TABLE 1.
Sequences of degenerate pools before and after passage
| Source of sequencesa | Sequenceb | Data |
|---|---|---|
| Wild typebc | TTTTATTTAGTCTCCAGAAAAAGGGGGG AAT | 5 |
| A (founding members of 179-member purine PPT poolc) | ||
| TTTTATTTAGTCTCCAGAGAGGGGGAGA AAT | 6 | |
| TTTTATTTAGTCTCCAGAAAAGGGAGGG AAT | 6 | |
| TTTTATTTAGTCTCCAGAAGGGGAGGGG AAT | 6 | |
| TTTTATTTAGTCTCCAGAAGGGGGAGGG AAT | 6 | |
| TTTTATTTAGTCTCCAGAAGAGGGAAGG AAT | 9 | |
| TTTTATTTAGTCTCCAGAAGGAGGGGAA AAT | 9 | |
| TTTTATTTAGTCTCCAGAGAGGGAGGGA AAT | 9 | |
| TTTTATTTAGTCTCCAGGGGAGGGGGGA AAT | 9 | |
| TTTTATTTAGTCTCCAG–AGAGGGGGAG AAT | 9 | |
| TTTTATTTAGTCTCCAGAGAGAGGAAGG AAT | 9 | |
| TTTTATTTAGTCTCCAGAAGGGGAGGAA AAT | 9 | |
| TTTTATTTAGTCTCCAGAAGGAAGGGAG AAT | 9 | |
| TTTTATTTAGTCTCCAGAGGGGAGGGGG AAT | 9 | |
| TTTTATTTAGTCTCCAGGGGAGGAAGGG AAT | 12 | |
| TTTTATTTAGTCTCCAGAGGGGGGGAGG AAT | 12 | |
| TTTTATTTAGTCTCCAGGGGAGGGGGAG AAT | 12 | |
| TTTTATTTAGTCTCCAGGGAGAGAGGAG AAT | 12 | |
| TTTTATTTAGTCTCCAGAGGGAGGGGAA AAT | 15 | |
| TTTTATTTAGTCTCCAGAGGGGGAGAAA AAT | 21 | |
| TTTTATTTAGTCTCCAGAGGGGAAGAGG AAT | 21 | |
| TTTTATTTAGTCTCCAGAGGGGAGGAAA AAT | 24 | |
| TTTTATTTAGTCTCCAGGGGAAGGGAAA AAT | 29 | |
| TTTTATTTAGTCTCCAGGGGGAAGGAGA AAT | >60 | |
| TTTTATTTAGTCTCCAGGGGGGGAAGAG AAT | >60 | |
| TTTTATTTAGTCTCCAGAGGGGAGGAGG AAT | >60 | |
| TTTTATCTAGTCTCCAGGGAGGGGAGGA AAT | >60 | |
| TTTTATTTAGTCTCCAGAGGGGGGAGAG AAT | >60 | |
| B (179-member purine PPT pool clones after first passaged) | ||
| TTTTATTTAGTCTCCAGAAGAAGGAGGG AAT | 10 | |
| TTTTATTTAGTCTCCAGAGAGGGGGAGA AAT | 2 | |
| TTTTATTTAGTCTCCAGAAAAGAGGAGG AAT | 4 | |
| TTTTATTTAGTCTCCAGAGGGGGGGGGG AAT | 1 | |
| TTTTATTTAGTCTCCAGGGAGGGGGGGA AAT | 1 | |
| TTTTATTTAGTCTCCAGAAGGGGGGGGA AAT | 1 | |
| TTTTATTTAGTCTCCAGGAAGGGGGGGG AAT | 1 | |
| TTTTATTTAGTCTCCAGAAGAAGGAAGG AAT | 1 | |
| C (predominant purine PPT pool sequences after passagec) | ||
| 179-member pool | TTTTATTTAGTCTCCAGAAGAAGGAGGG AAT | 5 |
| 500-member pool | TTTTATTTAGTCTCCAGAAAGAGGGGGG AAT | ∼5 |
| 6,300-member pool | TTTTATTTAGTCTCCAGRRRRRGGGGGG AAT | ∼5 |
| D (founding members of 530-member GATC PPT poolc) | ||
| TTTTATTTAGTCTCCAGAGATAGGGAGG AAT | 6 | |
| TTTTATTTAGTCTCCAGGGAGATGGAAA AAT | 12 | |
| TTTTATTTAGTCTCCAGCGGGAAGTGAG AAT | 12 | |
| TTTTATTTAGTCTCCAGAAGGAAAGGGG AAT | 12 | |
| TTTTATTTAGTCTCCAGAATAAAAGAGG AAT | 33 | |
| TTTTATTTAGTCTCCAGGACCGAATAAC AAT | >60 | |
| TTTTATTTAGTCTCCAGCGATTTAAAGG AAT | >60 | |
| TTTTATTTAGTCTCCAG–GAATAGCTTG AAT | >60 | |
| TTTTATTTAGTCTCCAGATTAGATAAGC AAT | >60 | |
| TTTTATTTAGTCTCCAGATTTAGAAGAA AAT | >60 | |
| TTTTATTTAGTCTCCAGCGGGAATAAAA AAT | >60 | |
| TTTTATTTAGTCTCCAGTTAAGAAGACA AAT | >60 | |
| TTTTATTTAGTCTCCAG––AGAAAAACT AAT | >60 | |
| E (predominant GATC PPT pool sequences after passagec) | ||
| Subset of 530-member pool | TTTTATTTAGTCTCCAGGTAAAGGGATA AAT | 7.5 |
| 530-member pool | TTTTATTTAGTCTCCAGARRWAGGGRRR AAT | NDe |
| 4,000-member pool | TTTTATTTAGTCTCCAGGGAGAGGGGGG AAT | ND |
| 5,000-member pool | TTTTATTTAGTCTCCAGAAAAAGGGGGG AAT | ND |
| F (founding members of GATC T-stretch pool) | ||
| ATTCTTCGAGTCTCCAGAAAAAGGGGGG AAT | ||
| ATTGTTCTAGTCTCCAGAAAAAGGGGGG AAT | ||
| CTTCTTGAAGTCTCCAGAAAAAGGGGGG AAT | ||
| GCCCACGTAGTCTCCAGAAAAAGGGGGG AAT | ||
| GTCTGCTTAGTCTCCAGAAAAAGGGGGG AAT | ||
| G (predominant GATC T-stretch pool sequences after passage) | ||
| Expt 1 | TTTTATWTAGTCTCCAGAAAAAGGGGGG AAT | |
| Expt 2 | TTTTATTYAGTCTCCAGAAAAAGGGGGG AAT | |
| H (founding members of TC T-stretch pool) | ||
| CTCCACCTAGTCTCCAGAAAAAGGGGGA AAT | ||
| TCCCGCCCAGTCTCCAGAAAAAGGGGGA AAT | ||
| CTCCATTCAGTCTCCAGAAAAAGGGGGA AAT | ||
| CTTCACTCAGTCTCCAGAAAAAGGGGGA AAT | ||
| TCCCGCCTAGTCTCCAGAAAAAGGGGGA AAT | ||
| I (TC T-stretch pool clones after first passaged) | ||
| TTTTATTCAGTCTCCAGAAAAAGGGGGA AAT | 4 | |
| TTTTATTCAGTCTCCAGAAAAAGGGGGG AAT | 1 | |
| J (founding members of TA T-stretch pool) | ||
| TTATTTAAAGTCTCCAGAAAAAGGGGGA AAT | ||
| ATTAATAAAGTCTCCAGAAAAAGGGGGA AAT | ||
| TAATTTTAAGTCTCCAGAAAAAGGGGGA AAT | ||
| ATTATATAAGTCTCCAGAAAAAGGGGGA AAT | ||
| ATAAAAATAGTCTCCAGAAAAAGGGGGA AAT | ||
| K (TA T-stretch pool clones after first passaged) | ||
| TTTTATTTAGTCTCCAGAAAAAGGGGGA AAT | 6 | |
| ATTTATTTAGTCTCCAGAAAAAGGGGGA GAT | 1 | |
| TTTTATTAAGTCTCCAGAAAAAGGGGGA AAT | 1 |
a
Founding members are sequences of clones that were part of the original transfected pool. Clones after first passage are sequences of individual clones after one passage of the pool. Predominant sequences are pool sequences when no further evolution of the pool was detectable.
b
Sequences varied in pools are underlined; positions that differ from wild type are in boldface. The space in each sequence denotes the PPT/U3 junction. R is any purine, Y is any pyrimidine, and W is T or A.
c
Data column shows replication efficiency measured as a function of days after infection that viral spread was detectable.
d
Data column shows the number of separate clones analyzed that possessed this sequence.
e
ND, not determined.