Table 1. Top-ranked and enriched sequences as evaluated by NGS.
| Name | Sequencea | ΔG (Kcal/mol)b |
Rankingc | Enrichmentc |
Kd (nM)d |
Δ MST (a.u.)e |
|---|---|---|---|---|---|---|
| PfR1 | GAGAAGGACTGCTTAGGCTTGCGATGTGAAATCTGTAATC | -3.92 | 1(14) | 4.13(14/10) | 175 ± 54 | 7.6 ± 0.6 |
| PfR2 | AGATGCAAAGGACTGCTCAGGCTTGCGATGGCAGCTTCAT | -5.72 | 2(14) | 32.05(14/10) | 778 ± 1020 | 4 ± 2 |
| PfR3 | CACTAGGTCTGCTTAGGATTGCGTAAGTGAAAGTCATTTA | -6.43 | 3(14) | 566.11(14/10) | 1930 ± 560 | 18 ± 3 |
| PfR4 | ACCGACTACGTCAACCTGGGTCTGCTCGGGATTGCGGATG | -6.92 | 1(10) | 8.68(10/8) | 41 ± 11 | 8.6 ± 0.6 |
| PfR5 | AGCCGTGGATTGCAAAGGGCTGCTGTGGCTTAGTTGAATG | -5.33 | 3(10) | 18.38(10/8) | 560 ± 120 | 8.5 ± 0.6 |
| PfR6 | CGCGTGGGTTTGGCTCCGGGCCTGGCGGATGCACGTATAG | -6.11 | 5(10) | 2.18(10/8) | 65 ± 15 | 7 ± 0.6 |
| PfE1 | GCCGACTACGTCAACCTGGGTCTGCTCGGGATTGCGGATG | -7.53 | 4(10) | 24.10(10/8) | 81 ± 20 | 8.8 ± 0.5 |
| PfE2 | ACCGACTACGTCAACTTGGGTCTGCTCGGGATTGCGGATG | -6.92 | 14(10) | 18.58(10/8) | 55 ± 20 | 7.8 ± 0.7 |
| PfE3 | AGTTTACACCAAGGACTGCTTAGGATTGCGTTAGGGTATT | -2.93 | 10(14) | 301.81(14/10) | 815 ± 158 | 17 ± 0.6 |
a Top-ranked and enriched sequences obtained by bioinformatic analysis. Here, we show the N40 central region of the aptamers, excluding the flanking 5’ (TAGGGAAGAGAAGGACATATGAT) and 3’ (TTGACTAGTACATGACCACTTGA) regions.
b Gibbs free energy was calculated considering the flanking regions using the Mfold web server (See S3 Fig for secondary structure predictions). Ranking and enrichment values were taken from the FASTAptamer toolkit [25].
c The cycle in which the aptamer was obtained, whether by Ranking or Enrichment, is shown in parenthesis.
d Aptamer Kd values were obtained by Microscale Thermophoresis (Fig 3A and 3B).
e Thermophoretic amplitude changes as an indicator of the extent of binding. Mean values and standard error were calculated from three independent measurements.