Table 1.
Affinity for Human Immunodeficiency Virus Reverse Transcriptase of PF1 Aptamer and Various Modifications
| Name | Sequence | Kd (nM) | ΔG (kcal/mol) |
|---|---|---|---|
| 5′-N30-3′ | 5′-NNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′ | ∼1000 | |
| PF1 | 5′-AGGAAGGCTTTAGGTCTGAGATCTCGGAAT-3′ | 82±7 | −0.61 |
| Diguanosine modifications of PF1 (Changes underlined) | |||
| PF1-GG>CC | 5′-ACCAACCCTTTACCTCTGAGATCTCCCAAT-3′ | >500 | >0 |
| PF1-GG>AA | 5′-AAAAAAACTTTAAATCTGAGATCTCAAAAT-3′ | >500 | −0.02 |
| PF1-terminal GG>CC | 5′-ACCAAGGCTTTAGGTCTGAGATCTCCCAAT-3′ | 140±10 | >0 |
| PF1-GCmid | 5′-AGGAACCCTTTACCTCTGAGATCTCGGAAT-3′ | ∼500 | −0.61 |
| PF1C6-7 | 5′-AGGAACCCTTTAGGTCTGAGATCTCGGAAT-3′ | ∼500 | −1.07 |
| PF1C13-14 | 5′-AGGAAGGCTTTACCTCTGAGATCTCGGAAT-3′ | >500 | −1.11 |
| PF1-C6 | 5′-AGGAACGCTTTAGGTCTGAGATCTCGGAAT-3′ | 420±70 | −0.61 |
| PF1-C14 | 5′-AGGAAGGCTTTAGCTCTGAGATCTCGGAAT-3′ | ∼500 | −0.73 |
| PF1-3G | 5′-AGGAAGGCTTTAGGGTCTGAGATCTCGGAAT-3′ | 310±90 | −0.61 |
| PF1-3G2 | 5′-AGGAAGGCTTTAGGGTCTGAGATCTCGGGAAT-3′ | 260±73 | −0.13 |
| PF1-4G | 5′-AGGAAGGCTTTAGGGGTCTGAGATCTCGGAAT-3′ | ∼500 | −0.61 |
| Truncated PF1 constructs (diguanosines and changes underlined) | |||
| PF1-25nt3′ cut | 5′-AGGAAGGCTTTAGGTCTGAGATCTC-3′ | ∼500 | >0 |
| PF1-25nt5′ cut | 5′-GGCTTTAGGTCTGAGATCTCGGAAT-3′ | >750 | −0.61 |
| PF1-20nt3′ cut | 5′-AGGAAGGCTTTAGGTCTGAG-3′ | >750 | >0 |
| PF1-20nt5′ cut | 5′-TAGGTCTGAGATCTCGGAAT-3′ | >750 | −0.61 |
| PF1-15nt3′ cut | 5′-AGGAAGGCTTTAGGT-3′ | >750 | >0 |
| PF1-15nt5′ cut | 5′-CTGAGATCTCGGAAT-3′ | >750 | −0.09 |
| PF1-27nt5′ cut | 5′-AAGGCTTTAGGTCTGAGATCTCGGAAT-3′ | ∼500 | −0.61 |
| PF1-26ntG | 5′-GGAAGGCTTTAGGTCTGAGATCTCGG-3′ | 233±29 | >0 |
| PF1-26ntC | 5′-CCAAGGCTTTAGGTCTGAGATCTCCC-3′ | ∼500 | >0 |
| PF1-26ntT | 5′-TTAAGGCTTTAGGTCTGAGATCTCTT-3′ | 131±24 | >0 |
| PF1-Δ (8–12) | 5′-AGGAAGGGGTCTGAGATCTCGGAAT-3′ | >750 | −0.61 |
| PF1-Δ (16–25) | 5′-AGGAAGGCTTTAGGTGGAAT-3′ | >750 | >0 |
| PF1-Δ (8–12/16–25) | 5′-AGGAAGGGGTGGAAT-3′ | >750 | >0 |
| PF1-15ntmidG | 5′-AAGGCTTTAGGTCTG-3′ | >750 | >0 |
| PF1-18ntTlinkG | 5′-AGGTTGGTTGGTTGGAAT-3′ | >750 | >0 |
| TBA (thrombin aptamer) | 5′-GGTTGGTGTGGTTGG-3′ | >750 | >0 |
| PF1-RNA | 5′-AGGAAGGCUUUAGGUCUGAGAUCUCGGAAU-3′ | >750 | −4.40 |
| Structural controls (diguanosines underlined) | |||
| PF1A | 5′-AGGAAGGCAAAAGGAAAAAAAAAAAGGAAA-3′ | >750 | 0 |
| PF1Flip | 5′-AGGAAGGCTTTAGGTTTCCTAAAGCCTTCC-3′ | 667±144 | −12.06 |
| PF1Loop | 5′-AGGAAGGCTTTAGGTCCGAGATCTCGGAAT-3′ | 558±3 | −3.38 |
| PF1N | 5′-NGGNNGGNNNNNGGNNNNNNNNNNNGGNNN-3′ | ∼500 | |
| PF1T | 5′-TGGTTGGTTTTTGGTTTTTTTTTTTGGTTT-3′ | 448±25 | −2.67 |
Repeated diguanosines are underlined in PF1, while changes to PF1 are underlined in the diguanosine-modified oligos. Both diguanosines and changes are underlined in the truncated oligos and diguanosines only in the structural controls.
Equilibrium dissociation constants (Kd) were determined using a gel-shift assay as described in Material and Methods. Results are an average of 3 experiments±standard deviation where indicated. Other results (denoted as ∼or>) were estimated based on at least 2 independent experiments.
Free energy of folding (ΔG) values were estimated using mfold (see Methods). If more than one structure was predicted, only the one with the lowest free energy is listed;>0 indicates a predicted positive value for ΔG.