1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Denisov, A.Y.
Gehring, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
n
CYTOSINE ARABINOSE-5'-PHOSPHATE
RNA 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
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
n
GUANINE ARABINOSE-5'-PHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
n
URACIL ARABINOSE-5'-PHOSPHATE
RNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
4284
4293
10.1093/nar/29.21.4284
11691916
Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.
2001
US
Nucleosides and Nucleotides
NUNUD5
0653
0732-8311
20
429
440
10.1081/NCN-100002317
Properties of Arabinonucleic Acids (ANA & 2'F-ANA): Implications for the Design of Antisense Therapeutics that Invoke RNase H Cleavage of RNA
2001
10.2210/pdb1ho6/pdb
pdb_00001ho6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
3768.350
DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR)P*(CAR)P*(CAR)-3')
1
syn
polymer
no
yes
GGAC(DT)(DT)(DC)(DG)(GAO)(UAR)(CAR)(CAR)
GGACTTCGGUCC
A
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
n
n
-7.333
1
19
A
1
A
12
0.817
A_G1:CAR12_A
1
0.809
-0.371
-0.113
-0.305
-4.260
1
19
A
2
A
11
-1.145
A_G2:CAR11_A
2
-9.783
-0.426
-0.097
-0.399
2.492
1
20
A
3
A
10
-0.919
A_A3:UAR10_A
3
-11.467
-0.051
0.073
-0.323
15.512
1
19
A
4
A
9
9.085
A_C4:GAO9_A
4
-16.413
1.175
-0.642
-0.393
2.923
31.711
A
A
1
2
2.013
A
A
12
11
3.054
1.097
-0.481
-1.624
AA_G1G2:CAR11CAR12_AA
1
3.702
-6.792
31.481
-3.157
1.505
2.859
34.766
A
A
2
3
3.245
A
A
11
10
2.935
1.937
-0.254
-0.959
AA_G2A3:UAR10CAR11_AA
2
2.098
-3.516
34.652
-1.868
0.709
2.625
36.921
A
A
3
4
5.702
A
A
10
9
2.642
3.578
0.438
-0.399
AA_A3C4:GAO9UAR10_AA
3
8.103
-12.912
35.878
-1.025
0.204
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2001-11-07
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
1FC8 contains the same hairpin but with 2'F-ANA instead of ANA
1HOQ contains the same hairpin but with RNA/DNA stem
RCSB
Y
RCSB
2000-12-08
REL
REL
Solid phase synthesis, phosphoramidite chemistry
sample
This structure was determined using standard 2D homo- and heteronuclear techniques: NOESY, DQF-COSY, TOCSY, H,C-HMQC and H,P-HetCOSY
all calculated structures submitted
10
10
DQF-COSY
2D-NOESY
7.0
1
atm
288
K
Starting A- and B-type stem hairpin structures with randomly organized loops were refined by 14 ps restrained molecular dynamics (300-1000 K) with final enegry minimization
simulated annealing
1
the hairpin stem structure closest to the average
1 mM hairpin
D2O
1 mM hairpin
9:1 H2O/D2O
Brunger
refinement
X-PLOR
3.843
Bruker
data analysis
X-PLOR
500
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
C
4
n
4
C
4
A
T
5
n
5
DT
5
A
T
6
n
6
DT
6
A
C
7
n
7
DC
7
A
G
8
n
8
DG
8
A
+G
9
n
9
GAO
9
A
+U
10
n
10
UAR
10
A
+C
11
n
11
CAR
11
A
+C
12
n
12
CAR
12
A
author_defined_assembly
1
monomeric
A
GAO
9
GUANINE ARABINOSE-5'-PHOSPHATE
A
GAO
9
G
A
UAR
10
URACIL ARABINOSE-5'-PHOSPHATE
A
UAR
10
U
A
CAR
11
CYTOSINE ARABINOSE-5'-PHOSPHATE
A
CAR
11
DC
A
CAR
12
CYTOSINE ARABINOSE-5'-PHOSPHATE
A
CAR
12
DC
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
2
A
A
H2'
O4'
DT
DT
5
6
1.57
2
A
A
HO2'
O5'
G
G
1
2
1.60
3
A
A
HO2'
O5'
G
A
2
3
1.59
4
A
A
HO2'
O5'
G
G
1
2
1.59
9
A
A
HO2'
O5'
G
A
2
3
1.55
1
4.44
0.50
113.10
117.54
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
1
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
2.74
0.30
108.30
111.04
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
DC
DC
DC
7
7
7
N
1
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.77
0.40
106.40
103.63
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
2
4.40
0.50
113.10
117.50
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
2
4.99
0.50
113.10
118.09
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
2
-2.42
0.40
106.40
103.98
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
2
3.61
0.50
113.80
117.41
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
2
3.73
0.30
108.30
112.03
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
2
-3.71
0.60
122.90
119.19
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
2
2.41
0.30
108.30
110.71
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
2
2.78
0.30
108.30
111.08
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
2
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
2
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
3
4.73
0.50
113.10
117.83
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
3
-2.62
0.40
106.40
103.78
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
3
4.42
0.50
113.10
117.52
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
3
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
3
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
3
2.71
0.30
108.30
111.01
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
3
2.21
0.30
108.30
110.51
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
3
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
3
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
4
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
4
4.79
0.50
113.10
117.89
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
4
3.59
0.50
113.80
117.39
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
4
3.76
0.30
108.30
112.06
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
4
1.86
0.30
108.30
110.16
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
-3.84
0.60
122.90
119.06
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
4
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
4
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
4
4.71
0.50
113.10
117.81
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
4
-2.44
0.40
106.40
103.96
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
5
4.65
0.50
113.10
117.75
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
5
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
5
4.72
0.50
113.10
117.82
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
5
-2.54
0.40
106.40
103.86
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
5
3.69
0.50
113.80
117.49
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
5
3.30
0.30
108.30
111.60
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
5
3.49
0.30
108.30
111.79
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
5
2.12
0.30
108.30
110.42
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
5
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
5
-2.55
0.40
106.40
103.85
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
6
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
6
4.95
0.50
113.10
118.05
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
6
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
6
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
6
2.59
0.30
108.30
110.89
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
6
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
6
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
6
-2.56
0.40
106.40
103.84
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
7
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
7
4.92
0.50
113.10
118.02
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
7
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
7
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
7
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
7
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
2.77
0.30
108.30
111.07
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
7
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
7
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
7
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
8
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
8
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
8
4.50
0.70
108.50
113.00
A
A
A
O4'
C1'
N9
G
G
G
2
2
2
N
8
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
8
-2.49
0.40
106.40
103.91
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
8
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
8
3.39
0.30
108.30
111.69
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
8
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
8
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
8
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
8
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
9
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
9
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
9
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
9
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
9
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
9
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
9
3.20
0.30
108.30
111.50
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
9
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
9
4.73
0.50
113.10
117.83
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
9
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
10
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
10
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
10
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
10
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
10
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
3
3
3
N
10
4.49
0.70
108.50
112.99
A
A
A
O4'
C1'
N1
C
C
C
4
4
4
N
10
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
10
3.26
0.30
108.30
111.56
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
10
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
10
2.82
0.30
108.30
111.12
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
10
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
10
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM
1
N
N
covale
1.609
both
A
DG
8
A
O3'
DG
8
1_555
A
GAO
9
A
P
GAO
9
1_555
covale
1.614
both
A
GAO
9
A
O3'
GAO
9
1_555
A
UAR
10
A
P
UAR
10
1_555
covale
1.614
both
A
UAR
10
A
O3'
UAR
10
1_555
A
CAR
11
A
P
CAR
11
1_555
covale
1.612
both
A
CAR
11
A
O3'
CAR
11
1_555
A
CAR
12
A
P
CAR
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
CAR
12
A
N3
CAR
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
CAR
12
A
O2
CAR
12
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
CAR
12
A
N4
CAR
12
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
CAR
11
A
N3
CAR
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
CAR
11
A
O2
CAR
11
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
CAR
11
A
N4
CAR
11
1_555
hydrog
WATSON-CRICK
A
A
3
A
N1
A
3
1_555
A
UAR
10
A
N3
UAR
10
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
UAR
10
A
O4
UAR
10
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
GAO
9
A
N1
GAO
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
GAO
9
A
O6
GAO
9
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
GAO
9
A
N2
GAO
9
1_555
hydrog
DT-GAO MISPAIR
A
DT
5
A
O2
DT
5
1_555
A
GAO
9
A
N1
GAO
9
1_555
hydrog
DG-GAO MISPAIR
A
DG
8
A
N2
DG
8
1_555
A
GAO
9
A
O6
GAO
9
1_555
DNA, RNA
Arabinonucleic acid, RNA, Hairpin, DNA
1HO6
PDB
1
1HO6
1
12
1HO6
1
12
1HO6
A
1
1
12