The MS2-aptamer selects EBER1-interacting proteins. (A–C) Three strategies for selecting EBER1 RNPs are depicted. (A) EBER1 was isolated using a complementary oligonucleotide covalently linked to adipic acid dihydrazide Agarose beads. Alternatively, an aptamer was inserted into stem–loop IV of EBER1. (B) The S1-aptamer (45 nt) or (C) three MS2-hairpin loops (82 nt) were used to select EBER1 RNPs on streptavidin beads or on MS2 coat-MBP fusion protein tethered to amylose resin, respectively. (D) For selection with complementary oligonucleotides, BJAB-B1 cell lysate was used. For aptamer-mediated selections, stable BJAB cell lines were generated that express either EBER1-S1 or EBER1-MS2. A Northern blot probed for EBER1 assessed the pull-down efficiency of aptamer-containing EBER1 RNAs versus unmodified EBER1. Western blots using antibodies against La and L22 asked whether known EBER1-interacting proteins were coselected.
