1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Johannsen, S.
Boehme, D.
Duepre, N.
Mueller, J.
Sigel, R.K.O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C8 H13 N2 O6 P
264.172
1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
To be Published
0353
Solution structure at different pHs of a DNA hairpin containing artificial nucleotides
DIH-DNA-17-mer
5015.311
DNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33)P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3')
1
syn
polymer
no
yes
(DT)(DT)(DA)(DA)(DT)(DT)(DT)(D33)(D33)(D33)(DA)(DA)(DA)(DT)(DT)(DA)(DA)
TTAATTTNNNAAATTAA
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-13.931
1
20
A
1
A
17
5.509
A_DT1:DA17_A
1
-20.617
-0.210
0.448
-0.159
-1.367
1
20
A
2
A
16
-3.860
A_DT2:DA16_A
2
-10.248
-0.227
0.463
-0.221
5.030
1
20
A
3
A
15
-1.907
A_DA3:DT15_A
3
-13.840
-0.161
0.331
-0.185
1.828
1
20
A
4
A
14
-7.915
A_DA4:DT14_A
4
-11.042
0.608
0.429
-0.061
-0.728
1
20
A
5
A
13
-4.357
A_DT5:DA13_A
5
-11.257
-0.776
0.352
-0.094
-1.363
1
20
A
6
A
12
-1.960
A_DT6:DA12_A
6
-12.363
-0.004
0.366
-0.110
2.600
1
20
A
7
A
11
9.165
A_DT7:DA11_A
7
-10.058
0.300
0.731
-0.422
2.873
35.985
A
A
1
2
-16.524
A
A
17
16
3.079
-10.070
-0.226
0.363
AA_DT1DT2:DA16DA17_AA
1
-2.840
4.661
34.478
1.921
-0.010
2.676
35.646
A
A
2
3
13.330
A
A
16
15
2.774
8.092
0.294
-0.173
AA_DT2DA3:DT15DA16_AA
2
1.367
-2.252
34.718
-1.275
-0.312
3.206
36.343
A
A
3
4
18.855
A
A
15
14
3.301
11.567
-0.674
0.149
AA_DA3DA4:DT14DT15_AA
3
-1.172
1.911
34.492
-1.411
0.914
3.505
29.678
A
A
4
5
15.327
A
A
14
13
3.664
7.756
0.217
-0.167
AA_DA4DT5:DA13DT14_AA
4
2.236
-4.418
28.583
-2.150
0.102
3.822
36.090
A
A
5
6
3.022
A
A
13
12
3.806
1.871
0.525
0.429
AA_DT5DT6:DA12DA13_AA
5
-0.077
0.124
36.043
0.383
-0.860
3.343
35.905
A
A
6
7
-4.022
A
A
12
11
3.427
-2.477
1.105
0.365
AA_DT6DT7:DA11DA12_AA
6
-1.645
2.672
35.785
0.959
-2.037
repository
Initial release
Version format compliance
1
0
2009-07-07
1
1
2011-07-13
NMR solution structure of modified DNA containing imidazole nucleosides at neutral pH
NMR solution structure of modified DNA containing imidazole nucleosides at basic pH
BMRB
Y
RCSB
2008-07-04
REL
REL
417
170
20
11
216
structures with the lowest energy
200
20
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D 1H-13C HSQC
2D 1H-1H NOESY
0.5
mM
120
mM
0.5
mM
120
mM
120 mM
4.7
ambient
298
K
120 mM
4.7
ambient
278
K
torsion angle dynamics, simulated annealing
1
lowest energy
0.5 mM DIH DNA 17-mer, 120 mM sodium perchlorate, 100% D2O
100% D2O
0.5 mM DIH DNA 17-mer, 120 mM sodium perchlorate, 90% H2O/10% D2O
90% H2O/10% D2O
Bruker Biospin
processing
TOPSPIN
1.3, 2.0, 2.1
Goddard
chemical shift assignment
SPARKY
3.1
Goddard
data analysis
SPARKY
3.1
Goddard
peak picking
SPARKY
3.1
Guntert, Braun and Wuthrich
structure solution
DYANA
1.5
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR_NIH
2.15
700
Bruker
Avance
Bruker Avance
T
1
n
1
DT
1
A
T
2
n
2
DT
2
A
A
3
n
3
DA
3
A
A
4
n
4
DA
4
A
T
5
n
5
DT
5
A
T
6
n
6
DT
6
A
T
7
n
7
DT
7
A
D33
8
n
8
D33
8
A
D33
9
n
9
D33
9
A
D33
10
n
10
D33
10
A
A
11
n
11
DA
11
A
A
12
n
12
DA
12
A
A
13
n
13
DA
13
A
T
14
n
14
DT
14
A
T
15
n
15
DT
15
A
A
16
n
16
DA
16
A
A
17
n
17
DA
17
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
OP2
H44
D33
D33
8
9
1.56
3
A
A
OP2
H44
D33
D33
8
9
1.54
5
A
A
H3
N1
DT
DA
1
17
1.60
8
A
A
OP2
H44
D33
D33
8
9
1.54
10
A
A
OP2
H44
D33
D33
8
9
1.56
17
A
A
H3
N1
DT
DA
7
11
1.59
20
A
A
H3
N1
DT
DA
1
17
1.59
1
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
1
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
2
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
2
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
2
-3.81
0.60
122.90
119.09
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
2
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
2
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
2
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
2
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
2
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
2
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
2
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
2
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
2
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
2
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
3
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
3
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
3
-3.82
0.60
122.90
119.08
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
3
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
3
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
2.85
0.30
108.30
111.15
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
3
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
3
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
3
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
3
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
3
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
3
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
3
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
3
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
4
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
4
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
4
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
4
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
4
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
4
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
4
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
4
2.14
0.30
108.30
110.44
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
4
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
4
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
4
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
4
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
5
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
5
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
5
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
5
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
5
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
5
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
5
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
5
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
5
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
5
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
5
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
5
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
5
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
14
14
14
N
5
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
5
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
5
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
6
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
6
-3.68
0.60
122.90
119.22
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
6
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
6
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
6
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
6
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
6
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
6
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
6
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
6
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
6
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
6
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
6
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
6
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
6
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
7
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
7
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
7
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
7
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
7
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
7
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
7
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
7
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
7
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
7
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
7
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
7
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
7
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
8
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
8
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
8
-3.60
0.60
122.90
119.30
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
8
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
8
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
8
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
8
-3.82
0.60
122.90
119.08
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
8
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.92
0.30
108.30
111.22
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
8
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
8
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
8
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
8
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
8
3.03
0.30
108.30
111.33
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
8
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
8
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
9
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
9
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
9
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
9
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
9
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
9
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
9
-3.71
0.60
122.90
119.19
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
9
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
9
3.03
0.30
108.30
111.33
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
9
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
9
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
9
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
9
2.14
0.30
108.30
110.44
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
9
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
9
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
9
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
10
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
10
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
10
-4.01
0.60
122.90
118.89
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
10
1.98
0.30
108.30
110.28
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
10
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
10
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
10
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
10
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
10
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
10
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
10
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
10
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
10
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
10
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
10
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
11
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
11
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
11
-3.89
0.60
122.90
119.01
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
11
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
11
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
11
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
11
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
11
3.34
0.30
108.30
111.64
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
11
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
11
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
11
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
11
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
11
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
11
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
11
2.85
0.30
108.30
111.15
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
12
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
12
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
12
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
12
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
12
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
12
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
12
3.11
0.30
108.30
111.41
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
12
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
12
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
12
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
12
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
12
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
12
2.96
0.30
108.30
111.26
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
12
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
13
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
13
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
13
-3.70
0.60
122.90
119.20
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
13
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
13
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
13
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
13
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
13
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
13
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
13
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
13
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
13
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
13
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
13
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
13
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
14
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
14
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
14
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
14
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
14
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
14
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
14
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
14
3.14
0.30
108.30
111.44
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
14
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
14
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
14
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
14
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
14
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
14
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
14
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
15
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
15
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
15
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
15
-4.04
0.60
122.90
118.86
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
15
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
15
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
15
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
15
-3.68
0.60
122.90
119.22
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
15
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
15
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
15
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
15
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
15
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
15
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
15
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
15
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
15
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
16
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
16
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
16
-3.67
0.60
122.90
119.23
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
16
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
16
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
16
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
16
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
16
-3.74
0.60
122.90
119.16
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
16
3.15
0.30
108.30
111.45
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
16
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
16
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
16
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
16
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
16
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
16
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
16
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
17
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
17
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
17
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
17
-3.68
0.60
122.90
119.22
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
17
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
17
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
17
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
17
2.90
0.30
108.30
111.20
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
17
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
17
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
17
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
17
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
17
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
17
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
17
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
17
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
18
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
18
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
18
-3.78
0.60
122.90
119.12
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
18
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
18
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
18
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
18
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
18
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
18
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
18
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
18
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
18
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
18
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
18
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
18
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
19
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
19
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
19
1.87
0.30
108.30
110.17
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
19
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
19
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
19
-3.69
0.60
122.90
119.21
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
19
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
19
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
19
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
19
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
19
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
19
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
19
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
19
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
20
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
20
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
20
-3.71
0.60
122.90
119.19
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
20
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
20
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
20
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
20
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
20
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
20
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
20
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
20
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
20
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
20
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
20
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
20
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
DIH-DNA-17-mer
NMR solution structure of modified DNA containing imidazole nucleosides at acidic pH
1
N
N
covale
1.611
A
DT
7
A
O3'
DT
7
1_555
A
D33
8
A
P
D33
8
1_555
covale
1.610
A
D33
8
A
O3'
D33
8
1_555
A
D33
9
A
P
D33
9
1_555
covale
1.610
A
D33
9
A
O3'
D33
9
1_555
A
D33
10
A
P
D33
10
1_555
covale
1.612
A
D33
10
A
O3'
D33
10
1_555
A
DA
11
A
P
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
A
DA
17
A
N1
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
A
DA
17
A
N6
DA
17
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
A
DA
16
A
N1
DA
16
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
A
DA
16
A
N6
DA
16
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
15
A
N3
DT
15
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
15
A
O4
DT
15
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
14
A
N3
DT
14
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
14
A
O4
DT
14
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
A
DA
13
A
N1
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
A
DA
13
A
N6
DA
13
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
A
DA
12
A
N1
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
A
DA
12
A
N6
DA
12
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
A
DA
11
A
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
A
DA
11
A
N6
DA
11
1_555
DNA
DNA 17-mer, hairpin, artificial nucleobase, imidazole nucleoside, shifted pKa, DNA
2K67
PDB
1
2K67
TTAATTTXXXAAATTAA
1
17
2K67
1
17
2K67
A
1
1
17
BINDING SITE FOR RESIDUE D33 A 8
Software
1
BINDING SITE FOR RESIDUE D33 A 9
Software
1
BINDING SITE FOR RESIDUE D33 A 10
Software
2
A
DT
7
A
DT
7
1
1_555
A
DT
7
A
DT
7
1
1_555
A
DT
6
A
DT
6
2
1_555
A
DA
11
A
DA
11
2
1_555