Zika virus has emerged
as a global concern because neither a vaccine nor antiviral compounds
targeting it exist. A structure for the positive-sense RNA genome
has not been established, leading us to look for potential G-quadruplex
sequences (PQS) in the genome. The analysis identified >60 PQSs
in the Zika genome. To minimize the PQS population, conserved sequences
in the Flaviviridae family were found by sequence alignment, identifying
seven PQSs in the prM, E, NS1, NS3, and NS5 genes. Next, alignment
of 78 Zika strain genomes identified a unique PQS near the end of
the 3′-UTR. Structural studies on the G-quadruplex sequences
found four of the conserved Zika virus sequences to adopt stable,
parallel-stranded folds that bind a G-quadruplex-specific compound,
and one that was studied caused polymerase stalling when folded to
a G-quadruplex. Targeting these PQSs with G-quadruplex binding molecules
validated in previous clinical trials may represent a new approach
for inhibiting viral replication.