1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Soliva, R.
Monaco, V.
Gomez-Pinto, I.
Meeuwenoord, N.J.
van der Marel, G.A.
van Boom, J.H.
Gonzalez, C.
Orozco, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C8 H18
114.229
N-OCTANE
non-polymer
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
2973
2985
10.1093/nar/29.14.2973
11452022
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety.
2001
10.2210/pdb1iey/pdb
pdb_00001iey
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2998.983
5'-D(P*CP*CP*AP*CP*CP*(OCT)GP*GP*AP*AP*C)-3'
1
syn
polymer
3092.013
5'-D(*GP*TP*TP*CP*CP*GP*GP*TP*GP*G)-3'
1
syn
polymer
114.229
N-OCTANE
1
syn
non-polymer
no
no
(DC)(DC)(DA)(DC)(DC)(DG)(DG)(DA)(DA)(DC)
CCACCGGAAC
A
polydeoxyribonucleotide
no
no
(DG)(DT)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DG)
GTTCCGGTGG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
9.180
1
19
A
1
B
20
-2.985
A_DC1:DG20_B
1
-23.031
-0.392
-0.317
0.077
4.787
1
19
A
2
B
19
0.671
A_DC2:DG19_B
2
-21.888
-0.790
-0.695
-0.199
-10.258
1
20
A
3
B
18
2.689
A_DA3:DT18_B
3
-19.625
0.192
-0.199
0.087
-22.116
1
19
A
4
B
17
-3.558
A_DC4:DG17_B
4
-12.381
-0.114
0.377
0.050
-12.911
1
19
A
5
B
16
4.077
A_DC5:DG16_B
5
4.370
0.109
-0.044
0.123
6.632
1
19
A
6
B
15
0.742
A_DG6:DC15_B
6
13.064
-0.168
-0.017
0.023
24.705
1
19
A
7
B
14
0.618
A_DG7:DC14_B
7
-1.261
0.243
0.565
0.193
3.694
1
20
A
8
B
13
1.223
A_DA8:DT13_B
8
-24.844
0.483
-0.046
0.003
-2.177
1
A
9
B
12
12.597
A_DA9:DT12_B
9
-27.685
-0.373
0.672
0.356
-22.112
1
19
A
10
B
11
-3.043
A_DC10:DG11_B
10
-17.334
0.908
0.225
-0.207
3.347
43.471
A
A
1
2
-2.121
B
B
20
19
3.353
-1.565
0.516
1.268
AA_DC1DC2:DG19DG20_BB
1
6.896
-9.348
42.919
1.868
-0.009
3.505
38.902
A
A
2
3
30.656
B
B
19
18
3.705
19.491
0.044
0.636
AA_DC2DA3:DT18DG19_BB
2
-5.152
8.104
33.444
-1.871
-0.813
3.243
30.413
A
A
3
4
7.025
B
B
18
17
3.322
3.658
-0.522
-0.813
AA_DA3DC4:DG17DT18_BB
3
-5.389
10.349
29.723
-2.294
-0.101
3.164
42.118
A
A
4
5
-3.763
B
B
17
16
3.148
-2.702
0.729
-0.014
AA_DC4DC5:DG16DG17_BB
4
1.361
-1.896
42.014
0.250
-0.878
2.225
19.651
A
A
5
6
35.675
B
B
16
15
2.812
11.422
-0.431
-0.136
AA_DC5DG6:DC15DG16_BB
5
-0.372
1.162
16.012
-5.092
1.111
3.150
33.745
A
A
6
7
2.390
B
B
15
14
3.115
1.387
-0.520
0.757
AA_DG6DG7:DC14DC15_BB
6
-0.489
0.843
33.714
1.089
0.820
3.646
42.915
A
A
7
8
14.909
B
B
14
13
3.777
10.785
-0.337
0.118
AA_DG7DA8:DT13DC14_BB
7
4.161
-5.752
41.400
-1.079
0.939
2.967
35.657
A
A
8
9
-2.242
B
B
13
12
3.044
-1.369
0.454
-0.190
AA_DA8DA9:DT12DT13_BB
8
-4.662
7.636
35.335
-0.127
-1.365
3.711
38.311
A
A
9
10
4.680
B
B
12
11
3.723
3.068
-0.552
0.123
AA_DA9DC10:DG11DT12_BB
9
0.722
-1.101
38.186
-0.250
0.944
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-07-25
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
diaestereoisomer S
RCSB
Y
RCSB
2001-04-11
REL
OCT
N-OCTANE
all calculated structures submitted
10
10
2D NOESY
2D NOESY
DQF-COSY
7.0
1
atm
278
K
7.0
1
atm
298
K
the structures are based on a total of 280 NOE-derived
distance constraints obtained from a complete relaxation
matrix refinement. The structures were calculated by using
restrained molecular dynamics with explicit solvent, and
applying the particle mesh Ewald method.
simulated, annealing molecular dynamics, matrix relaxation
2mM duplex; 10mM phosphate, 100mM NaCl
90% H20, 10% D2O
2mM duplex; 10mM phosphate, 100mM NaCl
D2O
James, T.L.
iterative matrix relaxation
MARDIGRAS
5.2
Kollman, P.A.
refinement
Amber
5.0
Bruker
collection
XwinNMR
1.3
600
Bruker
AMX
+G
6
3
OCT
OCT
11
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
C
4
n
4
DC
4
A
C
5
n
5
DC
5
A
+G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
A
9
n
9
DA
9
A
C
10
n
10
DC
10
A
G
11
n
1
DG
11
B
T
12
n
2
DT
12
B
T
13
n
3
DT
13
B
C
14
n
4
DC
14
B
C
15
n
5
DC
15
B
G
16
n
6
DG
16
B
G
17
n
7
DG
17
B
T
18
n
8
DT
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
author_defined_assembly
2
dimeric
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
DG
6
0.098
SIDE CHAIN
1
A
DC
10
0.081
SIDE CHAIN
1
B
DG
11
0.104
SIDE CHAIN
1
B
DT
13
0.069
SIDE CHAIN
1
B
DG
16
0.133
SIDE CHAIN
1
B
DG
19
0.059
SIDE CHAIN
2
A
DG
6
0.102
SIDE CHAIN
2
A
DC
10
0.076
SIDE CHAIN
2
B
DG
11
0.077
SIDE CHAIN
2
B
DT
13
0.072
SIDE CHAIN
2
B
DG
16
0.125
SIDE CHAIN
2
B
DG
19
0.062
SIDE CHAIN
3
A
DG
6
0.115
SIDE CHAIN
3
A
DC
10
0.076
SIDE CHAIN
3
B
DG
11
0.073
SIDE CHAIN
3
B
DT
13
0.080
SIDE CHAIN
3
B
DG
16
0.055
SIDE CHAIN
3
B
DG
19
0.074
SIDE CHAIN
4
A
DG
6
0.091
SIDE CHAIN
4
A
DC
10
0.077
SIDE CHAIN
4
B
DT
13
0.068
SIDE CHAIN
4
B
DG
16
0.130
SIDE CHAIN
4
B
DG
17
0.071
SIDE CHAIN
5
A
DG
6
0.097
SIDE CHAIN
5
A
DC
10
0.092
SIDE CHAIN
5
B
DT
13
0.085
SIDE CHAIN
5
B
DG
16
0.119
SIDE CHAIN
5
B
DG
17
0.067
SIDE CHAIN
5
B
DG
19
0.065
SIDE CHAIN
6
A
DA
9
0.066
SIDE CHAIN
6
A
DC
10
0.098
SIDE CHAIN
6
B
DT
13
0.077
SIDE CHAIN
6
B
DG
16
0.057
SIDE CHAIN
6
B
DG
19
0.067
SIDE CHAIN
7
A
DG
6
0.074
SIDE CHAIN
7
A
DC
10
0.092
SIDE CHAIN
7
B
DG
11
0.074
SIDE CHAIN
7
B
DT
13
0.073
SIDE CHAIN
7
B
DG
16
0.083
SIDE CHAIN
7
B
DG
19
0.069
SIDE CHAIN
8
A
DG
6
0.058
SIDE CHAIN
8
A
DC
10
0.076
SIDE CHAIN
8
B
DG
11
0.069
SIDE CHAIN
8
B
DT
13
0.071
SIDE CHAIN
8
B
DG
16
0.053
SIDE CHAIN
8
B
DG
17
0.070
SIDE CHAIN
8
B
DG
19
0.070
SIDE CHAIN
9
A
DG
6
0.057
SIDE CHAIN
9
A
DC
10
0.090
SIDE CHAIN
9
B
DT
13
0.068
SIDE CHAIN
9
B
DG
16
0.117
SIDE CHAIN
9
B
DG
17
0.069
SIDE CHAIN
9
B
DG
19
0.061
SIDE CHAIN
10
A
DC
10
0.099
SIDE CHAIN
10
B
DG
11
0.069
SIDE CHAIN
10
B
DT
13
0.091
SIDE CHAIN
10
B
DC
14
0.086
SIDE CHAIN
10
B
DG
16
0.128
SIDE CHAIN
10
B
DG
17
0.084
SIDE CHAIN
10
B
DG
19
0.064
SIDE CHAIN
1
-48.53
1.60
120.90
72.37
A
A
A
P
O5'
C5'
DC
DC
DC
1
1
1
N
1
4.33
0.30
108.30
112.63
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
2.92
0.30
108.30
111.22
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
6.00
0.30
108.30
114.30
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.42
0.30
108.30
110.72
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
2.76
0.30
108.30
111.06
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
1
-4.65
0.60
122.90
118.25
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
1
3.15
0.30
108.30
111.45
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
-3.98
0.60
122.90
118.92
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
1
3.54
0.30
108.30
111.84
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
1
-4.00
0.60
122.90
118.90
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
1
3.00
0.30
108.30
111.30
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
2
4.25
0.30
108.30
112.55
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
2
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
2
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
5.81
0.30
108.30
114.11
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
2
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
2
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
2
4.15
0.30
108.30
112.45
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
2
-4.55
0.60
122.90
118.35
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
2
3.13
0.30
108.30
111.43
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
2
-4.27
0.60
122.90
118.63
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
2
3.50
0.30
108.30
111.80
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
2
3.14
0.30
108.30
111.44
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
2
-4.54
0.60
122.90
118.36
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
2
2.69
0.30
108.30
110.99
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
2
1.85
0.30
108.30
110.15
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
3
4.27
0.30
108.30
112.57
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
3
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
6.06
0.30
108.30
114.36
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
3
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
3
4.26
0.30
108.30
112.56
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
3
4.12
0.30
108.30
112.42
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
3
-4.61
0.60
122.90
118.29
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
3
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
3
-4.13
0.60
122.90
118.77
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
3
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
3
1.84
0.30
108.30
110.14
B
B
B
O4'
C1'
N9
DG
DG
DG
17
17
17
N
3
3.00
0.30
108.30
111.30
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
3
-4.07
0.60
122.90
118.83
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
3
3.28
0.30
108.30
111.58
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
4
3.11
0.30
108.30
111.41
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
4
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
3.81
0.30
108.30
112.11
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
4
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
5.85
0.30
108.30
114.15
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
4
2.84
0.30
108.30
111.14
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
4
4.12
0.30
108.30
112.42
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
4
4.34
0.30
108.30
112.64
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
4
-4.70
0.60
122.90
118.20
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
4
3.45
0.30
108.30
111.75
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
4
-4.61
0.60
122.90
118.29
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
4
3.35
0.30
108.30
111.65
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
4
3.72
0.30
108.30
112.02
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
4
-3.99
0.60
122.90
118.91
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
4
8.07
1.20
119.70
127.77
B
B
B
C3'
O3'
P
DT
DT
DG
18
18
19
Y
5
3.52
0.30
108.30
111.82
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
5
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
5
3.70
0.30
108.30
112.00
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
5
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
5.81
0.30
108.30
114.11
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
5
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
5
3.83
0.30
108.30
112.13
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
5
4.32
0.30
108.30
112.62
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
5
-4.65
0.60
122.90
118.25
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
5
3.27
0.30
108.30
111.57
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
5
-3.93
0.60
122.90
118.97
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
5
7.99
1.20
119.70
127.69
B
B
B
C3'
O3'
P
DT
DT
DC
13
13
14
Y
5
3.30
0.30
108.30
111.60
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
5
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
5
-4.16
0.60
122.90
118.74
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
5
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
5
1.96
0.30
108.30
110.26
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
6
4.07
0.30
108.30
112.37
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
6
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
1.86
0.30
108.30
110.16
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
6
3.65
0.60
106.00
109.65
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
6
4.29
0.30
108.30
112.59
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
6
3.75
0.30
108.30
112.05
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
6
4.64
0.30
108.30
112.94
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
6
-4.12
0.60
122.90
118.78
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
6
2.53
0.30
108.30
110.83
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
6
-4.14
0.60
122.90
118.76
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
6
2.18
0.30
108.30
110.48
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
6
1.86
0.30
108.30
110.16
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
6
3.20
0.30
108.30
111.50
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
6
-4.03
0.60
122.90
118.87
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
6
3.03
0.30
108.30
111.33
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
7
4.09
0.30
108.30
112.39
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
7
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
7
3.26
0.30
108.30
111.56
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
7
3.76
0.30
108.30
112.06
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
7
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
7
7.38
1.20
119.70
127.08
A
A
A
C3'
O3'
P
DA
DA
DA
8
8
9
Y
7
3.82
0.30
108.30
112.12
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
7
4.30
0.30
108.30
112.60
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
7
-4.69
0.60
122.90
118.21
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
7
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
7
-4.72
0.60
122.90
118.18
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
7
7.41
1.20
119.70
127.11
B
B
B
C3'
O3'
P
DC
DC
DC
14
14
15
Y
7
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
7
2.85
0.30
108.30
111.15
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
7
-4.09
0.60
122.90
118.81
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
7
3.25
0.30
108.30
111.55
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
7
1.88
0.30
108.30
110.18
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
8
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
8
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
8
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
8
3.71
0.30
108.30
112.01
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
4.06
0.60
106.00
110.06
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
N
8
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
8
4.18
0.30
108.30
112.48
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
8
4.13
0.30
108.30
112.43
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
8
-4.74
0.60
122.90
118.16
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
8
2.71
0.30
108.30
111.01
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
8
-4.34
0.60
122.90
118.56
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
8
2.45
0.30
108.30
110.75
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
8
2.27
0.30
108.30
110.57
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
8
4.80
0.30
108.30
113.10
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
8
-4.83
0.60
122.90
118.07
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
8
3.37
0.30
108.30
111.67
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
8
1.90
0.30
108.30
110.20
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
9
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
9
2.58
0.30
108.30
110.88
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
9
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
9
3.97
0.30
108.30
112.27
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
3.75
0.60
106.00
109.75
A
A
A
O4'
C4'
C3'
DG
DG
DG
6
6
6
N
9
1.98
0.30
108.30
110.28
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
9
7.44
1.20
119.70
127.14
A
A
A
C3'
O3'
P
DA
DA
DA
8
8
9
Y
9
4.05
0.30
108.30
112.35
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
9
4.40
0.30
108.30
112.70
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
9
-4.75
0.60
122.90
118.15
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
9
2.88
0.30
108.30
111.18
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
9
-4.17
0.60
122.90
118.73
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
9
3.71
0.30
108.30
112.01
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
9
3.20
0.30
108.30
111.50
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
9
-4.27
0.60
122.90
118.63
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
9
2.82
0.30
108.30
111.12
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
9
1.83
0.30
108.30
110.13
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
10
3.90
0.30
108.30
112.20
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
10
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
10
3.24
0.30
108.30
111.54
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
10
3.79
0.60
106.00
109.79
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
10
4.48
0.30
108.30
112.78
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
10
7.41
1.20
119.70
127.11
A
A
A
C3'
O3'
P
DA
DA
DA
8
8
9
Y
10
3.59
0.30
108.30
111.89
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
10
3.77
0.30
108.30
112.07
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
10
-4.40
0.60
122.90
118.50
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
10
2.47
0.30
108.30
110.77
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
10
3.26
0.30
108.30
111.56
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
10
4.62
0.30
108.30
112.92
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
10
-4.40
0.60
122.90
118.50
B
B
B
C6
C5
C7
DT
DT
DT
18
18
18
N
10
3.14
0.30
108.30
111.44
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
10
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
A
A
P
O5'
DC
DC
1
1
10.673
0.010
1.593
12.266
N
SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER R)
1
N
N
2
N
N
3
N
N
covale
1.857
one
A
DG
6
A
P
DG
6
1_555
A
OCT
11
C
C1
OCT
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
20
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
20
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
20
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
17
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
17
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
17
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
16
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
16
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
16
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
15
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
15
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
15
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
14
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
14
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
14
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
13
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
13
B
O4
DT
3
1_555
hydrog
DA-DT PAIR
A
DA
9
A
N1
DA
9
1_555
B
DT
12
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
11
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
11
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
11
B
N2
DG
1
1_555
DNA
double helix, dna bending, modified oligonucleotide, charge neutralization, DNA
1IEY
PDB
1
1IEY
1IEY
PDB
2
1IEY
1
10
1IEY
1
10
1IEY
A
1
1
10
11
20
1IEY
11
20
1IEY
B
2
1
10
BINDING SITE FOR RESIDUE OCT A 11
A
OCT
11
Software
2
A
DC
5
A
DC
5
2
1_555
A
DG
6
A
DG
6
2
1_555