Flavivirus RNA replication: Probe development, structural dynamics, and role of zinc ions.

Abstract

Flaviviruses share a typical genome architecture where the highly conserved UTRs flank a central coding region. They also share a common genome replication strategy called genome cyclization where the UTRs interact to form a long-range, dynamic, 3D RNA interactome. Recent studies focused on the involvement of the capsid coding region in modulating these UTR interactions. Along similar lines, we have investigated the effect of CCR on the UTRs interactions in Dengue using ensemble FRET with cyanine dye-labeled Dengue UTRs. As a part of this study, we have developed a novel, generic chemoenzymatic, bead-based method for base-specific modification of RNA called “T7 RNA polymerase extension-based RNA modification (TERM)”. Here, we describe TERM development, demonstrate the synthesis of single, site-specific cyanine dye-labeled Dengue UTRs and discuss the UTR interaction studies performed using the TERM-synthesized cyanine dye-labeled UTRs. Our results bridge the knowledge gap in understanding the role of the capsid coding region in Flavivirus UTRs.