Table 1. Determination of Aptamer Binding Properties using the SPR-Based Characterization Platforma.
| target | reported KD | ka (M–1 s–1) | kd (s–1) | KD,kinetic | KD,equilibrium |
|---|---|---|---|---|---|
| In Vitro Selected RNA Aptamers | |||||
| arginine | 56 μM,15 76 μM15 | f | f | – | 140 ± 40 μM |
| citrulline | 62 μM,15 68 μM15 | f | f | – | 31 ± 1 μM |
| flavin mononucleotide | 500 nM16 | (7.6 ± 1.2) × 104 | (8.4 ± 1.8) × 10–2 | 1.1 ± 0.4 μM | 710 ± 20 nM |
| malachite green | 1 μM,28 1.03 μM,29 117 nM30 | (2.1 ± 0.3) × 104 | (2.0 ± 0.4) × 10–2 | 950 ± 340 nM | 2.0 ± 0.1 μM |
| theophylline | 320 nM,19 200–400 nM31c | (1.5 ± 0.1) × 105 | (6.3 ± 0.4) × 10–2 | 430 ± 40 nM | 340 ± 20 nM |
| tyrosine | 23 μM17g | f | f | – | 17 ± 6 μMh |
| In Vitro Selected DNA Aptamer | |||||
| ATP | 13 μM18i, 6 μM20j | f | f | – | 8.8 ± 3.0 μM |
| Natural RNA Aptamers | |||||
| c-di-GMP (class I) | 1 nM21b, 10 pM34c,k, 5.9 nM51c,k, 43 nM52d,k, 47 nM52d,k, 13.8 nM51e,k, 90 nM51e,k | (2.3 ± 0.2) × 104 | (2.3 ± 0.9) × 10–5 | 980 ± 470 pM | – |
| c-di-GMP (class II) | 200 pM22b | (1.6 ± 0.5) × 105 | (9.6 ± 1.9) × 10–3 | 60 ± 31 nM | 120 ± 20 nM |
| glycine | 3.5 μM53b, 20 μM23b | 28 ± 5 | (5.6 ± 2.5) × 10–3 | 200 ± 120 μM | – |
| (7.2 ± 1.0) × 102,b | (2.5 ± 0.3) × 10–3,b | 3.5 ± 1.0 μMb | – | ||
| TPP (Thi1) | 210 pM24b | (1.5 ± 0.4) × 105 | (2.1 ± 0.5) × 10–4 | 1.4 ± 0.7 nM | – |
| TPP (thiM) | 8.65 nM38e, 8.43 nM38c, 30 nM25b | (4.0 ± 1.4) × 105 | (3.6 ± 2.0) × 10–4 | 890 ± 800 pM | – |
All reported values are measured at 5 mM MgCl2 unless otherwise indicated. Reported ka, kd, and KD,equilibrium values are the mean and standard deviation of at least three independent experiments. Reported KD,kinetic values are calculated as kd/ka. Unreported KD,kinetic values are due to kinetic constants that cannot be uniquely determined. Unreported KD,equilibrium values are due to a slow approach to equilibrium.
Measured at 20 mM MgCl2.
Measured at 10 mM MgCl2.
Measured at 6 mM MgCl2.
Measured at 2.5 mM MgCl2.
Value cannot be uniquely determined as one kinetic parameter may be outside instrument measurement limits.
Value reported for the Tyr 1b aptamer.
Value reported for the Tyr 1 minimal aptamer, which removes a nonessential stem loop from the Tyr 1b aptamer.
Value reported for a modified aptamer internally labeled with fluorescein between two residues.
Value reported for adenosine.
Value reported for aptamer with a modified stem loop sequence.