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