RNA aptamers that specifically bind to a K ras-derived farnesylated peptide Original Research Article

RNA aptamers were selected against an affinity column containing a farnesylated peptide modeled after the carboxyl terminus of K ras, the major oncogenic form of this small G protein family. After 10-rounds of selection, 25% of the RNA applied to the column could be specifically eluted. Sequence analysis of the binding RNA aptamers revealed two consensus sequences—GGGUGGG and GGGAGG. Quantitative fluorescence binding studies on two of the high-affinity aptamers, showed a binding affinities of 139 nM and 0.93 μM, respectively for the farnesylated peptide. Binding to the nonfarnesylated peptide was at least 10-fold weaker, showing that the aptamers can recognize the hydrophobic farnesyl moiety. High affinity aptamers could be useful in specifically interfering with oncogenic ras function in particular, and G proteins in general.