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. 2001 Jan 15;29(2):455–463. doi: 10.1093/nar/29.2.455

Table 1. Kd of tectoRNA complexes.

Molecule number
 Loops/receptors
 Insert length (bp)
 Nature of linker (hinge)
 Substitutions
 Dimerization in conc. range <15 µM
 Kd value (nM) Comments
1 RL-GAAA 0 (all W.C. pairs) – Yes 4.3 ± 0.4  
2 RL-GAAA 0 U2/U2 – Yes 4.2 ± 0.8  
3 L-GUAA 0 U2/U2 – No –  
4 R-GUAA 0 U2/U2 – No –  
3 + 4 L-GUAA + R-GUAA       Yes 150 ± 21 Kinetic equilibrium
2 + 3 L-GUAA + RL-GAAA       Yes 4600 ± 1400 Kinetic equilibrium
2 + 4 R-GUAA + RL-GAAA       No –  
5 LL-GAAA +1 U/Nick – No –  
6 RR-GAAA –1 U/U – No    
5 + 6 LL-GAAA + RR-GAAA       Yes 210 ± 85 Kinetic equilibrium
7 RL-GAAA +3 GU4/U4C – No –  
8 RL-GAAA +11 (all W.C. pairs) – Yes 100 ± 3 Kinetic equilibrium
9 RL-GAAA +11 U2-U2/U2-U2 – Yes 500 ± 260 Kinetic equilibrium
10 RL-GAAA +11 U3-U3/U2-U2 – Yes 68 ± 28  
11 RL-GAAA +11 U3-U2/U3-U2 – Yes 60 ± 14  
12 RL-GAAA +10 U3-U2/U3-U2 – Yes 540 ± 65 Kinetic equilibrium
13 RL-GAAA +12 U3-U2/U3-U2 – Yes 68 ± 23  
14 RL-GAAA +22 U3-U2/U3-U2   No –  
15 RL-GAAA +11 A3-A2/A3-A2 – Yes 130 ± 15 Kinetic equilibrium
16 RL-GAAA +11 U3-U2/U3-U2 G29A and G30A Yes 70 Kinetic equilibrium
17 RL-GAAA +11 U3-U2/U3-U2 U24C and U51C Yes 70  
18 RL-GAAA +11 U3-U2/U3-U2 G18C, U20G, U21A, C22U, U24G, G44C, G46U, A47G, C49A, C50G, U51C Yes 26 ± 4  
19 L-GUAA +11 U3-U2/U3-U2   No –  
20 R-GUAA +11 U3-U2/U3-U2   No –  
  L-GUAA + R-GUAA       Yes 3500 Kinetic equilibrium
21 L-GUGA +11 U3-U2/U3-U2   No –  
22 R-GUGA +11 U3-U2/U3-U2   No –  
21 + 22 L-GUGA + R-GUGA       No –  

The structural features of each tectoRNA are summarized in columns 2–5, including the nature of the tetraloop and the specificity of the tetraloop receptor (column 2), the length of the linker insert (column 3), the nature of the linker (column 4) and base substitutions in the molecule (column 5). Kd were measured at 15 mM Mg(OAc)2, by quantitating bands from native gel electrophoresis as described in the Materials and Methods and are given in column 7. Kd values with standard deviations are averages of parameters measured from three independent experiments. For some constructs, the mobility of the dimer band increased as RNA concentration decreased, eventually merging with the monomer band. In these cases Kd was estimated from the mobility of the RNA dimer. This behavior was attributed to kinetic equilibrium between monomer and dimer, as indicated in column 8.