DNA secondary structures: stability and function of G-quadruplex structures

Abstract

In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription.

Figure 1. G-quadruplex DNA

a | An illustration of the interactions in a G-quartet. This quartet is represented schematically as a square in the other panels of this figure. M⁺ denotes a monovalent cation. b | Schematic diagrams of intramolecular (left) and intermolecular (right) G-quadruplex (G4) DNA structures. The arrowheads indicate the direction of the DNA strands. The intermolecular structures shown have two (upper) or four (lower) strands.

Figure 2. Putative functional roles of G-quadruplex structures at telomeres

Telomeric sequences can fold into G-quadruplex (G4) structures in vitro. Currently, many groups are investigating the physiological relevance of this phenomenon. a | G4 structures may form at the telomeric 3′ overhang and have a role in protecting telomeres from degradation by nucleases (red) or other events. b | Work in ciliates shows that G4 structures do form at telomeres and have a role in telomere protection and tethering to the nuclear scaffold. Formation, stabilization and tethering is faciliated by G4-binding proteins (green). c | Ligands (blue) that bind to telomeric G4 structures are currently being analysed for their ability to influence telomere length by altering telomerase (yellow) activity.

Figure 3. Putative functional roles of G-quadruplex structures during DNA replication

Computational studies show that in all tested organisms, many regions in the genome have the ability to form G-quadruplex (G4) structures. In vitro and in vivo studies indicate that unresolved G4 structures may influence DNA replication by slowing or stalling the replication fork machinery (replisome; blue).

Figure 4. Putative functional roles of G-quadruplex structures during transcription

Genome-wide bioinformatic analyses identified loci with high potential to form G-quadruplex (G4) structures. Among these loci, the promoters, transcription factor binding sites and 5′UTR regions of mRNAs are highly enriched for G4 motifs. These analyses, together with protein–G4 interaction studies, provide insights into predicted functions of G4 structures during transcription. a | G4 structures are postulated to block transcription by inhibiting polymerase (purple). b | G4 structures are postulated to facilitate transcription by keeping the transcribed strand in the single-stranded conformation. c | G4 DNA may stimulate transcription by recruiting proteins (green) that recruit or stimulate polymerase. d | G4 structures are suggested to block transcription via the recruitment of G4 binding proteins (blue), which directly or indirectly (red) repress transcription.

Figure 5. Putative roles for G-quadruplex structures in meiosis

a | It has been proposed that G-quadruplex (G4) structures might assist in the formation of the telomere-dependent bouquet structure during meiosis. G4-promoting proteins (pink) could be involved in the formation of G4 structures and tethering of the telomeric bouquet to the nuclear scaffold. b | It has also been suggested that G4 structures could promote meiotic homologous recombination^, if there is overlap between G4 motifs and preferred meiotic double-strand break sites. Sites of homologous recombination are indicated by the dashed lines.