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Secondary structure of dengue virus type 4 3' untranslated region: impact of deletion and substitution mutations

¹ Molecular Biology Program, New Mexico State University (NMSU), Las Cruces, NM 88003, USA
² School of Life Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia
³ Department of Biology, New Mexico State University (NMSU), Las Cruces, NM 88003, USA

Correspondence
Kathryn A. Hanley
khanley{at}nmsu.edu

Several studies have generated computer-based predictions of secondary structure of the 3' untranslated region (UTR) of Dengue virus (DEN); however, experimental verification of the formation of these structures in vitro is lacking. This study assessed the congruence of Mfold predictions of secondary structure of the core region of the DEN type 4 3' UTR with nuclease maps of this region. Maps and predictions were largely consistent. Maps supported the existence of previously predicted pseudoknots and identified putative regions of dynamic folding. Additionally, this study investigated previously identified conserved elements in the flavivirus 3' UTR that differ among viruses with different modes of transmission. Specific regions of mosquito-borne DEN type 4 were either deleted or replaced with homologous sequences from tick-borne Langat virus. All of these mutations caused substantial distortion of secondary structure, yet viruses carrying these mutations were viable.

A supplementary table showing post-transfection titres of wild-type DEN (rDEN4) and viruses carrying mutations in the 3' untranslated region is available in JGV Online.