Fig. 3: Comparison of DENV and ZIKV stem-loop A (SLA) structures.
From: Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase
a Sequence alignment of flavivirus SLAs. The SLA sequences from DENV1 (NCBI accession number, NC_001477), DENV2 (NC_001474), DENV3 (NC_001475), DENV4 (NC_002640), WNV (NC_001563), JEV (NC_001437) and ZIKV (KU527068) are aligned. The overall sequence identity among the seven listed SLAs is ~25%. Conserved nucleotides are shaded in pink. The top stem-loop, side loop, and the bottom stem are indicated for DENV2 (top) and ZIKV SLA (bottom). The AG motif and the U-bulge are boxed, and the side loop regions in DENV and ZIKV SLAs involved in the kissing-loop interaction are underlined. b Superposition of the DENV and ZIKV SLA structures. The DENV and ZIKV SLA structures were overlaid by the conserved bottom stem. DENV SLA is colored as in Fig. 2a and ZIKV SLA in light blue. The nucleotides in the AG motif and the U-bulge are indicated in DENV (black letters) and ZIKV (blue letters). The top stem-loops of DENV and ZIKV SLAs are related by ~180° rotation. c Kissing-loop interactions in the DENV SLA dimer. One tRNA-SLADENV molecule is shown as in Fig. 2a, and the other molecule is shown in yellow. The self-complementary, side loop sequence that forms kissing-loop interactions is shown below. d Kissing-loop interactions in the ZIKV SLA dimer. The tRNA-SLAZIKV dimer is colored as in Fig. 2c. The palindromic sequence that forms kissing loop interactions between the side loops is shown below.
