PMC

Calculated persistence of pre-existing structures involving SC or ML primer sequences in observed UAUU loop motifs.

(A) Estimated purification of the UAUU motif at particular selection cycles. (B) Calculated purification required to observe selection breakthrough and at cloning.

(A) Number of cycles of selection at breakthrough and at cloning. (B) Fraction of the UAUU motif in cloned pools. The dashed line is hypothetical and intended to be illustrative because breakthrough was not observed at 16 randomized nucleotides.

(A) Frequencies of both permutations of the conserved sequences within the UAUU motif. (B) Number of bits of information that was required in a randomized region to specify observed x- and y-stems around the UAUU motif in permutations P1 and P2.

Estimated initial abundance of functional UAUU loop motifs with SC (triangles) or ML (squares) primer sequences. The “predicted” curves are total probabilities for the UAUU motif calculated by summing those that are entirely in the random region, overlapping the 3^′ constant sequence, overlapping the 5^′ constant sequence, and overlapping both the 3^′ and 5^′ constant sequences (see Materials and Methods).

Secondary structures of the UAUU motif in permutation P1 supported by either SC (A) or ML (B) pre-formed primer sequences folded by BayesFold (). Conserved nucleotide positions of the motif are boldfaced. Primer sequences are in lowercase, and pre-existing structures are boxed. The N region in the y-stem has been counted as 10 nt for consistency of position numbering. (C) Permutation P2 of the UAUU motif. Position numbering has been broken in the middle for consistency.