Selection of high affinity RNA ligands to the bacteriophage R17 coat protein.
RNA ligands with high affinity for the bacteriophage R17 coat protein were isolated from a pool of random RNA molecules using SELEX. Of the 38 ligands isolated, 36 were found to contain a hairpin very similar to the naturally occurring coat protein binding site in the R17 genome. The common features of these 36 sequences provide a consensus binding site and predict components of a hairpin that promote favorable interaction with the coat protein. These include a tetraloop of primary sequence AUCA and a variable-length stem with a bulged adenosine residue at a specific stem position. The predicted consensus agrees well with the highest-affinity RNA binding site of the R17 coat protein, identified through classical but laborious techniques. These results demonstrate the value of SELEX as a tool for isolating high affinity RNA ligands to a specific target protein, and the further value of those ligands to point the researcher toward natural sequences for that target protein.
Schneider
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D
University of Colorado, Boulder 80309-0347.
Tuerk
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C
Gold
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L
D000494:Allosteric Regulation; D001435:Bacteriophages / Q000737:chemistry* / Q000648:ultrastructure; D001483:Base Sequence; D001665:Binding Sites; D002213:Capsid / Q000378:metabolism*; D016384:Consensus Sequence; D004586:Electrophoresis / Q000379:methods; D007536:Isomerism; D008024:Ligands; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid
D008024:Ligands; D046911:Macromolecular Substances; D009843:Oligoribonucleotides