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Updated: Apr 12, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
The HIV-1 leader RNA is exquisitely sensitive to structural changes
Nikki van Bel1, Anouar Ghabri1, Atze T Das1
1Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
Abstract:
The untranslated leader of the HIV-1 RNA genome is highly structured and contains multiple replication signals. We probed in detail the sequence requirements of a small single-stranded domain using a combination of in silico, in vitro and in vivo virus experiments. Although 'structure-neutral' mutations can be designed by RNA prediction algorithms, experimental follow-up studies nearly always demonstrate local or regional RNA structure changes. Our results indicate that the wild-type HIV-1 RNA sequence has been selected from total sequence space as a unique solution to present critical replication signals in the context of a complex leader structure with small intervening single-stranded segments.
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