Site-Selective Artificial Ribonucleases: Oligonucleotide Conjugates Containing Multiple Imidazole Residues in the Catalytic Domain
Table 2
Distances between active centers of the conjugates B-Im(4/m) and RNA target atoms.
Molecule
Final structure
Energy (kcal/mol)
ΔE (kcal/mol)
Dist. Pair 1(E)
Dist. Pair 2(E)
for O1
for O2
Im1-OH(a)
Im2-OP(b)
Im1-OH
Im2-OP
M-Im(4/1)
F1- Im(4/1)
47.3
18.2
13
6.2
11.4
26.6
21
F2- Im(4/1)
66.7
37.6
32.4
6.2
14.3
21.1
22.9
F3- Im(4/1)
48.3
19.2
14.0
6.6
16.3
23.0
33.9
F4- Im(4/1)
28.6
−0.6
−5.8
7.1
7.0
2.9
7.5
F5- Im(4/1)
60.2
31.1
25.9
7.5
17.2
11.8
11.5
F6- Im(4/1)
42.6
13.5
8.3
12.8
9
23.1
13.4
F7- Im(4/1)
54.9
25.8
20.5
11.9
12.7
15.7
25.9
F8- Im(4/1)
47.3
18.2
13.0
7.3
15.0
24.8
21.0
F9- Im(4/1)
49.8
20.7
15.5
10.7
17.0
16.5
23.7
O1- Im(4/1)
29.1
—
—
3.0
3.0
12.9
23.1
O2- Im(4/1)
34.3
—
—
23.5
25.7
3.2
3.3
M-Im(4/2a)
F1- Im(4/2a)
−6.7
−4.3
−5.8
12.4
25.1
26.4
19.8
F2- Im(4/2a)
24.0
26.3
24.8
23.1
15.6
23.2
34.8
F3- Im(4/2a)
0.5
2.9
1.4
21.1
11.6
21.3
19.8
F4- Im(4/2a)
9.7
12.0
10.5
6.4
15.8
23.3
27.8
F5- Im(4/2a)
1.7
4.0
2.5
5.6
10.1
21.6
26.7
F6- Im(4/2a)
23.4
25.8
24.3
26.1
30.6
16.2
8.6
F7- Im(4/2a)
23.4
25.8
24.3
26.1
30.6
16.2
8.6
F8- Im(4/2a)
0.5
2.9
1.4
21.2
11.6
24.4
17.4
F9- Im(4/2a)
13.3
15.6
14.1
14.4
18.4
28.2
27.8
O1- Im(4/2a)
−2.4
—
—
3.17
3.0
20.1
33.7
O2- Im(4/2a)
−0.9
—
—
17.7
17.6
3.0
3.2
M-Im(4/2b)
F1- Im(4/2b)
−4.7
6.9
−16.2
23.7
15.9
21.4
19.9
F2- Im(4/2b)
−17.9
−6.3
−29.3
30.9
32.7
21.9
30.7
F3- Im(4/2b)
−17.8
−6.2
−29.2
27.6
36.0
25.9
21.9
F4- Im(4/2b)
0.1
11.7
−11.3
5.3
23.3
14.5
14.3
F5- Im(4/2b)
−9.1
2.5
−20.5
21.1
26.2
23.5
25.8
F6- Im(4/2b)
0.1
11.7
−11.3
18.5
9.2
11.3
19.7
F7- Im(4/2b)
0.1
11.7
−11.3
18.5
9.2
11.3
19.7
F8- Im(4/2b)
−6.7
4.9
−18.1
9.0
10.6
20.7
23.3
F9- Im(4/2b)
−2.5
9.1
−13.9
14.9
30.4
27.9
31.8
O1-Type3
−11.6
—
—
3.1
3.0
13.4
14.9
O2-Type3
11.4
—
—
25.2
27.2
3.0
3.0
(a)Im1-OH represents the distance between N1 of one of the imidazole residues and the 2′OH group of C63.
(b)Im2-OP represents the distance between N1 of the other imidazole residue and the oxygen of the phosphate group connecting C63 and A64.
