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The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.

Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site., Ennifar E, Walter P, Dumas P, Nucleic Acids Res. 2010 Sep 1;38(17):5807-16. Epub 2010 May 11. PMID:020460458

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Categories: Dumas, P. | Ennifar, E. | Catalytic rna | Hiv-1 | Metal ion | Rna