Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site

Abstract

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 Ba2+, Mn2+, Co2+ and Zn2+ 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.

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA

“…High resolution is difficult to be achieved in larger amorphous systems, like the whole ribosomal subunits 11 . Thus, the chosen structures are either parts of larger biomolecules, or short synthetic sequences [34][35][36][50][51][52][53][54][55][56][57][58][59][60] . Molecules classified as small RNAs have not been included 61 .…”

“…Respective structure sources: PDB 1L2X 35 , 1J8G 52 and 3ND3 59 ; J, K, Lwith K + ions. Respective structure sources: PDB 2OIY (J and K) 34 and 2QEK 60 .…”

“…The K + -O(Н2О) distance is in the range of 251-321 pm (Table 4). The K + -О2' distance to the oxygen atom O2' of ribose is in the range of 280-320 pm, see PDB 3C44 and 2ОIY 34,60 . Furthermore, K + ions can be in direct contact with the О4 oxygen atoms of uracil or О6 oxygen atoms of guanine, with K + -О distances of 261-283 pm and 261-305 pm, respectively.…”

“…The locations of the metal ions in crystal phase can be determined by X-ray crystallography 8,9,11,12,[34][35][36][37][38] . However, it is often difficult to determine exact positions due to irregular distribution of the ions.…”

The Design of RNA Binders: Targeting the HIV Replication Cycle as a Case Study

“…Several NMR and X-ray structures have provided insights into both the DIS kissing-loop complex [104][105][106][107] and extended duplex structures (Figure 18 A, B). [104,[108][109][110][111] In addition, structure of the SL1 internal bulge was also investigated by NMR independently from the apical loop. [112][113][114] Crystal structures of the DIS kissing-loop complex opened the way to a rationale structure-based drug design of the DIS RNA.…”