PMID:10781065

Citation	Stelzl, U, Spahn, CM and Nierhaus, KH (2000) Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: application of a method called SERF. Proc. Natl. Acad. Sci. U.S.A. 97:4597-602
Abstract	Two-thirds of the 54 proteins of the Escherichia coli ribosome interact directly with the rRNAs, but the rRNA binding sites of only a very few proteins are known. We present a method (selection of random RNA fragments; SERF) that can identify the minimal binding region for proteins within ribonucleo-protein complexes such as the ribosome. The power of the method is exemplified with the ribosomal proteins L4 and L6. Binding sequences are identified for both proteins and characterized by phosphorothioate footprinting. Surprisingly, the binding region of L4, a 53-nt rRNA fragment of domain I of 23S rRNA, can simultaneously and independently bind L24, one of the two assembly initiator proteins of the large subunit.
Links	PubMed PMC18278 Online version:10.1073/pnas.090009297
Keywords	Base Sequence; Binding Sites; Escherichia coli/genetics; Escherichia coli/metabolism; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Oligoribonucleotides/chemistry; Operon; RNA, Bacterial/chemistry; RNA, Bacterial/metabolism; RNA, Ribosomal/chemistry; RNA, Ribosomal/metabolism; RNA, Ribosomal, 23S/chemistry; RNA, Ribosomal, 23S/metabolism; Ribosomal Proteins/chemistry; Ribosomal Proteins/metabolism
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