1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Robertson, S.A.
Harada, K.
Frankel, A.D.
Wemmer, D.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C6 H16 N5 O 1
174.224
n
ARGININEAMIDE
L-peptide linking
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
C
N
5
N
C
N
6
N
N
N
7
N
C
N
8
N
N
N
9
N
N
N
10
N
C
N
11
N
O
N
12
N
N
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
O
N
30
N
P
N
31
N
O
N
32
N
O
N
33
N
O
N
34
N
C
N
35
R
C
N
36
N
O
N
37
S
C
N
38
N
O
N
39
N
C
N
40
R
C
Y
41
N
N
Y
42
N
C
Y
43
N
N
Y
44
N
C
Y
45
N
C
N
46
N
N
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
O
N
66
N
P
N
67
N
O
N
68
N
O
N
69
N
O
N
70
N
C
N
71
R
C
N
72
N
O
N
73
S
C
N
74
N
O
N
75
N
C
N
76
R
C
N
77
N
N
N
78
N
C
N
79
N
O
N
80
N
N
N
81
N
C
N
82
N
N
N
83
N
C
N
84
N
C
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
O
N
100
N
P
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
C
N
105
R
C
N
106
N
O
N
107
S
C
N
108
N
O
N
109
N
C
N
110
R
C
Y
111
N
N
Y
112
N
C
Y
113
N
N
Y
114
N
C
N
115
N
C
N
116
N
O
N
117
N
N
N
118
N
C
N
119
N
N
N
120
N
N
Y
121
N
C
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
O
N
137
N
P
N
138
N
O
N
139
N
O
N
140
N
O
N
141
N
C
N
142
R
C
N
143
N
O
N
144
S
C
N
145
N
O
N
146
N
C
N
147
R
C
N
148
N
N
N
149
N
C
N
150
N
O
N
151
N
N
N
152
N
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
Y
51
N
sing
Y
52
N
sing
Y
53
N
doub
N
54
N
sing
Y
55
N
sing
Y
56
N
sing
Y
57
N
doub
N
58
N
sing
Y
59
N
doub
N
60
N
sing
N
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
Y
124
N
sing
Y
125
N
sing
Y
126
N
doub
N
127
N
sing
Y
128
N
sing
N
129
N
sing
Y
130
N
doub
N
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
39
946
954
10.1021/bi9915061
10653638
Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
2000
UK
Embo J.
EMJODG
0897
0261-4189
14
5798
5811
Identification of Two Novel Arginine Binding DNAs
1995
10.2210/pdb1db6/pdb
pdb_00001db6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
6729.329
DNA
1
syn
polymer
174.224
ARGININEAMIDE
1
syn
non-polymer
no
no
(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DG)(DC)(DC)(DT)(DG)(DG)(DT)
(DC)(DG)
CGACCAACGTGTCGCCTGGTCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-3.771
1
19
A
1
A
22
-4.012
A_DC1:DG22_A
1
-24.242
-0.142
0.457
-0.231
-0.483
1
19
A
2
A
21
-4.066
A_DG2:DC21_A
2
-21.954
0.573
0.238
-0.202
-0.558
1
20
A
3
A
20
-7.902
A_DA3:DT20_A
3
-20.722
0.292
0.274
-0.147
1.150
1
19
A
4
A
19
-6.733
A_DC4:DG19_A
4
-18.041
-0.514
0.614
-0.283
2.573
1
19
A
5
A
18
-5.733
A_DC5:DG18_A
5
-23.926
-0.528
0.392
-0.237
6.793
1
20
A
6
A
17
-11.897
A_DA6:DT17_A
6
-24.759
0.343
0.670
-0.270
-18.410
4
25
A
15
A
7
-85.381
A_DC15:DA7_A
7
17.961
3.167
1.555
-0.972
-12.807
1
19
A
9
A
16
-16.074
A_DG9:DC16_A
8
12.396
-0.010
-1.108
-0.358
-3.881
27
A
10
A
14
-156.465
A_DT10:DG14_A
9
6.053
-0.395
0.564
1.210
2.882
36.422
A
A
1
2
27.037
A
A
22
21
3.220
16.323
-0.094
-0.007
AA_DC1DG2:DC21DG22_AA
1
2.268
-3.757
32.594
-2.255
0.462
2.966
40.059
A
A
2
3
1.731
A
A
21
20
2.912
1.184
-0.820
-0.301
AA_DG2DA3:DT20DC21_AA
2
-3.840
5.615
39.865
-0.562
0.802
2.878
30.138
A
A
3
4
1.067
A
A
20
19
2.960
0.553
0.197
-1.224
AA_DA3DC4:DG19DT20_AA
3
-4.464
8.616
29.808
-2.454
-1.196
2.723
33.300
A
A
4
5
7.002
A
A
19
18
2.891
3.996
0.198
-1.313
AA_DC4DC5:DG18DG19_AA
4
3.622
-6.347
32.873
-2.867
0.176
2.827
37.349
A
A
5
6
9.697
A
A
18
17
3.032
6.183
-0.093
-1.038
AA_DC5DA6:DT17DG18_AA
5
-0.107
0.168
36.851
-2.357
0.133
-1.504
-176.358
A
A
6
15
27.626
A
A
17
7
-1.464
-55.149
0.653
-2.805
AA_DA6DC15:DA7DT17_AA
6
-147.382
-73.827
-161.365
1.362
0.438
-1.143
-129.806
A
A
15
9
-10.192
A
A
7
16
-2.500
15.949
0.542
6.654
AA_DC15DG9:DC16DA7_AA
7
-125.948
-80.484
-36.457
-3.497
1.691
3.058
107.525
A
A
9
10
-27.625
A
A
16
14
4.086
-43.400
-1.459
3.519
AA_DG9DT10:DG14DC16_AA
8
-37.403
23.808
95.311
2.882
0.300
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2000-02-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
2ARG contains a different DNA aptamer complexed with argininamide
1OlD is a similar DNA aptamer
RCSB
Y
RCSB
1999-11-02
REL
AAR
ARGININEAMIDE
Sequence is derived from in-vitro selection experiments. Sequences were chemically sythethesized.
sample
Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14.
structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy
30
10
2D NOESY
DQF-COSY
TOCSY
2D NOESY
0-25 mM NaCl
6.2
ambient
293
K
0-25 mM NaCl
6.2
ambient
278
K
Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing and molecular dynamics
6
fewest violations
1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide
99.99% D2O
1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide
90% H2O/10% D2O
Molecular Simulations, Inc
data analysis
Felix
950
Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli
iterative matrix relaxation
MARDIGRAS
3.2
Molecular Simulations, Inc
refinement
Discover
2.97
500
GE
OMEGA
600
Bruker
AMX
AAR
23
2
AAR
AAR
23
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
C
4
n
4
DC
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
T
10
n
10
DT
10
A
G
11
n
11
DG
11
A
T
12
n
12
DT
12
A
C
13
n
13
DC
13
A
G
14
n
14
DG
14
A
C
15
n
15
DC
15
A
C
16
n
16
DC
16
A
T
17
n
17
DT
17
A
G
18
n
18
DG
18
A
G
19
n
19
DG
19
A
T
20
n
20
DT
20
A
C
21
n
21
DC
21
A
G
22
n
22
DG
22
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
H3
O6
DT
DG
10
14
1.57
2
A
A
O2
H2'
DT
DT
10
12
1.55
2
A
A
H3
O6
DT
DG
10
14
1.58
3
A
A
O2
H2'
DT
DT
10
12
1.58
1
A
DC
1
0.067
SIDE CHAIN
1
A
DC
15
0.068
SIDE CHAIN
1
A
DC
16
0.109
SIDE CHAIN
2
A
DC
1
0.071
SIDE CHAIN
2
A
DG
14
0.068
SIDE CHAIN
2
A
DC
15
0.084
SIDE CHAIN
2
A
DC
16
0.060
SIDE CHAIN
3
A
DC
1
0.069
SIDE CHAIN
3
A
DT
10
0.069
SIDE CHAIN
3
A
DG
14
0.077
SIDE CHAIN
3
A
DC
15
0.089
SIDE CHAIN
3
A
DC
16
0.066
SIDE CHAIN
4
A
DC
1
0.072
SIDE CHAIN
4
A
DG
14
0.079
SIDE CHAIN
4
A
DC
15
0.056
SIDE CHAIN
4
A
DC
16
0.061
SIDE CHAIN
5
A
DC
8
0.057
SIDE CHAIN
5
A
DT
12
0.068
SIDE CHAIN
5
A
DG
14
0.076
SIDE CHAIN
5
A
DC
15
0.080
SIDE CHAIN
5
A
DC
16
0.079
SIDE CHAIN
6
A
DC
1
0.063
SIDE CHAIN
6
A
DG
14
0.079
SIDE CHAIN
6
A
DC
15
0.057
SIDE CHAIN
7
A
DC
1
0.070
SIDE CHAIN
7
A
DG
14
0.066
SIDE CHAIN
7
A
DC
15
0.101
SIDE CHAIN
7
A
DC
16
0.093
SIDE CHAIN
8
A
DC
1
0.068
SIDE CHAIN
8
A
DG
14
0.085
SIDE CHAIN
8
A
DC
15
0.113
SIDE CHAIN
8
A
DC
16
0.095
SIDE CHAIN
9
A
DC
1
0.068
SIDE CHAIN
9
A
DG
14
0.064
SIDE CHAIN
9
A
DC
15
0.089
SIDE CHAIN
9
A
DC
16
0.088
SIDE CHAIN
10
A
DC
1
0.064
SIDE CHAIN
10
A
DG
14
0.089
SIDE CHAIN
10
A
DC
15
0.080
SIDE CHAIN
10
A
DC
16
0.087
SIDE CHAIN
1
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
1
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
3.35
0.30
108.30
111.65
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
2.22
0.30
108.30
110.52
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
2
3.82
0.30
108.30
112.12
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
2
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
2
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
2
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
2
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
2
3.40
0.30
108.30
111.70
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
2
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
2
3.38
0.30
108.30
111.68
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
2
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
2
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
2
3.52
0.30
108.30
111.82
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
2
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
2
3.80
0.30
108.30
112.10
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
3
4.01
0.30
108.30
112.31
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
3
1.98
0.30
108.30
110.28
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
3
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
3
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
3
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
3
2.10
0.30
108.30
110.40
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
3
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
3
5.28
0.30
108.30
113.58
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
3
-3.64
0.60
122.90
119.26
A
A
A
C6
C5
C7
DT
DT
DT
12
12
12
N
3
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
3
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
3
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
3
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
3
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
3
3.70
0.30
108.30
112.00
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
4
4.25
0.30
108.30
112.55
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
4
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
4
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
1.89
0.30
108.30
110.19
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
4
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
4
2.37
0.30
108.30
110.67
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
4
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
4
3.16
0.30
108.30
111.46
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
4
3.73
0.30
108.30
112.03
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
4
-3.62
0.60
122.90
119.28
A
A
A
C6
C5
C7
DT
DT
DT
12
12
12
N
4
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
4
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
4
3.78
0.30
108.30
112.08
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
4
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
4
2.33
0.30
108.30
110.63
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
4
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
4
3.86
0.30
108.30
112.16
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
5
3.24
0.30
108.30
111.54
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
5
3.29
0.30
108.30
111.59
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
5
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
5
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
5
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
5
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
5
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
5
4.40
0.30
108.30
112.70
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
5
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
5
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
5
4.09
0.30
108.30
112.39
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
5
2.32
0.30
108.30
110.62
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
5
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
5
1.80
0.30
108.30
110.10
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
5
3.33
0.30
108.30
111.63
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
6
4.10
0.30
108.30
112.40
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
6
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
6
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
6
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
6
3.37
0.30
108.30
111.67
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
6
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
6
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
6
3.94
0.30
108.30
112.24
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
6
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
12
12
12
N
6
2.03
0.30
108.30
110.33
A
A
A
O4'
C1'
N1
DC
DC
DC
13
13
13
N
6
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
6
3.93
0.30
108.30
112.23
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
6
2.23
0.30
108.30
110.53
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
6
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
6
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
6
4.08
0.30
108.30
112.38
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
7
3.21
0.30
108.30
111.51
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
7
3.20
0.30
108.30
111.50
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
7
3.08
0.30
108.30
111.38
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
7
1.87
0.30
108.30
110.17
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
7
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
7
3.83
0.30
108.30
112.13
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
7
2.26
0.30
108.30
110.56
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
7
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
7
3.20
0.30
108.30
111.50
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
7
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
7
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
7
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
7
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
7
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
8
3.07
0.30
108.30
111.37
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
8
3.48
0.30
108.30
111.78
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
8
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
8
3.15
0.30
108.30
111.45
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
8
4.72
0.30
108.30
113.02
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
8
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
8
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
8
2.25
0.30
108.30
110.55
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
8
1.88
0.30
108.30
110.18
A
A
A
O4'
C1'
N1
DT
DT
DT
17
17
17
N
8
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
8
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
8
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
8
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
9
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
9
3.94
0.30
108.30
112.24
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
9
2.90
0.30
108.30
111.20
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
9
3.15
0.30
108.30
111.45
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
9
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
9
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
9
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
9
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N1
DT
DT
DT
17
17
17
N
9
3.42
0.30
108.30
111.72
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
9
1.93
0.30
108.30
110.23
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
9
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
9
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
9
3.25
0.30
108.30
111.55
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
10
3.39
0.30
108.30
111.69
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
10
4.10
0.30
108.30
112.40
A
A
A
O4'
C1'
N1
DC
DC
DC
4
4
4
N
10
2.69
0.30
108.30
110.99
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
10
4.37
0.30
108.30
112.67
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
10
2.60
0.30
108.30
110.90
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
10
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
10
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DT
DT
DT
12
12
12
N
10
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N1
DC
DC
DC
16
16
16
N
10
3.31
0.30
108.30
111.61
A
A
A
O4'
C1'
N9
DG
DG
DG
18
18
18
N
10
2.30
0.30
108.30
110.60
A
A
A
O4'
C1'
N9
DG
DG
DG
19
19
19
N
10
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N1
DT
DT
DT
20
20
20
N
10
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N1
DC
DC
DC
21
21
21
N
10
3.70
0.30
108.30
112.00
A
A
A
O4'
C1'
N9
DG
DG
DG
22
22
22
N
SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
22
A
N1
DG
22
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
22
A
O6
DG
22
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
22
A
N2
DG
22
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
21
A
N3
DC
21
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
21
A
O2
DC
21
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
21
A
N4
DC
21
1_555
hydrog
DA-DG MISPAIR
A
DA
3
A
N6
DA
3
1_555
A
DG
19
A
O6
DG
19
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
20
A
N3
DT
20
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
20
A
O4
DT
20
1_555
hydrog
DC-DG PAIR
A
DC
4
A
N4
DC
4
1_555
A
DG
18
A
O6
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
A
DG
19
A
N1
DG
19
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
A
DG
19
A
O6
DG
19
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
A
DG
19
A
N2
DG
19
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
18
A
N1
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
18
A
O6
DG
18
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
18
A
N2
DG
18
1_555
hydrog
TYPE_25_PAIR
A
DA
6
A
N6
DA
6
1_555
A
DC
15
A
N3
DC
15
1_555
hydrog
TYPE_25_PAIR
A
DA
6
A
N7
DA
6
1_555
A
DC
15
A
N4
DC
15
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
A
DT
17
A
N3
DT
17
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
A
DT
17
A
O4
DT
17
1_555
hydrog
TYPE_25_PAIR
A
DA
7
A
N6
DA
7
1_555
A
DC
15
A
N3
DC
15
1_555
hydrog
TYPE_25_PAIR
A
DA
7
A
N7
DA
7
1_555
A
DC
15
A
N4
DC
15
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
16
A
N3
DC
16
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
16
A
O2
DC
16
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
16
A
N4
DC
16
1_555
hydrog
TYPE_27_PAIR
A
DT
10
A
N3
DT
10
1_555
A
DG
14
A
O6
DG
14
1_555
hydrog
TYPE_27_PAIR
A
DT
10
A
O4
DT
10
1_555
A
DG
14
A
N1
DG
14
1_555
DNA
APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA
1DB6
PDB
1
1DB6
1
22
1DB6
1
22
1DB6
A
1
1
22
BINDING SITE FOR RESIDUE AAR A 23
A
AAR
23
Software
8
A
DC
8
A
DC
8
8
1_555
A
DG
9
A
DG
9
8
1_555
A
DT
12
A
DT
12
8
1_555
A
DC
13
A
DC
13
8
1_555
A
DG
14
A
DG
14
8
1_555
A
DC
16
A
DC
16
8
1_555
A
DT
17
A
DT
17
8
1_555
A
DG
18
A
DG
18
8
1_555
1
P 1