Table 4.
Most relevant available experimental results of (A) native, (B) S3′, and (C) S5′ reactions in solution to compare with the calculated barriers of our simplest models of RNA phosphate transesterification. “--” denotes the experimental data could not be found.
|
Native pH |
Liu et al.[a] | Harris et al.[b] | Iyer et al.[c] | Thomson et al.[d] | Weinstein et al.[e] | Dantzman et al.[f] | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
|
|
|
|
|
|
|
|
|
||||||
| 8 | -- | -- | 54266 | 27.6 | -- | -- | -- | -- | -- | -- | 12[m] | 21.5 |
| 9 | -- | -- | 5427 | 26.2 | -- | -- | -- | -- | -- | -- | -- | -- |
| 10 | -- | -- | 543 | 24.8 | -- | -- | -- | -- | 7289[j] | 24.1 | -- | -- |
| 10.06 | 4800[i] | 27.3[i] | 473 | 24.7 | -- | -- | -- | -- | -- | -- | -- | -- |
| 11 | -- | -- | 54 | 23.4 | -- | -- | -- | -- | 729[k] | 22.8 | -- | -- |
| 11.5 | -- | -- | 17 | 22.7 | -- | -- | 825 | 25.1 | -- | -- | -- | -- |
| 12 | -- | -- | 6 | 22 | -- | -- | -- | -- | -- | -- | -- | -- |
| 13 | -- | -- | 0.7 | 20.7 | -- | -- | -- | -- | 37[l] | 21.1 | -- | -- |
| Infinity | -- | -- | 0.2 | 19.9 | -- | -- | -- | -- | -- | -- | -- | -- |
| (A) | ||||||||||||
|
S3′ pH |
Liu et al.[a] | Harris et al.[b] | Iyer et al.[c] | Thomson et al.[d] | Weinstein et al.[e] | Dantzman et al.[f] | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
|
|
|
|
|
|
|
|
|
||||||
| 8 | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 9 | -- | -- | -- | -- | 11552[i] | 30.5 | -- | -- | -- | -- | -- | -- |
| 10 | -- | -- | -- | -- | 5403[j] | 30 | -- | -- | 7[o] | 20.2 | -- | -- |
| 10.06 | 25 | 23.9 | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 11 | -- | -- | -- | -- | 650[k] | 28.5 | -- | -- | 0.4[p] | 18.5 | -- | -- |
| 11.5 | -- | -- | -- | -- | 249[l] | 27.8 | -- | -- | -- | -- | -- | -- |
| 12 | -- | -- | -- | -- | 87[m] | 27.1 | -- | -- | -- | -- | -- | -- |
| 13 | -- | -- | -- | -- | 20.5[n] | 26 | -- | -- | 0.02[q] | 16.8 | -- | -- |
| Infinity | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| (B) | ||||||||||||
|
S5′ pH |
Liu et al.[a] | Harris et al.[b] | Iyer et al.[c] | Thomson et al.[d] | Weinstein et al.[e] | Dantzman et al.[f] | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
t1/2[g] (min) |
Barrier[h] (kcal/mol) |
|
|
|
|
|
|
|
|
|
||||||
| 8 | 132 | 23.4 | -- | -- | 9176[i] | 30.3 | 46[o] | 23.3 | -- | -- | -- | -- |
| 9 | 29 | 22.5 | -- | -- | 6496[j] | 30.1 | 4 | 21.7 | -- | -- | -- | -- |
| 10 | -- | -- | -- | -- | 1155[k] | 28.9 | -- | -- | -- | -- | -- | -- |
| 10.06 | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| 11 | -- | -- | -- | -- | 116[l] | 27.3 | -- | -- | -- | -- | -- | -- |
| 11.5 | -- | -- | -- | -- | 32.6[m] | 26.4 | -- | -- | -- | -- | -- | -- |
| 12 | -- | -- | -- | -- | 15.4[n] | 25.8 | -- | -- | -- | -- | -- | -- |
| 13 | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| Infinity | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
| (C) | ||||||||||||
37°C, UpG, Eq. (1) in Ref.[[14]].
80°C, mNB, Ref.[[91]].
37°C, UpU, Ref.[[95]].
10°C, IpU, Ref.[[90]].
25°C, UppNp, Ref.[[96]].
If the time of half life (t1/2) is not given in the reference papers, then t1/2 is derived from the first order rate constant k as follows: t1/2 = (ln 2)/k.
The energy barrier is converted from the rate constant by conventional transition-state theory.
4800 to 5400 min, 27.3 to 27.4 kcal/mol.
The extracted value of k is ~10−5.8 s−1, from the Fig. 4 in Ref. [[90]].
The extracted value of k is ~10−4.8 s−1, from the Fig.4 in Ref. [[90]].
The extracted value of k is ~10−3.5 s−1, from the Fig. 4 in Ref. [[90]].
The extracted value of k is ~10−3 s−1, from the Fig. 3 in Ref. [[96]].
37°C, UspG, Eq. (1) in Ref.[[14]].
80°C, S3′mNB, Ref.[[91]].
37°C, UspU, Ref.[[95]].
10°C, IspU, Ref.[[90]].
25°C, UsppNp, Ref.[[96]].
If the time of half life (t1/2) is not given in the reference papers, then t1/2 is derived from the first order rate constant k as follows: t1/2 = (ln 2)/k.
The energy barrier is converted from the rate constant by conventional transition state theory.
The extracted value of k is ~10−2.8 s−1, from the Fig. 4 in Ref. [[90]].
The extracted value of k is ~10−1.5 s−1, from the Fig. 4 in Ref. [[90]].
The extracted value of k is ~10−0.2 s−1, from the Fig. 4 in Ref. [[90]].
37°C, UpsG, Eq. (1) in Ref.[[14]].
80°C, S5′mNB, Ref.[[91]].
37°C, UpsU, Ref.[[95]].
10°C, IpsU, Ref.[[90]].
25°C, UpspNp, Ref.[[96]].
If the time of half life (t1/2) is not given in the reference papers, then t1/2 is derived from the first order rate constant k as follows: t1/2 = (ln 2)/k.
The energy barrier is converted from the rate constant by conventional transition state theory.
The extracted value of k is ~10−3.6 s−1, from the Fig. 2 in Ref. [[95]].