New Macrocyclic Terbium(III) Complex for Use in RNA Footprinting Experiments

Reaction of terbium triflate with a heptadentate ligand derivative of cyclen, L1 = 2-[7-ethyl-4,10-bis(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, produced a new synthetic ribonuclease, [Tb(L1)(OTf)(OH2)](OTf)2·MeCN (C1). X-ray crystal structure analysis indicates that the terbium(III) center in C1 is 9-coordinate, with a capped square-antiprism geometry. While the terbium(III) center is tightly bound by the L1 ligand, two of the coordination sites are occupied by labile water and triflate ligands. In water, the triflate ligand is likely to be displaced, forming [Tb(L1)(OH2)2]3+, which is able to effectively promote RNA cleavage. This complex greatly accelerates the rate of intramolecular transesterification of an activated model RNA phosphodiester, uridine-3′-p-nitrophenylphosphate (UpNP), with kobs = 5.5(1) × 10−2 s−1 at 21 °C and pH 7.5, corresponding to an apparent second-order rate constant of 277(5) M−1s−1. By contrast, the analogous complex of an octadentate derivative of cyclen featuring only a single labile coordination site, [Tb(L2)(OH2)](OTf)3 (C2), where L2 = 2-[4,7,10-tris(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, is inactive. [Tb(L1)(OH2)2]3+ is also capable of hydrolyzing short transcripts of the HIV-1 transactivation response (TAR) element, HIV-1 dimerization initiation site (DIS) and ribosomal A-site, as well as formyl methionine tRNA (tRNAfMet), albeit at a considerably slower rate than UpNP transesterification (kobs = 2.78(8) × 10−5 s−1 for TAR cleavage at 37 °C, pH 6.5, corresponding to an apparent second-order rate constant of 0.56(2) M−1s−1). Cleavage is concentrated at the single-stranded “bulge” regions of these RNA motifs. Exploiting this selectivity, [Tb(L1)(OH2)2]3+ was successfully employed in footprinting experiments, in which binding of the Tat peptide and neomycin B to the bulge region of the TAR stem-loop was confirmed.