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
10.2210/pdb2k68/pdb
pdb_00002k68
DID_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
-7.459
1
20
A
1
A
17
9.745
A_DT1:DA17_A
1
-16.575
-0.096
0.085
-0.163
-3.733
1
20
A
2
A
16
-4.027
A_DT2:DA16_A
2
-11.549
0.534
0.302
-0.336
2.423
1
20
A
3
A
15
-2.636
A_DA3:DT15_A
3
-11.860
0.547
0.380
-0.087
4.326
1
20
A
4
A
14
-2.731
A_DA4:DT14_A
4
-9.260
0.308
0.526
-0.132
-4.941
1
20
A
5
A
13
-3.464
A_DT5:DA13_A
5
-10.836
0.108
0.618
-0.129
-3.876
1
20
A
6
A
12
-0.462
A_DT6:DA12_A
6
-10.608
-0.288
0.515
-0.163
-1.043
1
20
A
7
A
11
-1.698
A_DT7:DA11_A
7
-2.701
0.114
1.044
-0.513
3.409
37.337
A
A
1
2
-14.498
A
A
17
16
3.546
-9.182
-0.553
0.282
AA_DT1DT2:DA16DA17_AA
1
-3.102
4.898
36.101
1.753
0.420
2.984
32.503
A
A
2
3
1.468
A
A
16
15
3.045
0.819
-0.175
-0.297
AA_DT2DA3:DT15DA16_AA
2
4.577
-8.205
32.178
-0.663
1.054
3.053
32.691
A
A
3
4
30.428
A
A
15
14
3.294
16.389
-0.163
0.372
AA_DA3DA4:DT14DT15_AA
3
-0.114
0.211
28.384
-2.299
0.269
4.195
31.786
A
A
4
5
16.748
A
A
14
13
4.123
9.051
-0.126
0.838
AA_DA4DT5:DA13DT14_AA
4
-0.702
1.299
30.494
-0.623
0.063
3.377
32.320
A
A
5
6
18.225
A
A
13
12
3.488
9.973
0.329
0.120
AA_DT5DT6:DA12DA13_AA
5
3.022
-5.522
30.636
-1.689
-0.014
3.866
33.165
A
A
6
7
5.625
A
A
12
11
3.856
3.203
0.130
0.545
AA_DT6DT7:DA11DA12_AA
6
-2.810
4.936
32.897
0.317
-0.787
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2009-07-07
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NMR solution structure of modified DNA containing imidazole nucleosides at acidic pH
NMR solution structure of modified DNA containing imidazole nucleosides at basic pH
BMRB
Y
RCSB
2008-07-04
REL
REL
28
354
147
20
12
185
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
7.2
ambient
298
K
120 mM
7.2
ambient
278
K
torsion angle dynamics, simulated annealing
1
lowest energy
0.5 mM DID DNA 17-mer, 120 mM sodium perchlorate, 100% D2O
100% D2O
0.5 mM DID 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
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
-3.68
0.60
122.90
119.22
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
1
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
1
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
-3.64
0.60
122.90
119.26
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
1
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
1
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
1
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
2
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
2
-3.75
0.60
122.90
119.15
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
2
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
2
-3.79
0.60
122.90
119.11
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
2
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
2
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
2
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
2
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
2
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
2
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
2
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
2
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
2
2.05
0.30
108.30
110.35
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
2
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
3
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
3
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
3
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
3
2.14
0.30
108.30
110.44
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
3
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
3
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
3
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
3
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
3
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
3
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
3
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
3
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
4
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
4
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
4
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
4
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
4
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
-3.60
0.60
122.90
119.30
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
4
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
4
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
4
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
4
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
4
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
4
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
4
2.38
0.30
108.30
110.68
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
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
5
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
5
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
5
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
5
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
5
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
5
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
5
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
5
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
5
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
5
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
6
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
6
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
6
-3.76
0.60
122.90
119.14
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
6
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
6
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
6
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.96
0.30
108.30
111.26
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
6
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
6
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
6
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
6
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
6
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
6
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
6
2.59
0.30
108.30
110.89
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
7
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
7
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
7
-3.67
0.60
122.90
119.23
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
7
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
7
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
7
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
7
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
7
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
7
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
7
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
7
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
7
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
7
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
7
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
8
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
8
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
8
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
8
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
8
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
8
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
8
-3.67
0.60
122.90
119.23
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
8
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
8
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
8
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
8
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
8
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
8
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
8
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
8
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
9
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
9
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
9
-3.74
0.60
122.90
119.16
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
9
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
9
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
9
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
9
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
9
2.95
0.30
108.30
111.25
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
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
9
2.01
0.30
108.30
110.31
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
9
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
9
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
9
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
9
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
10
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
10
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
10
-3.60
0.60
122.90
119.30
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
10
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
10
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
10
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
10
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
10
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
10
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
10
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
10
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
10
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
10
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
11
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
11
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
11
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
11
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
11
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
11
2.50
0.30
108.30
110.80
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
11
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
11
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
11
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
11
2.41
0.30
108.30
110.71
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
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
11
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
11
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
12
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
12
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
12
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
12
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
12
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
12
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
12
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
12
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
12
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
12
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
12
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
12
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
12
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
12
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
12
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
13
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
13
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
13
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
13
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
13
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
13
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
13
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
13
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
13
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
13
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
13
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
13
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
13
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
13
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
14
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
14
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
14
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
14
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
14
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
14
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
14
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
14
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
14
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
14
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
14
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
14
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
14
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
14
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
15
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
15
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
15
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
15
2.31
0.30
108.30
110.61
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
15
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
15
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
15
2.59
0.30
108.30
110.89
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
15
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
15
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
15
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
15
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
15
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
15
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
15
2.52
0.30
108.30
110.82
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
16
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
16
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
16
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
16
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
16
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
16
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
16
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
16
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
16
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
16
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
16
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
16
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
16
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
16
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
14
14
14
N
16
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
16
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
16
2.88
0.30
108.30
111.18
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
17
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
17
2.35
0.30
108.30
110.65
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
17
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
17
2.14
0.30
108.30
110.44
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
17
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
17
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
17
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
17
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
17
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
17
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
17
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
17
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
17
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
17
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
18
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
18
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
18
-3.71
0.60
122.90
119.19
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
18
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
18
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
18
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
18
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
18
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
18
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
18
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
18
2.36
0.30
108.30
110.66
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
18
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
18
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
18
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
18
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
18
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
19
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
19
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
19
-3.86
0.60
122.90
119.04
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
19
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
19
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
19
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
19
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
19
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
19
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
19
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
19
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
19
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
19
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
19
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
19
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
19
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
20
2.63
0.30
108.30
110.93
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
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
20
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
20
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
20
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
20
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
20
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DA
DA
DA
11
11
11
N
20
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DA
DA
DA
12
12
12
N
20
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N9
DA
DA
DA
13
13
13
N
20
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
14
14
14
N
20
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
20
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N9
DA
DA
DA
16
16
16
N
20
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DA
DA
DA
17
17
17
N
NMR solution structure of modified DNA containing imidazole nucleosides at neutral pH
1
N
N
covale
1.609
both
A
DT
7
A
O3'
DT
7
1_555
A
D33
8
A
P
D33
8
1_555
covale
1.610
both
A
D33
8
A
O3'
D33
8
1_555
A
D33
9
A
P
D33
9
1_555
covale
1.609
both
A
D33
9
A
O3'
D33
9
1_555
A
D33
10
A
P
D33
10
1_555
covale
1.611
both
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
2K68
PDB
1
2K68
TTAATTTXXXAAATTAA
1
17
2K68
1
17
2K68
A
1
1
17
BINDING SITE FOR RESIDUE D33 A 8
A
D33
8
Software
1
BINDING SITE FOR RESIDUE D33 A 9
A
D33
9
Software
1
BINDING SITE FOR RESIDUE D33 A 10
A
D33
10
Software
1
A
DT
7
A
DT
7
1
1_555
A
DT
7
A
DT
7
1
1_555
A
DA
11
A
DA
11
1
1_555