1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Ghosh, M.
Kumar, N.V.
Varshney, U.
Chary, K.V.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C9 H13 N2 O8 P
308.182
y
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
28
1906
1912
10.1093/nar/28.9.1906
10756190
Structural basis for uracil DNA glycosylase interaction with uracil: NMR study.
2000
10.2210/pdb1dgo/pdb
pdb_00001dgo
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
5483.537
URACIL CONTAINING HAIRPIN DNA
1
syn
polymer
no
no
(DA)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DU)(DT)(DT)(DG)(DG)(DA)(DT)(DC)(DC)(DT)
AGGATCCTUTTGGATCCT
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
6.191
1
20
A
1
A
18
1.406
A_DA1:DT18_A
1
-7.528
0.095
0.032
-0.084
2.904
1
19
A
2
A
17
-0.646
A_DG2:DC17_A
2
2.122
-0.539
-0.125
-0.228
-0.919
1
19
A
3
A
16
-1.088
A_DG3:DC16_A
3
6.947
-0.508
-0.252
-0.234
-1.170
1
20
A
4
A
15
0.541
A_DA4:DT15_A
4
3.862
0.085
-0.371
-0.110
0.568
1
20
A
5
A
14
0.660
A_DT5:DA14_A
5
4.375
-0.034
-0.410
-0.132
-4.430
1
19
A
6
A
13
-0.642
A_DC6:DG13_A
6
6.985
0.561
-0.251
-0.232
-3.110
1
19
A
7
A
12
-0.230
A_DC7:DG12_A
7
9.643
0.717
-0.252
-0.300
3.169
29.839
A
A
1
2
1.788
A
A
18
17
3.223
0.920
0.201
-1.616
AA_DA1DG2:DC17DT18_AA
1
-0.586
1.139
29.820
-3.325
-0.509
3.278
34.044
A
A
2
3
0.987
A
A
17
16
3.294
0.578
0.464
-1.714
AA_DG2DG3:DC16DC17_AA
2
1.115
-1.905
34.022
-3.021
-0.614
3.234
37.156
A
A
3
4
1.929
A
A
16
15
3.275
1.228
0.285
-1.539
AA_DG3DA4:DT15DC16_AA
3
1.798
-2.823
37.094
-2.578
-0.209
3.551
31.153
A
A
4
5
-7.270
A
A
15
14
3.372
-3.894
0.076
-1.672
AA_DA4DT5:DA14DT15_AA
4
-0.124
0.232
30.914
-2.324
-0.166
2.980
35.203
A
A
5
6
10.568
A
A
14
13
3.330
6.358
0.166
-1.709
AA_DT5DC6:DG13DA14_AA
5
0.146
-0.243
34.641
-3.746
-0.253
2.989
30.495
A
A
6
7
6.879
A
A
13
12
3.209
3.609
-0.033
-1.683
AA_DC6DC7:DG12DG13_AA
6
1.252
-2.386
30.260
-3.884
0.300
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-05-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
Solution structure of a uracil containing hairpin DNA.
RCSB
Y
RCSB
1999-11-24
REL
REL
Custom made by Ransom Hill Biosciences, Inc.,Ramona CA (USA)
sample
This structure was determined using standard 2D homonuclear techniques
structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
200
9
2D NOESY
E-COSY
2D NOESY
7.0
1
atm
305
K
7.0
1
atm
295
K
The structures are based on a total of 225 restraints, 145 are NOE-derived distance constraints, 64 dihedral aangle restraints, 16 distance restraints from hydrogen bonds.
Restrained molecular dynamics and Energy minimization.
1
zero violations and lowest energy
5 mM oligo; no buffer; pH = 7.0 Temp = 305K; 99% D2O
99% D2O
5 mM oligo; no buffer; pH = 7.0 Temp = 305K; 90% H20 +10% D2O
90% H20 +10% D2O
varian
collection
VNMR
6.1
MSI
structure solution
Discover
97
varian
data analysis
VNMR
6.1
Bruker
collection
UXNMR
3.0
MSI
processing
Felix
97
MSI
data analysis
Felix
97
MSI
refinement
Discover
97
600
Varian
UNITYPLUS
500
Bruker
AMX
A
1
n
1
DA
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
T
5
n
5
DT
5
A
C
6
n
6
DC
6
A
C
7
n
7
DC
7
A
T
8
n
8
DT
8
A
U
9
n
9
DU
9
A
T
1
n
10
DT
10
A
T
2
n
11
DT
11
A
G
3
n
12
DG
12
A
G
4
n
13
DG
13
A
A
5
n
14
DA
14
A
T
6
n
15
DT
15
A
C
7
n
16
DC
16
A
C
8
n
17
DC
17
A
T
9
n
18
DT
18
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
DT
8
0.117
SIDE CHAIN
1
A
DU
9
0.106
SIDE CHAIN
1
A
DT
10
0.181
SIDE CHAIN
2
A
DT
8
0.117
SIDE CHAIN
2
A
DU
9
0.106
SIDE CHAIN
2
A
DT
10
0.181
SIDE CHAIN
3
A
DT
8
0.117
SIDE CHAIN
3
A
DU
9
0.111
SIDE CHAIN
3
A
DT
10
0.174
SIDE CHAIN
4
A
DT
8
0.118
SIDE CHAIN
4
A
DU
9
0.109
SIDE CHAIN
4
A
DT
10
0.181
SIDE CHAIN
5
A
DT
8
0.119
SIDE CHAIN
5
A
DU
9
0.107
SIDE CHAIN
5
A
DT
10
0.185
SIDE CHAIN
6
A
DT
8
0.117
SIDE CHAIN
6
A
DU
9
0.106
SIDE CHAIN
6
A
DT
10
0.183
SIDE CHAIN
7
A
DT
8
0.116
SIDE CHAIN
7
A
DU
9
0.105
SIDE CHAIN
7
A
DT
10
0.180
SIDE CHAIN
8
A
DT
8
0.113
SIDE CHAIN
8
A
DU
9
0.109
SIDE CHAIN
8
A
DT
10
0.172
SIDE CHAIN
9
A
DT
8
0.117
SIDE CHAIN
9
A
DU
9
0.109
SIDE CHAIN
9
A
DT
10
0.189
SIDE CHAIN
1
-3.23
0.50
117.00
113.77
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
1
3.59
0.50
117.70
121.29
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
1
-4.23
0.60
118.60
114.37
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
1
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-3.10
0.50
117.00
113.90
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
1
3.57
0.50
117.70
121.27
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
-4.04
0.60
118.60
114.56
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
1
-4.23
0.70
121.90
117.67
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
1
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-4.21
0.70
121.90
117.69
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
1
-6.19
0.80
105.90
99.71
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
1
8.02
0.30
108.30
116.32
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
8.60
0.30
108.30
116.90
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
1
4.81
0.30
108.30
113.11
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
-5.22
0.60
122.30
117.08
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
1
-4.23
0.60
122.90
118.67
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
1
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-4.05
0.60
122.30
118.25
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
1
-3.88
0.60
122.90
119.02
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
1
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
-3.09
0.50
117.00
113.91
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
1
3.52
0.50
117.70
121.22
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
1
-3.93
0.60
118.60
114.67
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
1
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
1
-3.80
0.60
122.30
118.50
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
2
-3.23
0.50
117.00
113.77
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
2
3.59
0.50
117.70
121.29
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
2
-4.23
0.60
118.60
114.37
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
2
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
2
2.17
0.30
108.30
110.47
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
2
-3.10
0.50
117.00
113.90
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
2
3.57
0.50
117.70
121.27
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
2
-4.04
0.60
118.60
114.56
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
2
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
2
-4.23
0.70
121.90
117.67
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
2
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
-4.21
0.70
121.90
117.69
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
2
-6.19
0.80
105.90
99.71
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
2
8.02
0.30
108.30
116.32
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
2
8.60
0.30
108.30
116.90
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
2
4.81
0.30
108.30
113.11
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
2
-5.22
0.60
122.30
117.08
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
2
-4.23
0.60
122.90
118.67
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
2
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
2
-4.05
0.60
122.30
118.25
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
2
-3.88
0.60
122.90
119.02
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
2
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
2
-3.09
0.50
117.00
113.91
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
2
3.52
0.50
117.70
121.22
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
2
-3.93
0.60
118.60
114.67
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
2
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
2
-3.80
0.60
122.30
118.50
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
3
-3.24
0.50
117.00
113.76
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
3
3.60
0.50
117.70
121.30
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
3
-4.23
0.60
118.60
114.37
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
3
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
3
3.02
0.50
111.50
114.52
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
3
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
3
-3.11
0.50
117.00
113.89
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
3
3.60
0.50
117.70
121.30
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
3
-4.14
0.60
118.60
114.46
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
3
-3.71
0.60
122.30
118.59
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
3
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
-4.28
0.70
121.90
117.62
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
3
-5.98
0.80
105.90
99.92
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
3
7.99
0.30
108.30
116.29
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
3
8.40
0.30
108.30
116.70
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
3
4.09
0.30
108.30
112.39
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
3
-5.19
0.60
122.30
117.11
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
3
-4.05
0.60
122.90
118.85
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
3
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
3
-4.27
0.60
122.30
118.03
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
3
-3.82
0.60
122.90
119.08
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
3
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
3
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
3
3.03
0.50
111.50
114.53
A
A
A
C5
C6
N1
DG
DG
DG
13
13
13
N
3
-3.15
0.50
117.00
113.85
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
3
3.56
0.50
117.70
121.26
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
3
-3.92
0.60
118.60
114.68
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
3
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
3
-3.76
0.60
122.30
118.54
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
4
-3.22
0.50
117.00
113.78
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
4
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
4
-4.18
0.60
118.60
114.42
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
4
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
4
3.05
0.50
111.50
114.55
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
4
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
4
-3.10
0.50
117.00
113.90
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
4
3.59
0.50
117.70
121.29
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
4
-4.09
0.60
118.60
114.51
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
4
-3.63
0.60
122.30
118.67
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
4
-4.23
0.70
121.90
117.67
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
4
2.19
0.30
108.30
110.49
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
4
-5.30
0.80
105.90
100.60
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
4
7.51
0.30
108.30
115.81
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
4
8.47
0.30
108.30
116.77
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
4
4.22
0.30
108.30
112.52
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
4
-5.18
0.60
122.30
117.12
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
4
-3.97
0.60
122.90
118.93
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
4
3.21
0.30
108.30
111.51
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
4
-4.19
0.60
122.30
118.11
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
4
-3.94
0.60
122.90
118.96
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
4
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
4
-3.06
0.50
117.00
113.94
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
4
3.50
0.50
117.70
121.20
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
4
-3.97
0.60
118.60
114.63
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
4
-3.81
0.60
122.30
118.49
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
4
-4.20
0.70
121.90
117.70
A
A
A
N3
C2
O2
DC
DC
DC
17
17
17
N
4
-3.77
0.60
122.30
118.53
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
5
-3.25
0.50
117.00
113.75
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
5
3.59
0.50
117.70
121.29
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
5
-4.17
0.60
118.60
114.43
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
5
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
5
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
5
-3.16
0.50
117.00
113.84
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
5
3.61
0.50
117.70
121.31
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
5
-3.93
0.60
118.60
114.67
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
5
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
-5.53
0.80
105.90
100.37
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
5
7.69
0.30
108.30
115.99
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
5
8.57
0.30
108.30
116.87
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
5
4.98
0.30
108.30
113.28
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
5
-5.19
0.60
122.30
117.11
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
5
-4.24
0.60
122.90
118.66
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
5
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
5
-4.02
0.60
122.30
118.28
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
5
-3.99
0.60
122.90
118.91
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
5
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
5
-3.13
0.50
117.00
113.87
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
5
3.57
0.50
117.70
121.27
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
5
-4.19
0.60
118.60
114.41
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
5
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
5
-3.99
0.60
122.90
118.91
A
A
A
C6
C5
C7
DT
DT
DT
15
15
15
N
5
-4.25
0.70
121.90
117.65
A
A
A
N3
C2
O2
DC
DC
DC
17
17
17
N
5
-3.75
0.60
122.30
118.55
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
6
-3.26
0.50
117.00
113.74
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
6
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
6
-4.22
0.60
118.60
114.38
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
6
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
6
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
6
-3.19
0.50
117.00
113.81
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
6
3.64
0.50
117.70
121.34
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
6
-3.86
0.60
118.60
114.74
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
6
-3.68
0.60
122.30
118.62
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
6
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
-4.23
0.70
121.90
117.67
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
6
-5.76
0.80
105.90
100.14
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
6
7.89
0.30
108.30
116.19
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
6
8.65
0.30
108.30
116.95
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
6
5.34
0.30
108.30
113.64
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
6
-5.21
0.60
122.30
117.09
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
6
-4.26
0.60
122.90
118.64
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
6
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
6
-4.01
0.60
122.30
118.29
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
6
-3.97
0.60
122.90
118.93
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
6
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
6
-3.13
0.50
117.00
113.87
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
6
3.59
0.50
117.70
121.29
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
6
-4.16
0.60
118.60
114.44
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
6
-3.79
0.60
122.30
118.51
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
6
-3.99
0.60
122.90
118.91
A
A
A
C6
C5
C7
DT
DT
DT
15
15
15
N
6
-4.27
0.70
121.90
117.63
A
A
A
N3
C2
O2
DC
DC
DC
17
17
17
N
6
-3.76
0.60
122.30
118.54
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
7
-3.21
0.50
117.00
113.79
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
7
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
7
-4.21
0.60
118.60
114.39
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
7
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
7
3.02
0.50
111.50
114.52
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
7
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
7
-3.10
0.50
117.00
113.90
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
7
3.64
0.50
117.70
121.34
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
7
-4.09
0.60
118.60
114.51
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
7
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
7
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
7
-4.22
0.70
121.90
117.68
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
7
3.20
0.30
108.30
111.50
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
7
-4.30
0.70
121.90
117.60
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
7
-6.35
0.80
105.90
99.55
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
7
8.24
0.30
108.30
116.54
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
7
8.65
0.30
108.30
116.95
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
7
5.20
0.30
108.30
113.50
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
7
-5.20
0.60
122.30
117.10
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
7
-4.27
0.60
122.90
118.63
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
7
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
7
-4.04
0.60
122.30
118.26
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
7
-3.87
0.60
122.90
119.03
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
7
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
7
-3.08
0.50
117.00
113.92
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
7
3.54
0.50
117.70
121.24
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
7
-3.91
0.60
118.60
114.69
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
7
-3.81
0.60
122.30
118.49
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
7
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
8
-3.25
0.50
117.00
113.75
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
8
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
8
-4.21
0.60
118.60
114.39
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
8
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
8
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
8
-3.16
0.50
117.00
113.84
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
8
3.62
0.50
117.70
121.32
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
8
-3.85
0.60
118.60
114.75
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
8
-3.74
0.60
122.30
118.56
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
8
-3.60
0.60
122.90
119.30
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
8
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
8
2.98
0.30
108.30
111.28
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
8
-6.04
0.80
105.90
99.86
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
8
8.08
0.30
108.30
116.38
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
8
8.46
0.30
108.30
116.76
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
8
4.00
0.30
108.30
112.30
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
8
-5.26
0.60
122.30
117.04
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
8
-3.97
0.60
122.90
118.93
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
8
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
11
11
11
N
8
-4.29
0.60
122.30
118.01
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
8
-3.78
0.60
122.90
119.12
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
8
2.04
0.30
108.30
110.34
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
8
-3.09
0.50
117.00
113.91
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
8
3.54
0.50
117.70
121.24
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
8
-4.04
0.60
118.60
114.56
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
8
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N1
DT
DT
DT
15
15
15
N
8
-3.80
0.60
122.30
118.50
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
8
-4.05
0.60
122.90
118.85
A
A
A
C6
C5
C7
DT
DT
DT
15
15
15
N
8
-4.22
0.70
121.90
117.68
A
A
A
N3
C2
O2
DC
DC
DC
17
17
17
N
8
-3.76
0.60
122.30
118.54
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
9
-3.23
0.50
117.00
113.77
A
A
A
C4
C5
C6
DA
DA
DA
1
1
1
N
9
3.56
0.50
117.70
121.26
A
A
A
C5
C6
N1
DA
DA
DA
1
1
1
N
9
-4.14
0.60
118.60
114.46
A
A
A
N1
C6
N6
DA
DA
DA
1
1
1
N
9
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
9
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
9
-3.11
0.50
117.00
113.89
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
9
3.58
0.50
117.70
121.28
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
9
-4.07
0.60
118.60
114.53
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
9
-3.72
0.60
122.30
118.58
A
A
A
N3
C2
O2
DT
DT
DT
5
5
5
N
9
-4.22
0.70
121.90
117.68
A
A
A
N3
C2
O2
DC
DC
DC
6
6
6
N
9
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
9
-4.28
0.70
121.90
117.62
A
A
A
N3
C2
O2
DC
DC
DC
7
7
7
N
9
-5.89
0.80
105.90
100.01
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
9
8.13
0.30
108.30
116.43
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
9
8.53
0.30
108.30
116.83
A
A
A
O4'
C1'
N1
DU
DU
DU
9
9
9
N
9
4.65
0.30
108.30
112.95
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
9
-5.17
0.60
122.30
117.13
A
A
A
N3
C2
O2
DT
DT
DT
10
10
10
N
9
-4.31
0.60
122.90
118.59
A
A
A
C6
C5
C7
DT
DT
DT
10
10
10
N
9
-4.00
0.60
122.30
118.30
A
A
A
N3
C2
O2
DT
DT
DT
11
11
11
N
9
-3.91
0.60
122.90
118.99
A
A
A
C6
C5
C7
DT
DT
DT
11
11
11
N
9
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DG
DG
DG
13
13
13
N
9
-3.14
0.50
117.00
113.86
A
A
A
C4
C5
C6
DA
DA
DA
14
14
14
N
9
3.56
0.50
117.70
121.26
A
A
A
C5
C6
N1
DA
DA
DA
14
14
14
N
9
-3.98
0.60
118.60
114.62
A
A
A
N1
C6
N6
DA
DA
DA
14
14
14
N
9
-3.80
0.60
122.30
118.50
A
A
A
N3
C2
O2
DT
DT
DT
15
15
15
N
9
-3.73
0.60
122.30
118.57
A
A
A
N3
C2
O2
DT
DT
DT
18
18
18
N
4
A
A
C5
C7
DT
DT
10
10
0.037
0.006
1.496
1.533
N
8
A
A
C5
C7
DT
DT
10
10
0.036
0.006
1.496
1.532
N
SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA
1
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
A
DT
18
A
N3
DT
18
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
A
DT
18
A
O4
DT
18
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
17
A
N3
DC
17
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
17
A
O2
DC
17
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
17
A
N4
DC
17
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
16
A
N3
DC
16
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
16
A
O2
DC
16
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
16
A
N4
DC
16
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
15
A
N3
DT
15
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
15
A
O4
DT
15
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
A
DA
14
A
N1
DA
14
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
A
DA
14
A
N6
DA
14
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
13
A
N1
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
13
A
O6
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
13
A
N2
DG
13
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N3
DC
7
1_555
A
DG
12
A
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
7
A
N4
DC
7
1_555
A
DG
12
A
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
7
A
O2
DC
7
1_555
A
DG
12
A
N2
DG
12
1_555
DNA
Uracil, Hairpin DNA, Hairpin loop, Double helix, UDG-Uracil interaction, DNA
1DGO
PDB
1
1DGO
1
18
1DGO
1
18
1DGO
A
1
1
18
1
P 1