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Nucleic Acids Research, 1985, Vol. 13, No. 23 8339-8357
© 1985

Articles

Conformation of yeast 18S rRNA. Direct chemical probing of the 5' domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible sites

Laurence Lempereur1, Monique Nicoloso1, Nadine Riehl2, Chantal Ehresmann2, Bernard Ehresmann2 and Jean-Pierre Bachellerie1,*

1Centre de Recherche de Biochimie et de Génétique Cellulaires du CNRS, Université Paul Sabatier 118 route de Narbonne, 31062 Toulouse Cedex 2Institut de Biologie Moléculaire et Cellulaire du CNRS, Laboratoire de Biochimie 15 rue René Descartes, 67084 Strasbourg Cedex, France

*To whom correspondence should be addressed

Received September 27, 1985. Revised October 31, 1985. Accepted October 31, 1985.

The structure of the 5' domain of yeast 18S rRNA has been probed by dimethyl sulfate (DMS), either in "native" deproteinized molecules or in the 40S ribosomal subunits. DMS-reacted RNA has been used as a template for reverse transcription and a large number of reactive sites, corresponding to all types of bases have been mapped by a primer extension procedure, taking advantage of blocks in cDNA elongation immediately upstream from bases methy-Lated at atom positions involved in the base-pair recognition of the template. Since the same atom positions are protected from DMS in base-paired nucleotides, the secondary structure status of each nucleotide can be directly assessed in this procedure, thus allowing to evaluate the potential contribution of proteins in modulating subunit rRNA conformation. While the DMS probing of deproteinized rRNA confirms a number of helical stems predicted by phylogenetic comparisons, it is remarkable that a few additional base-pairings, while proven by the comparative analysis, appear to require the presence of the bound ribosomal subunit proteins to be stabilized.


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