Sequence and symmetry in ribosome binding sites of bacteriophage f1 RNA

RNA was synthesized in vitro from α-³²P-labeled ribonucleoside triphosphates with Escherichia coli RNA polymerase from covalently closed, circular, double-stranded DNA isolated from cells infected with bacteriophage f1. This RNA, which serves as an efficient message in vitro, was bound to ribosomes and the initiation complexes were digested with bovine pancreatic ribonuclease. Ribosome-protected fragments were isolated, purified and separated by two-dimensional analysis using electrophoresis and homochromatography. Sequence analysis, taking advantage of the ability to determine nearest neighbors, was done by conventional techniques. The sequences of the ribosome-protected fragments were found to fall into three classes. One sequence corresponds to the amino-terminal region of the protein product of f1 gene V, a DNA binding protein. It is proposed that a second sequence may correspond to the amino-terminal region of a precursor to the major coat protein. No assignment has yet been made for the third sequence. Comparisons are made between these three sequences and others that are available, both in terms of sequence features that have been pointed out earlier, and in terms of certain considerations of symmetry and syntax^† † The term syntax is used here to mean a connected or orderly system; a harmonious arrangement of parts or elements. In many cases involving nucleic acids, syntax would be detectable only following determination of the primary structure of the nucleic acid in question. The most straight-forward example of such an arrangement is the genetic code. Less obvious examples of syntactical order might be groups of nucleotides so arranged as to give rise to the "internal terminators" or true palindromes to be discussed here. Pieczenik (1973 and unpublished results) has more completely considered the implications of the existence of nucleic acid syntax. prominent in these binding site sequences that have not been discussed before.