G4-Interacting DNA Helicases and Polymerases: Potential Therapeutic Targets

Abstract

Background: Guanine-rich DNA can fold into highly stable four-stranded DNA structures called G-quadruplexes (G4). In recent years, the G-quadruplex field has blossomed as new evidence strongly suggests that such alternately folded DNA structures are likely to exist in vivo. G4 DNA presents obstacles for the replication machinery, and both eukaryotic DNA helicases and polymerases have evolved to resolve and copy G4 DNA in vivo. In addition, G4-forming sequences are prevalent in gene promoters, suggesting that G4-resolving helicases act to modulate transcription.

Methods: We have searched the PubMed database to compile an up-to-date and comprehensive assessment of the field's current knowledge to provide an overview of the molecular interactions of Gquadruplexes with DNA helicases and polymerases implicated in their resolution.

Results: Novel computational tools and alternative strategies have emerged to detect G4-forming sequences and assess their biological consequences. Specialized DNA helicases and polymerases catalytically act upon G4-forming sequences to maintain normal replication and genomic stability as well as appropriate gene regulation and cellular homeostasis. G4 helicases also resolve telomeric repeats to maintain chromosomal DNA ends. Bypass of many G4-forming sequences is achieved by the action of translesion DNS polymerases or the PrimPol DNA polymerase. While the collective work has supported a role of G4 in nuclear DNA metabolism, an emerging field centers on G4 abundance in the mitochondrial genome.

Conclusion: Discovery of small molecules that specifically bind and modulate DNA helicases and polymerases or interact with the G4 DNA structure itself may be useful for the development of anticancer regimes.

Keywords: G-quadruplex; G4 DNA; PrimPol; helicase; polymerase; replication; translesion synthesis..

Fig. (1).

A timeline of G-quadruplex nucleic acid discovery.

Fig. (2).

Processing of G4 by replicative and translesion DNA polymerases. A) A G4 site in template strand stalls the replicative polymerases pol δ and pol ε. B) Pol δ and pol ε are replaced by a translesion polymerase. The translesion polymerase adds a nucleotide opposite the G4 site and synthesis continues without resolving the G4. C) A G4 site in the template strand stalls pol δ and pol ε. Synthesis resumes when PrimPol synthesizes a short dNTP primer downstream of the G-quadruplex.

Fig. (3).

Coordinated action of DNA replication proteins during synthesis past G4 obstacle. A) A G-quadruplex DNA structure impedes leading strand synthesis during replication. As the CMG complex unwinds duplex DNA at the replication fork, RPA binds to stabilize the exposed single-stranded DNA. A 3′ to 5′ helicase, such as WRN or BLM, helps smooth over the G4 site, allowing the polymerase to synthesize the complementary strand. RPA heterotrimer is represented by spheres of orange (RPA70), blue (RPA32), and yellow (RPA14). B) Leading strand replication is again stalled by a G-quadruplex. The action of a 5’ to 3’ helicase, such as FANCJ, RTEL1, or PIF1, helps smooth the G-quadruplex in the direction opposite synthesis, resolving the replication block. The helicase dissociates from the DNA to allows the polymerase to proceed as synthesis continues.