Role of a Bulged A Residue in a Specific RNA-Protein Interaction

Huey Nan Wu, Olke C. Uhlenbeck

Research output: Contribution to journalArticlepeer-review

118 Scopus citations


The translational operator of the R17 replicase gene contains a bulged A residue that is essential for the specific binding to R17 coat protein. A large number of operator variants have been synthesized to more precisely examine the role of the bulged A residue on this specific protein-RNA interaction. By use of RNA ligase and transcription of synthetic DNA templates by T7 RNA polymerase, 14 different nucleotides were introduced to the bulged A position of three different coat protein binding fragments. The affinity between coat protein and each fragment was determined by a nitrocellulose filter binding assay. The data indicate that while functional groups on N1, C2, C6, N7, and 2’OH of the bulged A can be substituted without greatly changing protein binding, bulky substituents cannot be tolerated at these positions. Data from additional fragments that have base-pair changes adjacent to the bulged A suggest that the propensity of the bulged A to intercalate into the helix can affect protein binding.

Original languageEnglish (US)
Pages (from-to)8221-8227
Number of pages7
Issue number25
StatePublished - 1987

ASJC Scopus subject areas

  • Biochemistry

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