Selection and characterization of RNAs replicated by Q beta replicase.

RNAs replicated by Q beta replicase were isolated from two random sequence RNA populations (one 56 nucleotides in length, the second 83) using a replication/dilution protocol. The selected molecules were cloned and sequenced, generating data set of 54 replicatable RNAs bound with higher affinity to Q beta replicase than did the random populations from which they were selected. Deletion analyses on two of the molecules indicated that internal regions of the RNAs were responsible for the specific binding of Q beta replicase. Truncated molecules representing the minimized RNA binding sites could inhibit replication of the full-length molecules, apparently by obstructing their binding to the replicase. The binding regions of the two RNAs were dominated by extended runs of pyrimidines. Similar C/U-rich regions existed in 85% of the sequences in the data set as well as in all of the previously published replicatable sequences. Mutation of the polypyrimidine domain of one of the replicatable sequences reduced the affinity of the molecule for Q beta replicase by 10-fold and completely abolished its ability to be replicated.