Table 1. Sequences generated from RBM-SU, log-likelihoods, binding predictions (based on the comparison of the RBM-SU log-likelihood and the threshold in Fig 5D), and results from gel shift assay (B for binders, NB for non binders) and exosite binding assays.
For comparison, data for ThA, ThB, ThC and ThD sequences from Ref [41] are shown. ThB and ThC have not been tested for binding with our experimental setup (so NA is used in the corresponding column), although they are expected to bind thrombin given the results obtained in Ref [41].
| Label | Sequence | Log-likelihood | Binding Pred. | Binding Result | Exosite | Distance round 8 | |
|---|---|---|---|---|---|---|---|
| RBM-SC | RBM-SU | ||||||
| r1 | AGTGATGATGTGTGGTAGGC | -11.5 | -23.4 | NB | NB* | NA | 0 |
| r2 | AGTGTAGGTGTGGATGATGC | -11.4 | -24.0 | NB | NB | NA | 0 |
| r3 | TAGGTTTTGGGTAGCGTGGT | -13.0 | -22.3 | NB | NB | NA | 1 |
| r4 | AGGGATGATGTGTGGCAGGA | -17.3 | -23.6 | NB | NB | NA | 1 |
| r5 | CTAGGACGGGTAGGGCGGTG | -15.9 | -21.2 | NB | NB | NA | 1 |
| r6 | AGGGATGTGTGTGGTAGGCT | -14.1 | -23.9 | NB | NB* | NA | 0 |
| r7 | AGGGATGCTGCGTGGTAGGC | -10.2 | -20.0 | B | B | II | 0 |
| r8 | GAGGGTTGGTGTGGTTGGCA | -10.6 | -11.0 | B | B | I | 0 |
| r9 | AGGGTTGGTGTGTGGTTGGC | - 9.8 | -11.8 | B | B | I | 0 |
| r10 | ATGGTTGGTTTATGGTTGGC | -15.2 | -14.7 | B | B | I | 1 |
| r11 | GAAGGGTGGTCAGGGTGGGA | -16.5 | -15.7 | B | B | I | 2 |
| r12 | GGAGGGTGGGTCGGGTGGGA | -15.2 | -15.0 | B | B | NA | 1 |
| r13 | GGGGTTGGTACAGGGTTGGC | -16.3 | -14.9 | B | B | I | 2 |
| r14 | AGATGGGCAGGTTGGTGCGG | -16.3 | -16.3 | B | B | I | 2 |
| r15 | AGATGGGTGGGTAGGGTGGG | -13.9 | -14.3 | B | B | NA | 2 |
| r16 | ATAGGGTGGGTGGGTGGGTA | -13.1 | -15.0 | B | B | NA | 1 |
| r17 | TGGTGGTTGGGTTGGGTTGG | -12.8 | -12.3 | B | B | I | 1 |
| r18 | TGGGATGGGATTGGTAGGCG | -12.2 | -20.4 | B | NB | NA | 0 |
| r19 | AGGGTTGGTTATGTGGTTGG | -19.3 | -20.0 | B | B | I | 0 |
| r20 | ATTGGTTGGGTAGGGTGGTT | -10.4 | -12.2 | B | B | I | 0 |
| r21 | AAACGGTTGGTGAGGTTGGT | -11.2 | -12.4 | B | B | I | 0 |
| r22 | CGGGGTGGTGTGGGTGGGAG | -15.1 | -14.7 | B | B | NA | 2 |
| r23 | TATTGGTTGGATAGGTTGGT | -13.8 | -13.1 | B | B | I | 1 |
| r24 | AGGGTTGGGTGGTTGGATGA | -14.9 | -14.1 | B | B | I | 1 |
| r25 | CGGGTTGGGGGGTTGGATTC | -17.0 | -15.0 | B | B | I | 1 |
| r26 | CGGTTGGGGGGGTTGGATAC | -18.8 | -15.5 | B | B | I | 1 |
| r27 | TGTGGGTTGGTGAGGTAGGT | -18.0 | -17.0 | B | NB | NA | 1 |
| ThA | AGGGATGATGTGTGGTAGGC | -6.0 | -19.8 | B | B | II | 0 |
| ThB | AGGGTAGGTGTGGATGATGC | -5.7 | -20.7 | NB | NA | II | 0 |
| ThC | TAGGTTTTGGGTAGGGTGGT | -6.8 | -18.1 | B | NA | I | 0 |
| ThD | GTAGGATGGGTAGGGTGGTC | -5.7 | -13.9 | B | B | I | 0 |
| p1 | AGGGATGATGTGTGGTTGGC | -10.3 | -17.1 | B | B | I | 0 |
| p2 | AGGGATGGTGTGTGGTAGGC | - 9.2 | -16.2 | B | B | II | 0 |
| p3 | AGGGTTGATGTGTGGTAGGC | - 7.2 | -19.1 | B | B | II | 0 |
| p4 | AGGGATGGTGTGTGGTTGGC | - 9.3 | -13.1 | B | B | I | 0 |
| p5 | AGGGTTGATGTGTGGTTGGC | -11.1 | -16.2 | B | B | I | 0 |
| p6 | AGGGTTGGTGTGTGGTAGGC | - 9.7 | -15.2 | B | B | II | 0 |
*Aptamers and r1 and r6 did not show thrombin binding gel band, but their pattern indicates a possible weak interaction with thrombin.