A potential long-range RNA-RNA interaction in the HIV-1 RNA

Abstract

It is well-established that viral and cellular mRNAs alike harbour functional long-range intra-molecular RNA-RNA interactions. Despite the biological importance of such interactions, their identification and characterization remain challenging. Here we present a computational method for the identification of certain kinds of long-range intra-molecular RNA-RNA interactions involving the loop nucleotides of a hairpin loop. Using the computational method, we analysed 4272 HIV-1 genomic mRNAs. A potential long-range intra-molecular RNA-RNA interaction within the HIV-1 genomic RNA was identified. The long-range interaction is mediated by a kissing loop structure between two stem-loops of the previously reported SHAPE-based secondary structure of the entire HIV-1 genome. Structural modelling studies were carried out to show that the kissing loop structure not only is sterically feasible, but also contains a conserved RNA structural motif often found in compact RNA pseudoknots. The computational method should be generally applicable to the identification of potential long-range intra-molecular RNA-RNA interactions in any viral or cellular mRNA sequence.

Communicated by Ramaswamy H. Sarma

Keywords:

• RNA pseudoknot
• intramolecular interaction
• HIV-1
• genomic RNA
• long-range
• kissing-loop

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The work was partially supported by a grant from the National Institute of Health (1R15GM131366-01) to Z. Du.