Protonation of non-Watson–Crick base pairs and encapsidation of turnip yellow mosaic virus RNA

AUTOR(ES)

Bink, Hugo H. J.

FONTE

The National Academy of Sciences

RESUMO

The 5′ UTR of turnip yellow mosaic virus RNA contains two conserved hairpins with internal loops consisting of C⋅C and C⋅A mismatches. In this article, evidence is presented indicating that the 5′ proximal hairpin functions as an encapsidation initiation signal. Extensive mutagenesis studies on this hairpin and sequencing of virus progeny showed a clear preference for C⋅C and C⋅A mismatches within the internal loop. The importance of these mismatches lies in their pH-dependent protonation and stable base pair formation. Encapsidation efficiency was found to be severely affected for several mutants lacking the protonatable mismatches in the internal loop of the 5′ proximal hairpin. Furthermore, gel mobility-shift assays were performed with various RNA hairpins and empty capsids with a hole. Protonatable hairpins containing C⋅C and/or C⋅A pairs were found to bind specifically to the interior of the protein shell under acidic conditions (pH 4.5) in the presence of spermidine. Based on these results we propose that this binding of protonated cytosines to the coat protein of turnip yellow mosaic virus may represent a new motif in RNA–protein interactions.

Documentos Relacionados

• Characterization of imperfect DNA duplexes containing unpaired bases and non-Watson-Crick base pairs.
• SURVEY AND SUMMARY: The non-Watson–Crick base pairs and their associated isostericity matrices
• RNA tertiary structure of the HIV RRE domain II containing non-Watson-Crick base pairs GG and GA: molecular modeling studies.
• A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson–Crick base pairing
• Efficient construction of long DNA duplexes with internal non-Watson–Crick motifs and modifications