Table 3.
Inhibition of Human Immunodeficiency Virus Reverse Transcriptase Primer Extension by Various Aptamers
| Name | Sequence | IC50 (nM) |
|---|---|---|
| Starting material: 5′-N30-3′ | 5′-NNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3′ | >500 |
| PF1 | 5′-AGGAAGGCTTTAGGTCTGAGATCTCGGAAT-3′ | 63±24 |
| Primer-template aptamer | ||
| 38 NT SELEX (3′ ddG) | 5′-TAATACCCCCCCTTCGGTGCAAAGCACCGAAGGGGGGG-3′ | 3.7±1.1 |
| G-quadruplex aptamers | ||
| R1T | 5′-CGCCTGATTAGCGATACTCAGGCGTTGGGTGGGTGGGTGGG-3′ | 0.9±0.3 |
| S4 | 5′-CGCCTGACCCTTCAGGCGTTGGGTGGGTGGGTGGG-3′ | 0.5±0.1 |
| Large DNA aptamer | ||
| RT1 | 5′-ATCCGCCTGATTAGCGATACTCAGAAGGATAAACTGTCCAGAACTTGGATATATACACTTGAGCAAAATCACCTGCAGGGG-3′ | 0.3±0.1 |
| RNA pseudoknot aptamer | ||
| 1.1 | 5′-UCCGUUUUCAGUCGGGAAAAACUG-3′ | 4.7±0.2 |
| Modified constructs | ||
| PF1-terminal GG>CC | 5′-ACCAAGGCTTTAGGTCTGAGATCTCCCAAT-3′ | ∼250 |
| PF1-26ntG | 5′-GGAAGGCTTTAGGTCTGAGATCTCGG-3′ | ∼250 |
| PF1-26ntT | 5′-TTAAGGCTTTAGGTCTGAGATCTCTT-3′ | >250 |
Underlined nucleotides indicate the polypurine tract-like sequence in the primer-template aptamer and the region that forms the G-quadruplex in the G-quadruplex aptamers.
The half-maximal inhibitory value (IC50) values were determined using a reverse transcriptase inhibition assay as described under Material and Methods. Results for the experimental and control oligonucleotides were an average of 3 experiments±standard deviation. The results for the starting material and modified constructs were estimates based on 2–3 independent experiments.