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Science 6 August 1993:
Vol. 261. no. 5122, pp. 762 - 765
DOI: 10.1126/science.7688143
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Articles

Science, Vol 261, Issue 5122, 762-765
Copyright © 1993 by American Association for the Advancement of Science

articles

Circularly permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure

JM Nolan, DH Burke, and NR Pace

Department of Biology, Indiana University, Bloomington 47405.

Regions of Escherichia coli ribonuclease P (RNase P) RNA in proximity to a bound transfer RNA (tRNA) substrate were mapped by photoaffinity. A photoaffinity cross-linking reagent was introduced at specific sites in the interior of the native tRNA structure by modification of the 5' ends of circularly permuted tRNAs (cptRNAs). The polymerase chain reaction was used for the production of cptRNA templates. After the amplification of a segment of a tandemly duplicated tRNA gene, the cptRNA gene was transcribed in vitro to produce cptRNA. Modified cptRNAs were cross-linked to RNase P RNA, and the conjugation sites in RNase P RNA were determined by primer extension. These sites occur in phylogenetically conserved structures and sequences and identify regions of the ribozyme that form part of the tRNA binding site. The use of circularly permuted molecules to position specific modifications is applicable to the study of many inter- and intramolecular interactions.


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