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. Author manuscript; available in PMC: 2010 Aug 1.
Published in final edited form as: Expert Opin Biol Ther. 2009 Aug;9(8):975–989. doi: 10.1517/14712590903052877

FIG. 6.

FIG. 6

Proposed mechanism of PNA-Neamine conjugate-mediated cleavage of transactivation response element (TAR) RNA. The PNA attached to the 5-position of ring I of the neamine moiety through an 11-atom linker is shown as a circle. The numbers shown are the pKa value of amino groups at positions 3 and 6 of ring 1 and ring 6 of the neamine moiety. The deprotonated amino group at position 3 of ring I is shown extracting a proton from the 2 OH group of the ribose moiety of the RNA backbone. The activated 2 O is shown interacting intra-molecularly with a phosphorus atom, while the protonated amino group at the 6 -position in ring II is shown interacting with the negatively charged oxygen atom of the phosphate group. The arrows indicate the direction of interaction leading to final cleavage of the phosphodiester bond [54].