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 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 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 NUCLEOTIDES NUCLEIC ACIDS 1525-7770 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/pdb1hoq/pdb pdb_00001hoq 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 3718.377 DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*GP*GP*TP*CP*C)-3') 1 syn polymer no no GGAC(DT)(DT)(DC)(DG)(DG)(DT)(DC)(DC) GGACTTCGGTCC A polydeoxyribonucleotide/polyribonucleotide hybrid n n n n n n n n n n n n -4.042 1 19 A 1 A 12 -3.249 A_G1:DC12_A 1 1.652 -0.602 -0.085 -0.431 -9.401 1 19 A 2 A 11 5.181 A_G2:DC11_A 2 -17.732 -0.894 -0.347 -0.447 -6.301 1 20 A 3 A 10 1.313 A_A3:DT10_A 3 -7.846 -0.274 0.038 -0.367 16.958 1 19 A 4 A 9 -1.050 A_C4:DG9_A 4 -13.137 0.681 -0.152 -0.470 -18.946 A 6 A 8 -63.008 A_DT6:DG8_A 5 10.208 -0.941 0.016 3.679 3.113 36.100 A A 1 2 7.879 A A 12 11 3.348 4.853 0.277 -1.627 AA_G1G2:DC11DC12_AA 1 5.194 -8.433 35.416 -3.310 0.286 2.662 31.658 A A 2 3 12.294 A A 11 10 2.949 6.652 0.038 -1.034 AA_G2A3:DT10DC11_AA 2 -2.520 4.657 30.869 -2.962 -0.474 2.569 36.166 A A 3 4 3.786 A A 10 9 2.635 2.346 -0.200 -0.518 AA_A3C4:DG9DT10_AA 3 3.396 -5.482 35.937 -1.098 0.703 4.594 89.226 A A 4 6 14.760 A A 9 8 4.834 19.891 0.584 0.604 AA_C4DT6:DG8DG9_AA 4 47.516 -35.258 75.556 -0.247 1.201 database_2 pdbx_struct_assembly pdbx_struct_oper_list 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 1HO6 contains the same hairpin but with ANA/RNA stem 1FC8 contains the same hairpin but with 2'F-ANA/RNA stem RCSB Y RCSB 2000-12-11 REL REL Solid phase synthesis, phosphoramidite chemistry sample This structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY all calculated structures submitted 10 10 DQF-COSY 2D-NOESY 7.0 1 atm 293 K The structures were refined by NMR-restrained molecular dynamics (14 ps, 300-1000 K) with final energy minimization simulated annealing the hairpin stem structure closest to the average 1mM hairpin D2O 1mM hairpin H2O/D2O Brunger refinement X-PLOR 3.843 Brunger 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 DG 9 A T 10 n 10 DT 10 A C 11 n 11 DC 11 A C 12 n 12 DC 12 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 2 A A HO2' O5' G G 1 2 1.53 3 A A HO2' O5' G G 1 2 1.54 4 A A HO2' O5' G G 1 2 1.52 4 A A H1' O6 DT DG 5 8 1.59 5 A A HO2' O5' G G 1 2 1.55 6 A A HO2' O5' G G 1 2 1.50 6 A A N1 H3 A DT 3 10 1.59 7 A A HO2' O5' G G 1 2 1.51 8 A A HO2' O5' G G 1 2 1.49 9 A A HO2' O5' G G 1 2 1.51 9 A A O2 H21 C DG 4 9 1.56 10 A A O2 H21 C DG 4 9 1.58 1 4.88 0.50 113.10 117.98 A A A N7 C8 N9 G G G 1 1 1 N 1 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 G G G 1 1 1 N 1 4.72 0.50 113.10 117.82 A A A N7 C8 N9 G G G 2 2 2 N 1 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 2 2 2 N 1 3.71 0.50 113.80 117.51 A A A N7 C8 N9 A A A 3 3 3 N 1 3.26 0.30 108.30 111.56 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 2.68 0.30 108.30 110.98 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 2.74 0.30 108.30 111.04 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 2.14 0.30 108.30 110.44 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 4.59 0.50 113.10 117.69 A A A N7 C8 N9 DG DG DG 8 8 8 N 1 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 DG DG DG 8 8 8 N 1 3.58 0.30 108.30 111.88 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 4.69 0.50 113.10 117.79 A A A N7 C8 N9 DG DG DG 9 9 9 N 1 -2.45 0.40 106.40 103.95 A A A C8 N9 C4 DG DG DG 9 9 9 N 1 2.66 0.30 108.30 110.96 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 3.39 0.30 108.30 111.69 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 2.85 0.30 108.30 111.15 A A A O4' C1' N1 DC DC DC 12 12 12 N 2 4.41 0.50 113.10 117.51 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 3.85 0.50 113.80 117.65 A A A N7 C8 N9 A A A 3 3 3 N 2 2.78 0.30 108.30 111.08 A A A O4' C1' N1 DT DT DT 5 5 5 N 2 3.02 0.30 108.30 111.32 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DC DC DC 7 7 7 N 2 3.42 0.30 108.30 111.72 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 8 8 8 N 2 -2.64 0.40 106.40 103.76 A A A C8 N9 C4 DG DG DG 8 8 8 N 2 3.52 0.30 108.30 111.82 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 4.71 0.50 113.10 117.81 A A A N7 C8 N9 DG DG DG 9 9 9 N 2 -2.44 0.40 106.40 103.96 A A A C8 N9 C4 DG DG DG 9 9 9 N 2 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 3.87 0.30 108.30 112.17 A A A O4' C1' N1 DC DC DC 11 11 11 N 2 2.92 0.30 108.30 111.22 A A A O4' C1' N1 DC DC DC 12 12 12 N 3 4.50 0.50 113.10 117.60 A A A N7 C8 N9 G G G 1 1 1 N 3 5.04 0.50 113.10 118.14 A A A N7 C8 N9 G G G 2 2 2 N 3 -2.56 0.40 106.40 103.84 A A A C8 N9 C4 G G G 2 2 2 N 3 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 3 3 3 N 3 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DT DT DT 5 5 5 N 3 3.14 0.30 108.30 111.44 A A A O4' C1' N1 DC DC DC 7 7 7 N 3 3.16 0.30 108.30 111.46 A A A O4' C1' N9 DG DG DG 8 8 8 N 3 4.65 0.50 113.10 117.75 A A A N7 C8 N9 DG DG DG 8 8 8 N 3 -2.76 0.40 106.40 103.64 A A A C8 N9 C4 DG DG DG 8 8 8 N 3 3.43 0.30 108.30 111.73 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 4.67 0.50 113.10 117.77 A A A N7 C8 N9 DG DG DG 9 9 9 N 3 -2.58 0.40 106.40 103.82 A A A C8 N9 C4 DG DG DG 9 9 9 N 3 2.90 0.30 108.30 111.20 A A A O4' C1' N1 DT DT DT 10 10 10 N 3 3.41 0.30 108.30 111.71 A A A O4' C1' N1 DC DC DC 11 11 11 N 3 2.77 0.30 108.30 111.07 A A A O4' C1' N1 DC DC DC 12 12 12 N 4 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 1 1 1 N 4 5.00 0.50 113.10 118.10 A A A N7 C8 N9 G G G 2 2 2 N 4 3.81 0.50 113.80 117.61 A A A N7 C8 N9 A A A 3 3 3 N 4 2.97 0.30 108.30 111.27 A A A O4' C1' N1 DT DT DT 5 5 5 N 4 3.09 0.30 108.30 111.39 A A A O4' C1' N1 DT DT DT 6 6 6 N 4 2.87 0.30 108.30 111.17 A A A O4' C1' N1 DC DC DC 7 7 7 N 4 4.54 0.30 108.30 112.84 A A A O4' C1' N9 DG DG DG 8 8 8 N 4 4.76 0.50 113.10 117.86 A A A N7 C8 N9 DG DG DG 8 8 8 N 4 -2.63 0.40 106.40 103.77 A A A C8 N9 C4 DG DG DG 8 8 8 N 4 3.68 0.30 108.30 111.98 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 4.68 0.50 113.10 117.78 A A A N7 C8 N9 DG DG DG 9 9 9 N 4 -2.68 0.40 106.40 103.72 A A A C8 N9 C4 DG DG DG 9 9 9 N 4 2.94 0.30 108.30 111.24 A A A O4' C1' N1 DT DT DT 10 10 10 N 4 3.78 0.30 108.30 112.08 A A A O4' C1' N1 DC DC DC 11 11 11 N 4 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DC DC DC 12 12 12 N 5 4.52 0.50 113.10 117.62 A A A N7 C8 N9 G G G 1 1 1 N 5 5.04 0.50 113.10 118.14 A A A N7 C8 N9 G G G 2 2 2 N 5 3.83 0.50 113.80 117.63 A A A N7 C8 N9 A A A 3 3 3 N 5 3.13 0.30 108.30 111.43 A A A O4' C1' N1 DT DT DT 5 5 5 N 5 2.74 0.30 108.30 111.04 A A A O4' C1' N1 DT DT DT 6 6 6 N 5 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DC DC DC 7 7 7 N 5 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DG DG DG 8 8 8 N 5 4.82 0.50 113.10 117.92 A A A N7 C8 N9 DG DG DG 8 8 8 N 5 -2.81 0.40 106.40 103.59 A A A C8 N9 C4 DG DG DG 8 8 8 N 5 3.23 0.30 108.30 111.53 A A A O4' C1' N9 DG DG DG 9 9 9 N 5 4.54 0.50 113.10 117.64 A A A N7 C8 N9 DG DG DG 9 9 9 N 5 -2.47 0.40 106.40 103.93 A A A C8 N9 C4 DG DG DG 9 9 9 N 5 2.93 0.30 108.30 111.23 A A A O4' C1' N1 DT DT DT 10 10 10 N 5 3.53 0.30 108.30 111.83 A A A O4' C1' N1 DC DC DC 11 11 11 N 5 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DC DC DC 12 12 12 N 6 4.48 0.50 113.10 117.58 A A A N7 C8 N9 G G G 1 1 1 N 6 5.08 0.50 113.10 118.18 A A A N7 C8 N9 G G G 2 2 2 N 6 -2.42 0.40 106.40 103.98 A A A C8 N9 C4 G G G 2 2 2 N 6 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 3 3 3 N 6 3.11 0.30 108.30 111.41 A A A O4' C1' N1 DT DT DT 5 5 5 N 6 2.67 0.30 108.30 110.97 A A A O4' C1' N1 DT DT DT 6 6 6 N 6 2.58 0.30 108.30 110.88 A A A O4' C1' N1 DC DC DC 7 7 7 N 6 2.48 0.30 108.30 110.78 A A A O4' C1' N9 DG DG DG 8 8 8 N 6 4.70 0.50 113.10 117.80 A A A N7 C8 N9 DG DG DG 8 8 8 N 6 -2.70 0.40 106.40 103.70 A A A C8 N9 C4 DG DG DG 8 8 8 N 6 4.25 0.30 108.30 112.55 A A A O4' C1' N9 DG DG DG 9 9 9 N 6 4.59 0.50 113.10 117.69 A A A N7 C8 N9 DG DG DG 9 9 9 N 6 2.86 0.30 108.30 111.16 A A A O4' C1' N1 DT DT DT 10 10 10 N 6 3.78 0.30 108.30 112.08 A A A O4' C1' N1 DC DC DC 11 11 11 N 6 2.97 0.30 108.30 111.27 A A A O4' C1' N1 DC DC DC 12 12 12 N 7 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 1 1 1 N 7 5.04 0.50 113.10 118.14 A A A N7 C8 N9 G G G 2 2 2 N 7 -2.50 0.40 106.40 103.90 A A A C8 N9 C4 G G G 2 2 2 N 7 3.80 0.50 113.80 117.60 A A A N7 C8 N9 A A A 3 3 3 N 7 3.21 0.30 108.30 111.51 A A A O4' C1' N1 DT DT DT 5 5 5 N 7 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DT DT DT 6 6 6 N 7 2.56 0.30 108.30 110.86 A A A O4' C1' N1 DC DC DC 7 7 7 N 7 3.34 0.30 108.30 111.64 A A A O4' C1' N9 DG DG DG 8 8 8 N 7 4.68 0.50 113.10 117.78 A A A N7 C8 N9 DG DG DG 8 8 8 N 7 -2.72 0.40 106.40 103.68 A A A C8 N9 C4 DG DG DG 8 8 8 N 7 3.15 0.30 108.30 111.45 A A A O4' C1' N9 DG DG DG 9 9 9 N 7 4.59 0.50 113.10 117.69 A A A N7 C8 N9 DG DG DG 9 9 9 N 7 2.73 0.30 108.30 111.03 A A A O4' C1' N1 DT DT DT 10 10 10 N 7 3.79 0.30 108.30 112.09 A A A O4' C1' N1 DC DC DC 11 11 11 N 7 2.84 0.30 108.30 111.14 A A A O4' C1' N1 DC DC DC 12 12 12 N 8 4.47 0.50 113.10 117.57 A A A N7 C8 N9 G G G 1 1 1 N 8 5.03 0.50 113.10 118.13 A A A N7 C8 N9 G G G 2 2 2 N 8 -2.44 0.40 106.40 103.96 A A A C8 N9 C4 G G G 2 2 2 N 8 3.79 0.50 113.80 117.59 A A A N7 C8 N9 A A A 3 3 3 N 8 3.04 0.30 108.30 111.34 A A A O4' C1' N1 DT DT DT 5 5 5 N 8 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DT DT DT 6 6 6 N 8 3.18 0.30 108.30 111.48 A A A O4' C1' N1 DC DC DC 7 7 7 N 8 3.11 0.30 108.30 111.41 A A A O4' C1' N9 DG DG DG 8 8 8 N 8 4.72 0.50 113.10 117.82 A A A N7 C8 N9 DG DG DG 8 8 8 N 8 -2.69 0.40 106.40 103.71 A A A C8 N9 C4 DG DG DG 8 8 8 N 8 3.84 0.30 108.30 112.14 A A A O4' C1' N9 DG DG DG 9 9 9 N 8 4.71 0.50 113.10 117.81 A A A N7 C8 N9 DG DG DG 9 9 9 N 8 2.91 0.30 108.30 111.21 A A A O4' C1' N1 DT DT DT 10 10 10 N 8 3.62 0.30 108.30 111.92 A A A O4' C1' N1 DC DC DC 11 11 11 N 8 2.95 0.30 108.30 111.25 A A A O4' C1' N1 DC DC DC 12 12 12 N 9 4.59 0.50 113.10 117.69 A A A N7 C8 N9 G G G 1 1 1 N 9 4.95 0.50 113.10 118.05 A A A N7 C8 N9 G G G 2 2 2 N 9 -2.41 0.40 106.40 103.99 A A A C8 N9 C4 G G G 2 2 2 N 9 3.67 0.50 113.80 117.47 A A A N7 C8 N9 A A A 3 3 3 N 9 2.87 0.30 108.30 111.17 A A A O4' C1' N1 DT DT DT 5 5 5 N 9 3.12 0.30 108.30 111.42 A A A O4' C1' N1 DT DT DT 6 6 6 N 9 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DC DC DC 7 7 7 N 9 2.14 0.30 108.30 110.44 A A A O4' C1' N9 DG DG DG 8 8 8 N 9 4.80 0.50 113.10 117.90 A A A N7 C8 N9 DG DG DG 8 8 8 N 9 -2.77 0.40 106.40 103.63 A A A C8 N9 C4 DG DG DG 8 8 8 N 9 4.34 0.30 108.30 112.64 A A A O4' C1' N9 DG DG DG 9 9 9 N 9 4.65 0.50 113.10 117.75 A A A N7 C8 N9 DG DG DG 9 9 9 N 9 2.97 0.30 108.30 111.27 A A A O4' C1' N1 DT DT DT 10 10 10 N 9 3.64 0.30 108.30 111.94 A A A O4' C1' N1 DC DC DC 11 11 11 N 9 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DC DC DC 12 12 12 N 10 4.93 0.50 113.10 118.03 A A A N7 C8 N9 G G G 1 1 1 N 10 -2.65 0.40 106.40 103.75 A A A C8 N9 C4 G G G 1 1 1 N 10 4.68 0.50 113.10 117.78 A A A N7 C8 N9 G G G 2 2 2 N 10 -2.71 0.40 106.40 103.69 A A A C8 N9 C4 G G G 2 2 2 N 10 3.92 0.50 113.80 117.72 A A A N7 C8 N9 A A A 3 3 3 N 10 -2.42 0.40 105.80 103.38 A A A C8 N9 C4 A A A 3 3 3 N 10 3.61 0.30 108.30 111.91 A A A O4' C1' N1 DT DT DT 5 5 5 N 10 2.58 0.30 108.30 110.88 A A A O4' C1' N1 DT DT DT 6 6 6 N 10 2.47 0.30 108.30 110.77 A A A O4' C1' N1 DC DC DC 7 7 7 N 10 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DG DG DG 8 8 8 N 10 4.83 0.50 113.10 117.93 A A A N7 C8 N9 DG DG DG 8 8 8 N 10 -2.77 0.40 106.40 103.63 A A A C8 N9 C4 DG DG DG 8 8 8 N 10 3.70 0.30 108.30 112.00 A A A O4' C1' N9 DG DG DG 9 9 9 N 10 4.64 0.50 113.10 117.74 A A A N7 C8 N9 DG DG DG 9 9 9 N 10 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DT DT DT 10 10 10 N 10 3.56 0.30 108.30 111.86 A A A O4' C1' N1 DC DC DC 11 11 11 N 10 2.91 0.30 108.30 111.21 A A A O4' C1' N1 DC DC DC 12 12 12 N CHIMERIC RNA/DNA HAIRPIN 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A DC 12 A N3 DC 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A DC 12 A O2 DC 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A DC 12 A N4 DC 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A DC 11 A N3 DC 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A DC 11 A O2 DC 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A DC 11 A N4 DC 11 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A DT 10 A N3 DT 10 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A DT 10 A O4 DT 10 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A DG 9 A N1 DG 9 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A DG 9 A O6 DG 9 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A DG 9 A N2 DG 9 1_555 hydrog DT-DG MISPAIR A DT 5 A O4 DT 5 1_555 A DG 9 A N1 DG 9 1_555 hydrog DT-DG MISPAIR A DT 6 A N3 DT 6 1_555 A DG 8 A N7 DG 8 1_555 DNA, RNA Hairpin, DNA, RNA 1HOQ PDB 1 1HOQ 1 12 1HOQ 1 12 1HOQ A 1 1 12