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Nucleic Acids Research, Vol 27, Issue 22 4376-4384, Copyright © 1999 by Oxford University Press

ARTICLES

Identification of 23S rRNA nucleotides neighboring the P-loop in the Escherichia coli 50S subunit

Y Bukhtiyarov, Z Druzina and BS Cooperman
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

We report the synthesis of a radioactive, photolabile 2'-O- methyloligoRNA probe, 2258-53/52(SAz)-48, PHONT1, and its exploitation in identifying 23S rRNA nucleotides neighboring the so-called 'P-loop'. The probe is complementary to nt 2248-2258 in Escherichia coli 50S subunits. PHONT1 contains a p-azidophenacyl group attached to a phosphorothioate bridge between the nucleotides complementary to the positions 2252-2253, such that the photogenerated nitrene is maximally 17-19 A from 23S RNA nucleotides G2252 and G2253. PHONT1 binds to the 50S subunit, and photoincorporates within or immediately adjacent to its target site, as well as into several nucleotides falling between G2357 and A2430. The significance of these results for the structure of the peptidyl transferase center is considered. The PHONT approach is generally applicable to studies of complex RNA-containing molecules.
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