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. Rumpal, N. Varshney, U. Chary, K.V. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 269 1886 1894 10.1046/j.1432-1033.2002.02837.x 11952790 Structural basis for poor uracil excision from hairpin DNA. An NMR study. 2002 10.2210/pdb1idx/pdb pdb_00001idx 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 Uracil containing hairpin DNA 5483.537 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*UP*TP*GP*GP*AP*TP*CP*CP*T)-3' 1 syn polymer no no (DA)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DT)(DU)(DT)(DG)(DG)(DA)(DT)(DC)(DC)(DT) AGGATCCTTUTGGATCCT A polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n -8.992 1 20 A 1 B A 9 0.917 A_DA1:DT9B_A 1 -16.415 0.024 -0.201 -0.100 -1.732 1 19 A 2 B A 8 -0.526 A_DG2:DC8B_A 2 -1.320 -0.394 0.091 -0.172 5.799 1 19 A 3 B A 7 -0.556 A_DG3:DC7B_A 3 -6.145 -0.471 0.074 -0.197 -3.990 1 20 A 4 B A 6 4.570 A_DA4:DT6B_A 4 -15.668 -0.035 -0.218 -0.110 -0.735 1 20 A 5 B A 5 -1.155 A_DT5:DA5B_A 5 -11.333 0.034 -0.249 -0.124 7.208 1 19 A 6 B A 4 0.711 A_DC6:DG4B_A 6 3.385 0.419 0.189 -0.180 26.964 1 19 A 7 B A 3 0.553 A_DC7:DG3B_A 7 -4.107 0.558 -0.808 -0.185 24.964 1 16 A 8 B A 2 -3.111 A_DT8:DT2B_A 8 53.017 -2.457 -0.750 -1.989 2.451 30.022 A A 1 2 11.123 B B A A 9 8 2.896 5.725 -0.004 -2.088 AA_DA1DG2:DC8BDT9B_AA 1 -1.728 3.358 29.434 -5.003 -0.286 2.385 31.678 A A 2 3 14.765 B B A A 8 7 2.894 7.976 0.687 -1.782 AA_DG2DG3:DC7BDC8B_AA 2 0.888 -1.644 30.670 -4.472 -1.124 2.367 32.916 A A 3 4 22.485 B B A A 7 6 3.301 12.429 0.421 -1.961 AA_DG3DA4:DT6BDC7B_AA 3 2.416 -4.370 30.446 -5.374 -0.371 2.959 26.479 A A 4 5 4.704 B B A A 6 5 3.128 2.152 -0.613 -1.801 AA_DA4DT5:DA5BDT6B_AA 4 0.623 -1.363 26.386 -4.464 1.492 2.333 30.071 A A 5 6 15.829 B B A A 5 4 3.022 8.062 -0.084 -2.055 AA_DT5DC6:DG4BDA5B_AA 5 -5.974 11.729 28.384 -5.354 -0.870 2.046 28.280 A A 6 7 13.650 B B A A 4 3 2.685 6.587 -0.444 -2.087 AA_DC6DC7:DG3BDG4B_AA 6 4.074 -8.441 27.220 -5.398 1.605 1.494 22.106 A A 7 8 -0.052 B B A A 3 2 4.714 -0.014 -0.638 -4.133 AA_DC7DT8:DT2BDG3B_AA 7 -21.740 79.624 4.030 -10.770 -11.786 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 2002-05-08 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name Structural Basis for Poor Uracil Excision from Hairpin DNA: NMR Study Solution structure of a uracil containing hairpin DNA. Structural basis for Uracil DNA Glycosylase interaction with Uracil: NMR study Structural basis for Uracil DNA Glycosylase interaction with Uracil: NMR study RCSB Y RCSB 2001-04-05 REL Custom made by Ransom Hill Biosciences, Inc., Ramona CA (USA) sample This structure was determined using 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 6 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 196 restraints, 122 are NOE-derived distance constraints, 64 dihedral angle restraints, 10 distance restraints from hydrogen bonds. Restrained molecular dynamics and Energy minimization 1 fewest violations,lowest energy 2 mM oligo; no buffer; pH = 7.0; 305K; 99% D2O 99% D2O 2 mM oligo; no buffer; pH = 7.0; 305K; 90% H2O + 10% D2O 90% H2O/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 T 9 n 9 DT 9 A U 1 n 10 B DU 1 A T 2 n 11 B DT 2 A G 3 n 12 B DG 3 A G 4 n 13 B DG 4 A A 5 n 14 B DA 5 A T 6 n 15 B DT 6 A C 7 n 16 B DC 7 A C 8 n 17 B DC 8 A T 9 n 18 B DT 9 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 DG 2 0.082 SIDE CHAIN 1 A DT 8 0.094 SIDE CHAIN 1 A DT 9 0.420 SIDE CHAIN B 1 A DT 2 0.073 SIDE CHAIN B 1 A DG 3 0.062 SIDE CHAIN 2 A DG 2 0.071 SIDE CHAIN 2 A DT 8 0.086 SIDE CHAIN 2 A DT 9 0.400 SIDE CHAIN B 2 A DT 2 0.153 SIDE CHAIN B 2 A DG 3 0.058 SIDE CHAIN 3 A DA 1 0.061 SIDE CHAIN 3 A DG 2 0.064 SIDE CHAIN 3 A DT 8 0.080 SIDE CHAIN 3 A DT 9 0.426 SIDE CHAIN B 3 A DT 2 0.065 SIDE CHAIN 4 A DG 2 0.076 SIDE CHAIN 4 A DT 8 0.090 SIDE CHAIN 4 A DT 9 0.406 SIDE CHAIN B 4 A DT 2 0.076 SIDE CHAIN B 4 A DG 3 0.065 SIDE CHAIN B 4 A DT 6 0.081 SIDE CHAIN 5 A DG 2 0.082 SIDE CHAIN 5 A DT 8 0.094 SIDE CHAIN 5 A DT 9 0.420 SIDE CHAIN B 5 A DT 2 0.073 SIDE CHAIN B 5 A DG 3 0.062 SIDE CHAIN 6 A DG 2 0.071 SIDE CHAIN 6 A DT 8 0.086 SIDE CHAIN 6 A DT 9 0.400 SIDE CHAIN B 6 A DT 2 0.153 SIDE CHAIN B 6 A DG 3 0.058 SIDE CHAIN 1 2.33 0.30 108.30 110.63 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 -3.20 0.50 117.00 113.80 A A A C4 C5 C6 DA DA DA 1 1 1 N 1 3.54 0.50 117.70 121.24 A A A C5 C6 N1 DA DA DA 1 1 1 N 1 -3.99 0.60 118.60 114.61 A A A N1 C6 N6 DA DA DA 1 1 1 N 1 1.90 0.30 108.30 110.20 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 3.17 0.30 108.30 111.47 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 -3.29 0.50 117.00 113.71 A A A C4 C5 C6 DA DA DA 4 4 4 N 1 3.40 0.50 117.70 121.10 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -4.78 0.60 118.60 113.82 A A A N1 C6 N6 DA DA DA 4 4 4 N 1 2.32 0.30 108.30 110.62 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 -3.79 0.60 122.90 119.11 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 4.64 0.30 108.30 112.94 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 1.88 0.30 108.30 110.18 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 -5.35 0.80 105.90 100.55 A A A O4' C1' C2' DT DT DT 8 8 8 N 1 2.81 0.30 108.30 111.11 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -4.84 0.60 122.30 117.46 A A A N3 C2 O2 DT DT DT 8 8 8 N 1 -4.57 0.60 122.90 118.33 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 -5.29 0.50 121.30 116.01 A A A C6 N1 C2 DT DT DT 9 9 9 N 1 -3.75 0.60 127.20 123.45 A A A C2 N3 C4 DT DT DT 9 9 9 N 1 -5.36 0.60 123.70 118.34 A A A C5 C6 N1 DT DT DT 9 9 9 N 1 10.64 1.50 120.40 131.04 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 1 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 1 5.68 0.60 114.90 120.58 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 1 -5.98 0.70 122.20 116.22 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 1 3.10 0.30 108.30 111.40 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 1 -4.56 0.60 122.30 117.74 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 1 -4.32 0.60 122.90 118.58 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 1 -4.95 0.80 105.90 100.95 A A A O4' C1' C2' DG DG DG 3 3 3 N B B B 1 6.71 0.30 108.30 115.01 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 1 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 1 -5.06 0.80 105.90 100.84 A A A O4' C1' C2' DA DA DA 5 5 5 N B B B 1 3.84 0.50 117.70 121.54 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 1 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DT DT DT 6 6 6 N B B B 1 -3.95 0.60 122.30 118.35 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 1 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 1 3.12 0.30 108.30 111.42 A A A O4' C1' N1 DC DC DC 7 7 7 N B B B 1 1.83 0.30 108.30 110.13 A A A O4' C1' N1 DC DC DC 8 8 8 N B B B 1 -3.65 0.60 122.30 118.65 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 1 -3.89 0.60 122.90 119.01 A A A C6 C5 C7 DT DT DT 9 9 9 N 2 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DA DA DA 1 1 1 N 2 -3.14 0.50 117.00 113.86 A A A C4 C5 C6 DA DA DA 1 1 1 N 2 3.46 0.50 117.70 121.16 A A A C5 C6 N1 DA DA DA 1 1 1 N 2 -4.10 0.60 118.60 114.50 A A A N1 C6 N6 DA DA DA 1 1 1 N 2 -4.82 0.80 105.90 101.08 A A A O4' C1' C2' DG DG DG 2 2 2 N 2 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DG DG DG 2 2 2 N 2 3.04 0.50 111.50 114.54 A A A C5 C6 N1 DG DG DG 2 2 2 N 2 3.88 0.30 108.30 112.18 A A A O4' C1' N9 DA DA DA 4 4 4 N 2 -3.16 0.50 117.00 113.84 A A A C4 C5 C6 DA DA DA 4 4 4 N 2 3.73 0.50 117.70 121.43 A A A C5 C6 N1 DA DA DA 4 4 4 N 2 -3.94 0.60 118.60 114.66 A A A N1 C6 N6 DA DA DA 4 4 4 N 2 -4.09 0.60 122.30 118.21 A A A N3 C2 O2 DT DT DT 5 5 5 N 2 -3.80 0.60 122.90 119.10 A A A C6 C5 C7 DT DT DT 5 5 5 N 2 -5.45 0.80 105.90 100.45 A A A O4' C1' C2' DT DT DT 8 8 8 N 2 3.25 0.30 108.30 111.55 A A A O4' C1' N1 DT DT DT 8 8 8 N 2 -4.70 0.60 122.30 117.60 A A A N3 C2 O2 DT DT DT 8 8 8 N 2 -4.52 0.60 122.90 118.38 A A A C6 C5 C7 DT DT DT 8 8 8 N 2 -5.18 0.50 121.30 116.12 A A A C6 N1 C2 DT DT DT 9 9 9 N 2 -5.16 0.60 123.70 118.54 A A A C5 C6 N1 DT DT DT 9 9 9 N 2 -3.62 0.60 122.30 118.68 A A A N3 C2 O2 DT DT DT 9 9 9 N 2 10.51 1.50 120.40 130.91 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 2 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 2 5.86 0.60 114.90 120.76 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 2 -6.34 0.70 122.20 115.86 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 2 3.10 0.30 108.30 111.40 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 2 -4.10 0.60 122.30 118.20 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 2 -3.89 0.60 122.90 119.01 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 2 7.02 0.30 108.30 115.32 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 2 1.99 0.30 108.30 110.29 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 2 -5.25 0.80 105.90 100.65 A A A O4' C1' C2' DA DA DA 5 5 5 N B B B 2 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DA DA DA 5 5 5 N B B B 2 3.86 0.50 117.70 121.56 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 2 -4.30 0.60 122.30 118.00 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 2 -3.84 0.60 122.90 119.06 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 2 4.30 0.30 108.30 112.60 A A A O4' C1' N1 DC DC DC 7 7 7 N B B B 2 -3.76 0.60 122.30 118.54 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 2 -3.95 0.60 122.90 118.95 A A A C6 C5 C7 DT DT DT 9 9 9 N 3 -5.40 0.80 105.90 100.50 A A A O4' C1' C2' DA DA DA 1 1 1 N 3 6.28 0.30 108.30 114.58 A A A O4' C1' N9 DA DA DA 1 1 1 N 3 -3.45 0.50 117.00 113.55 A A A C4 C5 C6 DA DA DA 1 1 1 N 3 3.42 0.50 117.70 121.12 A A A C5 C6 N1 DA DA DA 1 1 1 N 3 -5.52 0.60 118.60 113.08 A A A N1 C6 N6 DA DA DA 1 1 1 N 3 2.22 0.30 108.30 110.52 A A A O4' C1' N9 DG DG DG 3 3 3 N 3 3.03 0.50 111.50 114.53 A A A C5 C6 N1 DG DG DG 3 3 3 N 3 -3.13 0.50 117.00 113.87 A A A C4 C5 C6 DA DA DA 4 4 4 N 3 3.52 0.50 117.70 121.22 A A A C5 C6 N1 DA DA DA 4 4 4 N 3 -4.41 0.60 118.60 114.19 A A A N1 C6 N6 DA DA DA 4 4 4 N 3 -3.80 0.60 122.30 118.50 A A A N3 C2 O2 DT DT DT 5 5 5 N 3 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 5 5 5 N 3 3.73 0.30 108.30 112.03 A A A O4' C1' N1 DC DC DC 6 6 6 N 3 2.52 0.30 108.30 110.82 A A A O4' C1' N1 DC DC DC 7 7 7 N 3 -5.89 0.80 105.90 100.01 A A A O4' C1' C2' DT DT DT 8 8 8 N 3 3.74 0.30 108.30 112.04 A A A O4' C1' N1 DT DT DT 8 8 8 N 3 -4.87 0.60 122.30 117.43 A A A N3 C2 O2 DT DT DT 8 8 8 N 3 -4.29 0.60 122.90 118.61 A A A C6 C5 C7 DT DT DT 8 8 8 N 3 -5.04 0.50 121.30 116.26 A A A C6 N1 C2 DT DT DT 9 9 9 N 3 -3.70 0.60 127.20 123.50 A A A C2 N3 C4 DT DT DT 9 9 9 N 3 -5.44 0.60 123.70 118.26 A A A C5 C6 N1 DT DT DT 9 9 9 N 3 10.07 1.50 120.40 130.47 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 3 2.61 0.30 108.30 110.91 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 3 5.65 0.60 114.90 120.55 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 3 -5.97 0.70 122.20 116.23 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 3 2.84 0.30 108.30 111.14 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 3 -4.40 0.60 122.30 117.90 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 3 -4.28 0.60 122.90 118.62 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 3 7.46 0.30 108.30 115.76 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 3 4.59 0.30 108.30 112.89 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 3 3.58 0.50 117.70 121.28 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 3 3.12 0.30 108.30 111.42 A A A O4' C1' N1 DT DT DT 6 6 6 N B B B 3 -3.71 0.60 122.30 118.59 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 3 -4.03 0.60 122.90 118.87 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 3 1.88 0.30 108.30 110.18 A A A O4' C1' N1 DT DT DT 9 9 9 N B B B 3 -3.74 0.60 122.30 118.56 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 3 -4.11 0.60 122.90 118.79 A A A C6 C5 C7 DT DT DT 9 9 9 N 4 2.04 0.30 108.30 110.34 A A A O4' C1' N9 DA DA DA 1 1 1 N 4 -3.12 0.50 117.00 113.88 A A A C4 C5 C6 DA DA DA 1 1 1 N 4 3.45 0.50 117.70 121.15 A A A C5 C6 N1 DA DA DA 1 1 1 N 4 -3.91 0.60 118.60 114.69 A A A N1 C6 N6 DA DA DA 1 1 1 N 4 2.06 0.30 108.30 110.36 A A A O4' C1' N9 DG DG DG 2 2 2 N 4 3.51 0.30 108.30 111.81 A A A O4' C1' N9 DA DA DA 4 4 4 N 4 -3.27 0.50 117.00 113.73 A A A C4 C5 C6 DA DA DA 4 4 4 N 4 3.37 0.50 117.70 121.07 A A A C5 C6 N1 DA DA DA 4 4 4 N 4 -4.54 0.60 118.60 114.06 A A A N1 C6 N6 DA DA DA 4 4 4 N 4 -3.99 0.60 122.30 118.31 A A A N3 C2 O2 DT DT DT 5 5 5 N 4 -3.80 0.60 122.90 119.10 A A A C6 C5 C7 DT DT DT 5 5 5 N 4 4.19 0.30 108.30 112.49 A A A O4' C1' N1 DC DC DC 6 6 6 N 4 -5.31 0.80 105.90 100.59 A A A O4' C1' C2' DT DT DT 8 8 8 N 4 3.09 0.30 108.30 111.39 A A A O4' C1' N1 DT DT DT 8 8 8 N 4 -4.81 0.60 122.30 117.49 A A A N3 C2 O2 DT DT DT 8 8 8 N 4 -4.46 0.60 122.90 118.44 A A A C6 C5 C7 DT DT DT 8 8 8 N 4 -5.17 0.50 121.30 116.13 A A A C6 N1 C2 DT DT DT 9 9 9 N 4 -5.19 0.60 123.70 118.51 A A A C5 C6 N1 DT DT DT 9 9 9 N 4 10.46 1.50 120.40 130.86 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 4 3.38 0.30 108.30 111.68 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 4 5.56 0.60 114.90 120.46 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 4 -5.74 0.70 122.20 116.46 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 4 3.05 0.30 108.30 111.35 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 4 -4.39 0.60 122.30 117.91 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 4 -4.31 0.60 122.90 118.59 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 4 -5.24 0.80 105.90 100.66 A A A O4' C1' C2' DG DG DG 3 3 3 N B B B 4 6.75 0.30 108.30 115.05 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 4 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 4 3.91 0.50 117.70 121.61 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 4 3.82 0.30 108.30 112.12 A A A O4' C1' N1 DT DT DT 6 6 6 N B B B 4 -3.97 0.60 122.30 118.33 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 4 -4.20 0.60 122.90 118.70 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 4 -3.70 0.60 122.30 118.60 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 4 -3.99 0.60 122.90 118.91 A A A C6 C5 C7 DT DT DT 9 9 9 N 5 2.33 0.30 108.30 110.63 A A A O4' C1' N9 DA DA DA 1 1 1 N 5 -3.20 0.50 117.00 113.80 A A A C4 C5 C6 DA DA DA 1 1 1 N 5 3.54 0.50 117.70 121.24 A A A C5 C6 N1 DA DA DA 1 1 1 N 5 -3.99 0.60 118.60 114.61 A A A N1 C6 N6 DA DA DA 1 1 1 N 5 1.90 0.30 108.30 110.20 A A A O4' C1' N9 DG DG DG 3 3 3 N 5 3.17 0.30 108.30 111.47 A A A O4' C1' N9 DA DA DA 4 4 4 N 5 -3.29 0.50 117.00 113.71 A A A C4 C5 C6 DA DA DA 4 4 4 N 5 3.40 0.50 117.70 121.10 A A A C5 C6 N1 DA DA DA 4 4 4 N 5 -4.78 0.60 118.60 113.82 A A A N1 C6 N6 DA DA DA 4 4 4 N 5 2.32 0.30 108.30 110.62 A A A O4' C1' N1 DT DT DT 5 5 5 N 5 -3.79 0.60 122.90 119.11 A A A C6 C5 C7 DT DT DT 5 5 5 N 5 4.64 0.30 108.30 112.94 A A A O4' C1' N1 DC DC DC 6 6 6 N 5 1.88 0.30 108.30 110.18 A A A O4' C1' N1 DC DC DC 7 7 7 N 5 -5.35 0.80 105.90 100.55 A A A O4' C1' C2' DT DT DT 8 8 8 N 5 2.81 0.30 108.30 111.11 A A A O4' C1' N1 DT DT DT 8 8 8 N 5 -4.84 0.60 122.30 117.46 A A A N3 C2 O2 DT DT DT 8 8 8 N 5 -4.57 0.60 122.90 118.33 A A A C6 C5 C7 DT DT DT 8 8 8 N 5 -5.29 0.50 121.30 116.01 A A A C6 N1 C2 DT DT DT 9 9 9 N 5 -3.75 0.60 127.20 123.45 A A A C2 N3 C4 DT DT DT 9 9 9 N 5 -5.36 0.60 123.70 118.34 A A A C5 C6 N1 DT DT DT 9 9 9 N 5 10.64 1.50 120.40 131.04 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 5 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 5 5.68 0.60 114.90 120.58 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 5 -5.98 0.70 122.20 116.22 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 5 3.10 0.30 108.30 111.40 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 5 -4.56 0.60 122.30 117.74 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 5 -4.32 0.60 122.90 118.58 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 5 -4.95 0.80 105.90 100.95 A A A O4' C1' C2' DG DG DG 3 3 3 N B B B 5 6.71 0.30 108.30 115.01 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 5 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 5 -5.06 0.80 105.90 100.84 A A A O4' C1' C2' DA DA DA 5 5 5 N B B B 5 3.84 0.50 117.70 121.54 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 5 3.06 0.30 108.30 111.36 A A A O4' C1' N1 DT DT DT 6 6 6 N B B B 5 -3.95 0.60 122.30 118.35 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 5 -3.77 0.60 122.90 119.13 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 5 3.12 0.30 108.30 111.42 A A A O4' C1' N1 DC DC DC 7 7 7 N B B B 5 1.83 0.30 108.30 110.13 A A A O4' C1' N1 DC DC DC 8 8 8 N B B B 5 -3.65 0.60 122.30 118.65 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 5 -3.89 0.60 122.90 119.01 A A A C6 C5 C7 DT DT DT 9 9 9 N 6 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DA DA DA 1 1 1 N 6 -3.14 0.50 117.00 113.86 A A A C4 C5 C6 DA DA DA 1 1 1 N 6 3.46 0.50 117.70 121.16 A A A C5 C6 N1 DA DA DA 1 1 1 N 6 -4.10 0.60 118.60 114.50 A A A N1 C6 N6 DA DA DA 1 1 1 N 6 -4.82 0.80 105.90 101.08 A A A O4' C1' C2' DG DG DG 2 2 2 N 6 4.31 0.30 108.30 112.61 A A A O4' C1' N9 DG DG DG 2 2 2 N 6 3.04 0.50 111.50 114.54 A A A C5 C6 N1 DG DG DG 2 2 2 N 6 3.88 0.30 108.30 112.18 A A A O4' C1' N9 DA DA DA 4 4 4 N 6 -3.16 0.50 117.00 113.84 A A A C4 C5 C6 DA DA DA 4 4 4 N 6 3.73 0.50 117.70 121.43 A A A C5 C6 N1 DA DA DA 4 4 4 N 6 -3.94 0.60 118.60 114.66 A A A N1 C6 N6 DA DA DA 4 4 4 N 6 -4.09 0.60 122.30 118.21 A A A N3 C2 O2 DT DT DT 5 5 5 N 6 -3.80 0.60 122.90 119.10 A A A C6 C5 C7 DT DT DT 5 5 5 N 6 -5.45 0.80 105.90 100.45 A A A O4' C1' C2' DT DT DT 8 8 8 N 6 3.25 0.30 108.30 111.55 A A A O4' C1' N1 DT DT DT 8 8 8 N 6 -4.70 0.60 122.30 117.60 A A A N3 C2 O2 DT DT DT 8 8 8 N 6 -4.52 0.60 122.90 118.38 A A A C6 C5 C7 DT DT DT 8 8 8 N 6 -5.18 0.50 121.30 116.12 A A A C6 N1 C2 DT DT DT 9 9 9 N 6 -5.16 0.60 123.70 118.54 A A A C5 C6 N1 DT DT DT 9 9 9 N 6 -3.62 0.60 122.30 118.68 A A A N3 C2 O2 DT DT DT 9 9 9 N 6 10.51 1.50 120.40 130.91 A A A C6 N1 C1' DT DT DT 9 9 9 N B B B 6 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DU DU DU 1 1 1 N B B B 6 5.86 0.60 114.90 120.76 A A A N1 C2 N3 DU DU DU 1 1 1 N B B B 6 -6.34 0.70 122.20 115.86 A A A N3 C2 O2 DU DU DU 1 1 1 N B B B 6 3.10 0.30 108.30 111.40 A A A O4' C1' N1 DT DT DT 2 2 2 N B B B 6 -4.10 0.60 122.30 118.20 A A A N3 C2 O2 DT DT DT 2 2 2 N B B B 6 -3.89 0.60 122.90 119.01 A A A C6 C5 C7 DT DT DT 2 2 2 N B B B 6 7.02 0.30 108.30 115.32 A A A O4' C1' N9 DG DG DG 3 3 3 N B B B 6 1.99 0.30 108.30 110.29 A A A O4' C1' N9 DG DG DG 4 4 4 N B B B 6 -5.25 0.80 105.90 100.65 A A A O4' C1' C2' DA DA DA 5 5 5 N B B B 6 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DA DA DA 5 5 5 N B B B 6 3.86 0.50 117.70 121.56 A A A C5 C6 N1 DA DA DA 5 5 5 N B B B 6 -4.30 0.60 122.30 118.00 A A A N3 C2 O2 DT DT DT 6 6 6 N B B B 6 -3.84 0.60 122.90 119.06 A A A C6 C5 C7 DT DT DT 6 6 6 N B B B 6 4.30 0.30 108.30 112.60 A A A O4' C1' N1 DC DC DC 7 7 7 N B B B 6 -3.76 0.60 122.30 118.54 A A A N3 C2 O2 DT DT DT 9 9 9 N B B B 6 -3.95 0.60 122.90 118.95 A A A C6 C5 C7 DT DT DT 9 9 9 N B B 1 A A N1 C6 DU DU 1 1 0.102 0.009 1.375 1.477 N B B 2 A A N1 C6 DU DU 1 1 0.103 0.009 1.375 1.478 N B B 3 A A N1 C6 DU DU 1 1 0.103 0.009 1.375 1.478 N B B 4 A A N1 C6 DU DU 1 1 0.101 0.009 1.375 1.476 N B B 5 A A N1 C6 DU DU 1 1 0.102 0.009 1.375 1.477 N B B 6 A A N1 C6 DU DU 1 1 0.103 0.009 1.375 1.478 N Structural Basis for Poor Excision from Hairpin DNA: NMR Study 1 N N hydrog WATSON-CRICK B A DA 1 A N1 DA 1 1_555 A DT 9 A N3 DT 18 1_555 hydrog WATSON-CRICK B A DA 1 A N6 DA 1 1_555 A DT 9 A O4 DT 18 1_555 hydrog WATSON-CRICK B A DG 2 A N1 DG 2 1_555 A DC 8 A N3 DC 17 1_555 hydrog WATSON-CRICK B A DG 2 A N2 DG 2 1_555 A DC 8 A O2 DC 17 1_555 hydrog WATSON-CRICK B A DG 2 A O6 DG 2 1_555 A DC 8 A N4 DC 17 1_555 hydrog WATSON-CRICK B A DG 3 A N1 DG 3 1_555 A DC 7 A N3 DC 16 1_555 hydrog WATSON-CRICK B A DG 3 A N2 DG 3 1_555 A DC 7 A O2 DC 16 1_555 hydrog WATSON-CRICK B A DG 3 A O6 DG 3 1_555 A DC 7 A N4 DC 16 1_555 hydrog WATSON-CRICK B A DA 4 A N1 DA 4 1_555 A DT 6 A N3 DT 15 1_555 hydrog WATSON-CRICK B A DA 4 A N6 DA 4 1_555 A DT 6 A O4 DT 15 1_555 hydrog WATSON-CRICK B A DT 5 A N3 DT 5 1_555 A DA 5 A N1 DA 14 1_555 hydrog WATSON-CRICK B A DT 5 A O4 DT 5 1_555 A DA 5 A N6 DA 14 1_555 hydrog WATSON-CRICK B A DC 6 A N3 DC 6 1_555 A DG 4 A N1 DG 13 1_555 hydrog WATSON-CRICK B A DC 6 A N4 DC 6 1_555 A DG 4 A O6 DG 13 1_555 hydrog WATSON-CRICK B A DC 6 A O2 DC 6 1_555 A DG 4 A N2 DG 13 1_555 hydrog WATSON-CRICK B A DC 7 A N3 DC 7 1_555 A DG 3 A N1 DG 12 1_555 hydrog WATSON-CRICK B A DC 7 A N4 DC 7 1_555 A DG 3 A O6 DG 12 1_555 hydrog WATSON-CRICK B A DC 7 A O2 DC 7 1_555 A DG 3 A N2 DG 12 1_555 hydrog TYPE_16_PAIR B A DT 8 A N3 DT 8 1_555 A DT 2 A O2 DT 11 1_555 hydrog TYPE_16_PAIR B A DT 8 A O4 DT 8 1_555 A DT 2 A N3 DT 11 1_555 DNA Uracil, Hairpin DNA, Hairpin loop, Double helix, UDG-Uracil interaction, DNA 1IDX PDB 1 1IDX 1 9 1IDX 1 9 1IDX B A 1 1 18