G-quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides.

Guanine-rich nucleic acid sequences can exert sequence- and/or structure-specific activities to influence biological and pathobiological cellular processes. As such, it has been reported that different G-rich oligonucleotides (both DNA and RNA) can have cytotoxic as well as cytoprotective effects on the cells. However, the mechanisms of such a biological outcome are unclear. Here, we report that G-rich DNA oligonucleotides (ODNs) that can form four-stranded secondary structures called G-quadruplexes (G4s) have a topology-dependent biological outcome. Using different biochemical, biophysical, and cellular approaches, we demonstrate that only the parallel topology G4-forming ODNs can repress eukaryotic messenger RNA (mRNA) translation by directly interacting with eukaryotic translation initiation protein 1 (EIF4G1), while the anti-parallel topology G4s do not have inhibitory effect on mRNA translation. These results directly connect the G4 topological differences within ODNs to differential functional impacts in mRNA translation intrans. Our study provides the foundation for the rational design of G-rich oligonucleotides for a desired therapeutic outcome.