurley, 2002; Mergny et al., 2002; Neidle and Parkinson, 2002). A number of proteins that interact specifically with G-quadruplexes have also been reported (Duquette et al., 2005; Fang and Cech, 1993; Fry, 2007; Giraldo and Rhodes, 1994; Maizels, 2006). Potential quadruplex forming sites in non-telomeric regions (double stranded) have also been identified. These include c-myc promoter (Simonsson et al., 1998), immunoglobin switch regions (Fukita et al., 1993; Yu et al., 2003), Fragile-X syndrome d (CGG)n repeat (Fry and Loeb, 1994; Fry and Loeb, 1999), cystatin B promoter (Saha and Usdin, 2001) which has a region with sequence (CGCG4CG4)4 and is involved in epilepsy.