1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Urbach, A.R. Love, J.J. Ross, S.A. Dervan, P.B. 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 C41 H56 N17 O8 1 914.992 IMIDAZOLE-PYRROLE-BETA ALANINE-IMIDAZOLE-BETA ALANINE-IMIDAZOLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE non-polymer UK J.Mol.Biol. JMOBAK 0070 0022-2836 320 55 71 10.1016/S0022-2836(02)00430-8 12079334 Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif. 2002 10.2210/pdb1lej/pdb pdb_00001lej 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 4018.652 5'-D(*CP*CP*AP*AP*AP*GP*AP*GP*AP*AP*GP*CP*G)-3' 1 syn polymer 3924.544 5'-D(*CP*GP*CP*TP*TP*CP*TP*CP*TP*TP*TP*GP*G)-3' 1 syn polymer 914.992 IMIDAZOLE-PYRROLE-BETA ALANINE-IMIDAZOLE-BETA ALANINE-IMIDAZOLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE 1 syn non-polymer no no (DC)(DC)(DA)(DA)(DA)(DG)(DA)(DG)(DA)(DA)(DG)(DC)(DG) CCAAAGAGAAGCG A polydeoxyribonucleotide no no (DC)(DG)(DC)(DT)(DT)(DC)(DT)(DC)(DT)(DT)(DT)(DG)(DG) CGCTTCTCTTTGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n 15.407 1 19 A 1 B 26 -1.723 A_DC1:DG26_B 1 -10.475 0.355 -0.074 -0.168 15.972 1 19 A 2 B 25 0.329 A_DC2:DG25_B 2 -15.351 0.263 -0.368 -0.144 1.392 1 20 A 3 B 24 2.377 A_DA3:DT24_B 3 -14.615 0.259 -0.477 -0.145 10.783 1 20 A 4 B 23 -4.341 A_DA4:DT23_B 4 -18.272 0.135 -0.167 -0.132 8.052 1 20 A 5 B 22 -3.614 A_DA5:DT22_B 5 -15.960 0.269 0.167 -0.053 -1.920 1 19 A 6 B 21 1.716 A_DG6:DC21_B 6 -18.542 -0.262 0.010 -0.198 -1.601 1 20 A 7 B 20 -0.846 A_DA7:DT20_B 7 -15.732 0.308 -0.002 -0.118 -4.802 1 19 A 8 B 19 0.701 A_DG8:DC19_B 8 -19.007 -0.145 -0.061 -0.186 -16.958 1 20 A 9 B 18 0.520 A_DA9:DT18_B 9 -18.652 0.394 -0.270 -0.054 -12.937 1 20 A 10 B 17 -2.503 A_DA10:DT17_B 10 -15.648 0.347 -0.347 -0.102 -11.424 1 19 A 11 B 16 1.325 A_DG11:DC16_B 11 -6.596 -0.003 0.064 -0.103 -2.689 1 19 A 12 B 15 0.039 A_DC12:DG15_B 12 -7.014 0.466 0.191 -0.215 -25.372 1 19 A 13 B 14 0.188 A_DG13:DC14_B 13 -24.829 -0.451 -0.278 -0.155 3.314 37.092 A A 1 2 2.621 B B 26 25 3.191 1.654 0.835 0.491 AA_DC1DC2:DG25DG26_BB 1 8.324 -13.194 36.141 0.548 -0.190 3.537 40.837 A A 2 3 20.194 B B 25 24 3.526 13.822 -1.001 0.436 AA_DC2DA3:DT24DG25_BB 2 -3.036 4.435 38.405 -1.073 1.061 2.958 31.452 A A 3 4 7.862 B B 24 23 2.972 4.247 -0.124 0.072 AA_DA3DA4:DT23DT24_BB 3 -2.008 3.717 31.108 -0.591 -0.115 3.127 42.863 A A 4 5 1.146 B B 23 22 3.099 0.837 -0.405 0.242 AA_DA4DA5:DT22DT23_BB 4 -4.240 5.811 42.655 0.252 0.151 3.248 38.577 A A 5 6 5.033 B B 22 21 3.323 3.321 0.138 -0.732 AA_DA5DG6:DC21DT22_BB 5 -0.582 0.881 38.435 -1.520 -0.282 3.048 36.000 A A 6 7 6.705 B B 21 20 3.090 4.135 -0.391 -0.260 AA_DG6DA7:DT20DC21_BB 6 -0.536 0.868 35.766 -0.975 0.561 3.222 34.622 A A 7 8 6.109 B B 20 19 3.244 3.629 0.435 -0.163 AA_DA7DG8:DC19DT20_BB 7 1.069 -1.800 34.421 -0.827 -0.568 3.436 45.538 A A 8 9 2.929 B B 19 18 3.370 2.265 -0.722 0.598 AA_DG8DA9:DT18DC19_BB 8 -3.295 4.261 45.371 0.566 0.631 3.069 39.629 A A 9 10 -1.026 B B 18 17 3.094 -0.695 -0.263 -0.024 AA_DA9DA10:DT17DT18_BB 9 2.764 -4.080 39.530 0.041 0.693 3.303 30.276 A A 10 11 -5.632 B B 17 16 3.213 -2.937 0.703 -1.087 AA_DA10DG11:DC16DT17_BB 10 0.072 -0.138 30.136 -1.489 -1.332 3.062 37.088 A A 11 12 1.486 B B 16 15 3.063 0.945 -0.745 -0.481 AA_DG11DC12:DG15DC16_BB 11 -0.643 1.011 37.071 -0.875 1.091 3.489 39.830 A A 12 13 20.152 B B 15 14 3.568 13.340 1.086 -0.116 AA_DC12DG13:DC14DG15_BB 12 9.940 -15.017 36.319 -1.920 -0.290 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2002-05-08 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _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 RCSB Y RCSB 2002-04-09 REL REL P11 IMIDAZOLE-PYRROLE-BETA ALANINE-IMIDAZOLE-BETA ALANINE-IMIDAZOLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE This sequence was designed and synthesized for this study. sample This sequence was designed and synthesized for this study. sample This structure was determined using standard 2D homonuclear techniques. structures with the least restraint violations 40 11 2D NOESY 10 Millimolar 7.0 ambient 298 K The structure calculations used 548 distance restraints. 508 were NOE-derived, and 40 were for Watson-Crick hydrogen bonds. restrained molecular dynamics/simulated annealing, matrix relaxation/NOE-derived distance restraints. 1 fewest violations 3.67 millimolar polyamide-DNA complex, 10 millimolar sodium phosphate, pH 7.0, 90% H2O, 10% D2O 90% H2O/10% D2O Varian Associates, Inc. collection VNMR 6.1 B Delalgio, grzesiek, Vuister, Zhu, Pfeifer, & Bax processing NMRPipe 1 Johnson, & Blevins data analysis NMRView 4.1.2 Borgias, & James iterative matrix relaxation MARDIGRAS 3.2 Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner structure solution Amber 6.0 Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner refinement SANDER MODULE OF AMBER 6.0 PACKAGE (2000) 600 Varian INOVA P11 27 3 P11 P11 27 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A A 4 n 4 DA 4 A A 5 n 5 DA 5 A G 6 n 6 DG 6 A A 7 n 7 DA 7 A G 8 n 8 DG 8 A A 9 n 9 DA 9 A A 10 n 10 DA 10 A G 11 n 11 DG 11 A C 12 n 12 DC 12 A G 13 n 13 DG 13 A C 14 n 1 DC 14 B G 15 n 2 DG 15 B C 16 n 3 DC 16 B T 17 n 4 DT 17 B T 18 n 5 DT 18 B C 19 n 6 DC 19 B T 20 n 7 DT 20 B C 21 n 8 DC 21 B T 22 n 9 DT 22 B T 23 n 10 DT 23 B T 24 n 11 DT 24 B G 25 n 12 DG 25 B G 26 n 13 DG 26 B author_defined_assembly 2 dimeric 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 HO5' OP1 DC DC 1 2 1.32 2 B B HO5' OP1 DC DG 14 15 1.35 3 B B HO5' OP1 DC DG 14 15 1.34 4 A A HO5' OP1 DC DC 1 2 1.35 5 B B HO5' OP1 DC DG 14 15 1.34 7 A A HO5' OP2 DC DC 1 2 1.37 8 A B OP1 HO3' DA DG 4 26 1.32 9 B B HO5' OP2 DC DG 14 15 1.35 10 A A HO5' OP1 DC DC 1 2 1.36 1 A DG 6 0.075 SIDE CHAIN 1 A DA 9 0.077 SIDE CHAIN 1 B DT 17 0.080 SIDE CHAIN 1 B DT 18 0.068 SIDE CHAIN 2 A DG 6 0.075 SIDE CHAIN 2 A DA 9 0.056 SIDE CHAIN 2 A DG 11 0.091 SIDE CHAIN 2 B DC 16 0.061 SIDE CHAIN 2 B DT 20 0.086 SIDE CHAIN 2 B DT 22 0.082 SIDE CHAIN 2 B DT 23 0.072 SIDE CHAIN 2 B DG 26 0.072 SIDE CHAIN 3 A DA 7 0.062 SIDE CHAIN 3 B DT 17 0.101 SIDE CHAIN 3 B DT 22 0.067 SIDE CHAIN 4 A DA 3 0.054 SIDE CHAIN 4 A DG 11 0.067 SIDE CHAIN 4 A DC 12 0.071 SIDE CHAIN 4 B DC 16 0.117 SIDE CHAIN 4 B DT 18 0.068 SIDE CHAIN 4 B DT 20 0.101 SIDE CHAIN 4 B DT 22 0.082 SIDE CHAIN 4 B DG 26 0.076 SIDE CHAIN 5 A DA 4 0.057 SIDE CHAIN 5 B DT 22 0.111 SIDE CHAIN 6 A DG 6 0.087 SIDE CHAIN 6 A DA 7 0.071 SIDE CHAIN 6 A DA 9 0.059 SIDE CHAIN 6 B DT 22 0.071 SIDE CHAIN 6 B DT 24 0.074 SIDE CHAIN 7 A DA 9 0.129 SIDE CHAIN 7 B DC 14 0.074 SIDE CHAIN 7 B DT 17 0.084 SIDE CHAIN 7 B DT 20 0.103 SIDE CHAIN 7 B DT 22 0.078 SIDE CHAIN 7 B DG 25 0.060 SIDE CHAIN 8 A DA 3 0.087 SIDE CHAIN 8 A DC 12 0.083 SIDE CHAIN 8 B DC 14 0.078 SIDE CHAIN 8 B DC 16 0.122 SIDE CHAIN 8 B DT 22 0.114 SIDE CHAIN 8 B DG 26 0.053 SIDE CHAIN 9 A DC 2 0.063 SIDE CHAIN 9 A DG 6 0.105 SIDE CHAIN 9 A DG 11 0.056 SIDE CHAIN 9 A DC 12 0.078 SIDE CHAIN 9 A DG 13 0.053 SIDE CHAIN 9 B DC 16 0.071 SIDE CHAIN 9 B DT 18 0.075 SIDE CHAIN 9 B DT 20 0.109 SIDE CHAIN 9 B DT 22 0.091 SIDE CHAIN 9 B DG 26 0.072 SIDE CHAIN 10 A DA 3 0.052 SIDE CHAIN 10 A DG 6 0.084 SIDE CHAIN 10 A DA 7 0.056 SIDE CHAIN 10 B DT 18 0.084 SIDE CHAIN 10 B DT 20 0.081 SIDE CHAIN 10 B DT 22 0.077 SIDE CHAIN 10 B DG 25 0.096 SIDE CHAIN 11 A DG 6 0.102 SIDE CHAIN 11 A DC 12 0.089 SIDE CHAIN 11 A DG 13 0.059 SIDE CHAIN 11 B DC 16 0.069 SIDE CHAIN 11 B DT 17 0.063 SIDE CHAIN 11 B DT 18 0.068 SIDE CHAIN 11 B DT 20 0.104 SIDE CHAIN 11 B DG 26 0.056 SIDE CHAIN 1 2.42 0.30 108.30 110.72 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 -4.22 0.70 121.90 117.68 A A A N3 C2 O2 DC DC DC 2 2 2 N 1 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 -4.37 0.60 118.60 114.23 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 2.40 0.30 108.30 110.70 A A A O4' C1' N9 DA DA DA 4 4 4 N 1 3.43 0.50 117.70 121.13 A A A C5 C6 N1 DA DA DA 4 4 4 N 1 -3.55 0.50 117.00 113.45 A A A C4 C5 C6 DA DA DA 5 5 5 N 1 4.05 0.50 117.70 121.75 A A A C5 C6 N1 DA DA DA 5 5 5 N 1 -5.29 0.60 118.60 113.31 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 -3.41 0.50 117.00 113.59 A A A C4 C5 C6 DA DA DA 7 7 7 N 1 3.04 0.50 117.70 120.74 A A A C5 C6 N1 DA DA DA 7 7 7 N 1 -5.17 0.60 118.60 113.43 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 2.24 0.30 108.30 110.54 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 -3.94 0.60 119.90 115.96 A A A N1 C6 O6 DG DG DG 8 8 8 N 1 -4.85 0.60 118.60 113.75 A A A N1 C6 N6 DA DA DA 9 9 9 N 1 -3.89 0.60 118.60 114.71 A A A N1 C6 N6 DA DA DA 10 10 10 N 1 4.54 0.30 108.30 112.84 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 1.87 0.30 108.30 110.17 A A A O4' C1' N1 DC DC DC 12 12 12 N 1 4.13 0.60 118.90 123.03 A A A N1 C2 O2 DC DC DC 12 12 12 N 1 -5.08 0.70 121.90 116.82 A A A N3 C2 O2 DC DC DC 12 12 12 N 1 3.72 0.30 108.30 112.02 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 2.17 0.30 108.30 110.47 B B B O4' C1' N1 DC DC DC 14 14 14 N 1 -4.64 0.70 121.90 117.26 B B B N3 C2 O2 DC DC DC 14 14 14 N 1 -3.73 0.60 122.90 119.17 B B B C6 C5 C7 DT DT DT 18 18 18 N 1 -4.29 0.70 121.90 117.61 B B B N3 C2 O2 DC DC DC 19 19 19 N 1 -3.72 0.60 122.90 119.18 B B B C6 C5 C7 DT DT DT 20 20 20 N 1 -3.80 0.60 122.90 119.10 B B B C6 C5 C7 DT DT DT 24 24 24 N 1 2.58 0.30 108.30 110.88 B B B O4' C1' N9 DG DG DG 25 25 25 N 1 1.91 0.30 108.30 110.21 B B B O4' C1' N9 DG DG DG 26 26 26 N 2 5.06 0.30 108.30 113.36 A A A O4' C1' N1 DC DC DC 1 1 1 N 2 -4.87 0.70 121.90 117.03 A A A N3 C2 O2 DC DC DC 1 1 1 N 2 -4.21 0.70 121.90 117.69 A A A N3 C2 O2 DC DC DC 2 2 2 N 2 3.30 0.30 108.30 111.60 A A A O4' C1' N9 DA DA DA 3 3 3 N 2 3.31 0.50 117.70 121.01 A A A C5 C6 N1 DA DA DA 3 3 3 N 2 -4.18 0.60 118.60 114.42 A A A N1 C6 N6 DA DA DA 3 3 3 N 2 4.66 0.30 108.30 112.96 A A A O4' C1' N9 DA DA DA 4 4 4 N 2 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 4 4 4 N 2 -3.67 0.60 118.60 114.93 A A A N1 C6 N6 DA DA DA 5 5 5 N 2 -3.65 0.60 119.90 116.25 A A A N1 C6 O6 DG DG DG 6 6 6 N 2 -3.82 0.60 118.60 114.78 A A A N1 C6 N6 DA DA DA 7 7 7 N 2 -4.15 0.60 119.90 115.75 A A A N1 C6 O6 DG DG DG 8 8 8 N 2 -3.35 0.50 117.00 113.65 A A A C4 C5 C6 DA DA DA 9 9 9 N 2 3.33 0.50 117.70 121.03 A A A C5 C6 N1 DA DA DA 9 9 9 N 2 -4.66 0.60 118.60 113.94 A A A N1 C6 N6 DA DA DA 9 9 9 N 2 3.01 0.50 117.70 120.71 A A A C5 C6 N1 DA DA DA 10 10 10 N 2 3.13 0.30 108.30 111.43 A A A O4' C1' N9 DG DG DG 11 11 11 N 2 2.01 0.30 108.30 110.31 A A A O4' C1' N9 DG DG DG 13 13 13 N 2 4.13 0.30 108.30 112.43 B B B O4' C1' N1 DC DC DC 14 14 14 N 2 -4.20 0.70 121.90 117.70 B B B N3 C2 O2 DC DC DC 14 14 14 N 2 -4.33 0.70 121.90 117.57 B B B N3 C2 O2 DC DC DC 16 16 16 N 2 -4.04 0.60 122.90 118.86 B B B C6 C5 C7 DT DT DT 24 24 24 N 2 4.30 0.30 108.30 112.60 B B B O4' C1' N9 DG DG DG 25 25 25 N 2 -4.06 0.60 119.90 115.84 B B B N1 C6 O6 DG DG DG 25 25 25 N 2 2.24 0.30 108.30 110.54 B B B O4' C1' N9 DG DG DG 26 26 26 N 3 2.91 0.30 108.30 111.21 A A A O4' C1' N1 DC DC DC 2 2 2 N 3 -4.52 0.70 121.90 117.38 A A A N3 C2 O2 DC DC DC 2 2 2 N 3 -4.27 0.60 118.60 114.33 A A A N1 C6 N6 DA DA DA 3 3 3 N 3 3.11 0.50 117.70 120.81 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 5 5 5 N 3 3.98 0.30 108.30 112.28 A A A O4' C1' N9 DG DG DG 6 6 6 N 3 2.24 0.30 108.30 110.54 A A A O4' C1' N9 DA DA DA 7 7 7 N 3 3.27 0.50 117.70 120.97 A A A C5 C6 N1 DA DA DA 7 7 7 N 3 -4.71 0.60 118.60 113.89 A A A N1 C6 N6 DA DA DA 7 7 7 N 3 3.34 0.30 108.30 111.64 A A A O4' C1' N9 DG DG DG 8 8 8 N 3 -3.72 0.60 118.60 114.88 A A A N1 C6 N6 DA DA DA 9 9 9 N 3 -3.04 0.50 117.00 113.96 A A A C4 C5 C6 DA DA DA 10 10 10 N 3 3.35 0.50 117.70 121.05 A A A C5 C6 N1 DA DA DA 10 10 10 N 3 2.71 0.30 108.30 111.01 A A A O4' C1' N9 DG DG DG 11 11 11 N 3 -4.74 0.70 121.90 117.16 A A A N3 C2 O2 DC DC DC 12 12 12 N 3 2.41 0.30 108.30 110.71 A A A O4' C1' N9 DG DG DG 13 13 13 N 3 4.77 0.30 108.30 113.07 B B B O4' C1' N1 DC DC DC 14 14 14 N 3 2.23 0.30 108.30 110.53 B B B O4' C1' N1 DC DC DC 16 16 16 N 3 7.97 1.20 119.70 127.67 B B B C3' O3' P DC DC DT 16 16 17 Y 3 -4.44 0.70 121.90 117.46 B B B N3 C2 O2 DC DC DC 19 19 19 N 3 7.31 1.20 119.70 127.01 B B B C3' O3' P DT DT DC 20 20 21 Y 3 3.88 0.60 118.90 122.78 B B B N1 C2 O2 DC DC DC 21 21 21 N 3 -4.57 0.70 121.90 117.33 B B B N3 C2 O2 DC DC DC 21 21 21 N 3 -3.81 0.60 122.30 118.49 B B B N3 C2 O2 DT DT DT 24 24 24 N 3 2.68 0.30 108.30 110.98 B B B O4' C1' N9 DG DG DG 25 25 25 N 3 3.01 0.30 108.30 111.31 B B B O4' C1' N9 DG DG DG 26 26 26 N 3 -3.72 0.60 119.90 116.18 B B B N1 C6 O6 DG DG DG 26 26 26 N 4 2.79 0.30 108.30 111.09 A A A O4' C1' N1 DC DC DC 1 1 1 N 4 3.69 0.60 118.90 122.59 A A A N1 C2 O2 DC DC DC 1 1 1 N 4 -4.63 0.70 121.90 117.27 A A A N3 C2 O2 DC DC DC 1 1 1 N 4 -4.06 0.60 118.60 114.54 A A A N1 C6 N6 DA DA DA 3 3 3 N 4 -4.81 0.80 102.40 97.59 A A A C3' C2' C1' DA DA DA 4 4 4 N 4 2.31 0.30 108.30 110.61 A A A O4' C1' N9 DA DA DA 4 4 4 N 4 -3.71 0.60 118.60 114.89 A A A N1 C6 N6 DA DA DA 4 4 4 N 4 -3.74 0.60 118.60 114.86 A A A N1 C6 N6 DA DA DA 5 5 5 N 4 -3.64 0.60 119.90 116.26 A A A N1 C6 O6 DG DG DG 6 6 6 N 4 -3.11 0.50 117.00 113.89 A A A C4 C5 C6 DA DA DA 7 7 7 N 4 -4.18 0.60 118.60 114.42 A A A N1 C6 N6 DA DA DA 7 7 7 N 4 -4.40 0.60 118.60 114.20 A A A N1 C6 N6 DA DA DA 9 9 9 N 4 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 10 10 10 N 4 1.95 0.30 108.30 110.25 A A A O4' C1' N9 DG DG DG 11 11 11 N 4 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DC DC DC 12 12 12 N 4 4.79 0.30 108.30 113.09 B B B O4' C1' N1 DC DC DC 14 14 14 N 4 -4.08 0.60 122.30 118.22 B B B N3 C2 O2 DT DT DT 18 18 18 N 4 2.54 0.30 108.30 110.84 B B B O4' C1' N1 DC DC DC 21 21 21 N 4 -4.60 0.70 121.90 117.30 B B B N3 C2 O2 DC DC DC 21 21 21 N 4 -3.62 0.60 122.30 118.68 B B B N3 C2 O2 DT DT DT 23 23 23 N 4 1.89 0.30 108.30 110.19 B B B O4' C1' N1 DT DT DT 24 24 24 N 4 3.05 0.30 108.30 111.35 B B B O4' C1' N9 DG DG DG 25 25 25 N 4 3.11 0.30 108.30 111.41 B B B O4' C1' N9 DG DG DG 26 26 26 N 5 3.75 0.60 118.90 122.65 A A A N1 C2 O2 DC DC DC 2 2 2 N 5 -3.00 0.50 117.00 114.00 A A A C4 C5 C6 DA DA DA 3 3 3 N 5 3.23 0.50 117.70 120.93 A A A C5 C6 N1 DA DA DA 3 3 3 N 5 3.19 0.50 117.70 120.89 A A A C5 C6 N1 DA DA DA 5 5 5 N 5 -3.62 0.60 118.60 114.98 A A A N1 C6 N6 DA DA DA 5 5 5 N 5 -3.61 0.60 119.90 116.29 A A A N1 C6 O6 DG DG DG 6 6 6 N 5 3.30 0.50 117.70 121.00 A A A C5 C6 N1 DA DA DA 10 10 10 N 5 1.91 0.30 108.30 110.21 A A A O4' C1' N9 DG DG DG 11 11 11 N 5 2.73 0.30 108.30 111.03 A A A O4' C1' N9 DG DG DG 13 13 13 N 5 2.88 0.30 108.30 111.18 B B B O4' C1' N1 DC DC DC 14 14 14 N 5 4.15 0.60 118.90 123.05 B B B N1 C2 O2 DC DC DC 14 14 14 N 5 -4.93 0.70 121.90 116.97 B B B N3 C2 O2 DC DC DC 14 14 14 N 5 -3.67 0.60 122.90 119.23 B B B C6 C5 C7 DT DT DT 17 17 17 N 5 2.41 0.30 108.30 110.71 B B B O4' C1' N1 DT DT DT 18 18 18 N 5 -4.24 0.70 121.90 117.66 B B B N3 C2 O2 DC DC DC 19 19 19 N 5 2.71 0.30 108.30 111.01 B B B O4' C1' N1 DC DC DC 21 21 21 N 5 -4.44 0.70 121.90 117.46 B B B N3 C2 O2 DC DC DC 21 21 21 N 5 1.82 0.30 108.30 110.12 B B B O4' C1' N9 DG DG DG 25 25 25 N 6 2.27 0.30 108.30 110.57 A A A O4' C1' N1 DC DC DC 1 1 1 N 6 -4.34 0.70 121.90 117.56 A A A N3 C2 O2 DC DC DC 1 1 1 N 6 -3.88 0.60 118.60 114.72 A A A N1 C6 N6 DA DA DA 3 3 3 N 6 2.60 0.30 108.30 110.90 A A A O4' C1' N9 DA DA DA 4 4 4 N 6 -3.11 0.50 117.00 113.89 A A A C4 C5 C6 DA DA DA 4 4 4 N 6 -4.92 0.60 118.60 113.68 A A A N1 C6 N6 DA DA DA 4 4 4 N 6 -4.62 0.60 118.60 113.98 A A A N1 C6 N6 DA DA DA 5 5 5 N 6 2.14 0.30 108.30 110.44 A A A O4' C1' N9 DG DG DG 6 6 6 N 6 3.22 0.50 117.70 120.92 A A A C5 C6 N1 DA DA DA 7 7 7 N 6 -4.52 0.60 118.60 114.08 A A A N1 C6 N6 DA DA DA 7 7 7 N 6 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DG DG DG 8 8 8 N 6 -3.96 0.60 118.60 114.64 A A A N1 C6 N6 DA DA DA 10 10 10 N 6 3.80 0.60 118.90 122.70 A A A N1 C2 O2 DC DC DC 12 12 12 N 6 -4.93 0.70 121.90 116.97 A A A N3 C2 O2 DC DC DC 12 12 12 N 6 2.52 0.30 108.30 110.82 A A A O4' C1' N9 DG DG DG 13 13 13 N 6 4.18 0.60 118.90 123.08 B B B N1 C2 O2 DC DC DC 14 14 14 N 6 -5.29 0.70 121.90 116.61 B B B N3 C2 O2 DC DC DC 14 14 14 N 6 -3.74 0.60 119.90 116.16 B B B N1 C6 O6 DG DG DG 15 15 15 N 6 -3.71 0.60 122.90 119.19 B B B C6 C5 C7 DT DT DT 18 18 18 N 6 -4.90 0.70 121.90 117.00 B B B N3 C2 O2 DC DC DC 19 19 19 N 6 7.50 1.20 119.70 127.20 B B B C3' O3' P DT DT DT 23 23 24 Y 6 2.93 0.30 108.30 111.23 B B B O4' C1' N9 DG DG DG 25 25 25 N 7 6.78 0.30 108.30 115.08 A A A O4' C1' N1 DC DC DC 1 1 1 N 7 2.95 0.30 108.30 111.25 A A A O4' C1' N1 DC DC DC 2 2 2 N 7 -4.71 0.70 121.90 117.19 A A A N3 C2 O2 DC DC DC 2 2 2 N 7 -3.63 0.60 118.60 114.97 A A A N1 C6 N6 DA DA DA 4 4 4 N 7 -3.10 0.50 117.00 113.90 A A A C4 C5 C6 DA DA DA 5 5 5 N 7 3.06 0.50 117.70 120.76 A A A C5 C6 N1 DA DA DA 5 5 5 N 7 -4.47 0.60 118.60 114.13 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 3.08 0.30 108.30 111.38 A A A O4' C1' N9 DG DG DG 8 8 8 N 7 -3.87 0.60 119.90 116.03 A A A N1 C6 O6 DG DG DG 8 8 8 N 7 -3.16 0.50 117.00 113.84 A A A C4 C5 C6 DA DA DA 9 9 9 N 7 3.05 0.50 117.70 120.75 A A A C5 C6 N1 DA DA DA 9 9 9 N 7 -4.70 0.60 118.60 113.90 A A A N1 C6 N6 DA DA DA 9 9 9 N 7 -3.62 0.60 118.60 114.98 A A A N1 C6 N6 DA DA DA 10 10 10 N 7 2.04 0.30 108.30 110.34 A A A O4' C1' N9 DG DG DG 11 11 11 N 7 -3.61 0.60 119.90 116.29 A A A N1 C6 O6 DG DG DG 11 11 11 N 7 3.72 0.30 108.30 112.02 A A A O4' C1' N9 DG DG DG 13 13 13 N 7 -3.66 0.60 119.90 116.24 A A A N1 C6 O6 DG DG DG 13 13 13 N 7 3.79 0.30 108.30 112.09 B B B O4' C1' N1 DC DC DC 16 16 16 N 7 -3.61 0.60 122.30 118.69 B B B N3 C2 O2 DT DT DT 18 18 18 N 7 2.30 0.30 108.30 110.60 B B B O4' C1' N1 DC DC DC 21 21 21 N 7 -4.39 0.60 122.30 117.91 B B B N3 C2 O2 DT DT DT 24 24 24 N 7 -3.60 0.60 122.90 119.30 B B B C6 C5 C7 DT DT DT 24 24 24 N 7 2.96 0.30 108.30 111.26 B B B O4' C1' N9 DG DG DG 25 25 25 N 7 2.06 0.30 108.30 110.36 B B B O4' C1' N9 DG DG DG 26 26 26 N 8 3.84 0.60 118.90 122.74 A A A N1 C2 O2 DC DC DC 1 1 1 N 8 -4.44 0.70 121.90 117.46 A A A N3 C2 O2 DC DC DC 1 1 1 N 8 4.22 0.30 108.30 112.52 A A A O4' C1' N1 DC DC DC 2 2 2 N 8 -4.20 0.70 121.90 117.70 A A A N3 C2 O2 DC DC DC 2 2 2 N 8 -4.18 0.60 118.60 114.42 A A A N1 C6 N6 DA DA DA 3 3 3 N 8 7.52 1.20 119.70 127.22 A A A C3' O3' P DA DA DA 3 3 4 Y 8 3.62 0.50 117.70 121.32 A A A C5 C6 N1 DA DA DA 4 4 4 N 8 -3.07 0.50 117.00 113.93 A A A C4 C5 C6 DA DA DA 5 5 5 N 8 -3.89 0.60 118.60 114.71 A A A N1 C6 N6 DA DA DA 5 5 5 N 8 2.79 0.30 108.30 111.09 A A A O4' C1' N9 DG DG DG 8 8 8 N 8 3.89 0.60 118.90 122.79 A A A N1 C2 O2 DC DC DC 12 12 12 N 8 -4.54 0.70 121.90 117.36 A A A N3 C2 O2 DC DC DC 12 12 12 N 8 2.83 0.30 108.30 111.13 A A A O4' C1' N9 DG DG DG 13 13 13 N 8 3.61 0.30 108.30 111.91 B B B O4' C1' N9 DG DG DG 15 15 15 N 8 5.20 0.30 108.30 113.50 B B B O4' C1' N1 DC DC DC 16 16 16 N 8 3.92 0.60 118.90 122.82 B B B N1 C2 O2 DC DC DC 16 16 16 N 8 -4.77 0.70 121.90 117.13 B B B N3 C2 O2 DC DC DC 16 16 16 N 8 -4.76 0.70 121.90 117.14 B B B N3 C2 O2 DC DC DC 19 19 19 N 8 -3.70 0.60 122.90 119.20 B B B C6 C5 C7 DT DT DT 22 22 22 N 8 -3.70 0.60 122.90 119.20 B B B C6 C5 C7 DT DT DT 23 23 23 N 8 -4.13 0.60 122.90 118.77 B B B C6 C5 C7 DT DT DT 24 24 24 N 9 1.89 0.30 108.30 110.19 A A A O4' C1' N1 DC DC DC 1 1 1 N 9 3.87 0.60 118.90 122.77 A A A N1 C2 O2 DC DC DC 1 1 1 N 9 -4.41 0.70 121.90 117.49 A A A N3 C2 O2 DC DC DC 1 1 1 N 9 7.88 1.20 119.70 127.58 A A A C3' O3' P DC DC DA 2 2 3 Y 9 -3.35 0.50 117.00 113.65 A A A C4 C5 C6 DA DA DA 3 3 3 N 9 -4.23 0.60 118.60 114.37 A A A N1 C6 N6 DA DA DA 3 3 3 N 9 3.64 0.50 117.70 121.34 A A A C5 C6 N1 DA DA DA 4 4 4 N 9 -4.55 0.60 118.60 114.05 A A A N1 C6 N6 DA DA DA 4 4 4 N 9 3.11 0.50 117.70 120.81 A A A C5 C6 N1 DA DA DA 5 5 5 N 9 -4.55 0.60 118.60 114.05 A A A N1 C6 N6 DA DA DA 5 5 5 N 9 -3.17 0.50 117.00 113.83 A A A C4 C5 C6 DA DA DA 9 9 9 N 9 4.21 0.50 117.70 121.91 A A A C5 C6 N1 DA DA DA 10 10 10 N 9 -4.23 0.60 118.60 114.37 A A A N1 C6 N6 DA DA DA 10 10 10 N 9 3.42 0.30 108.30 111.72 A A A O4' C1' N9 DG DG DG 11 11 11 N 9 6.77 0.30 108.30 115.07 B B B O4' C1' N1 DC DC DC 14 14 14 N 9 1.87 0.30 108.30 110.17 B B B O4' C1' N9 DG DG DG 15 15 15 N 9 3.61 0.60 118.90 122.51 B B B N1 C2 O2 DC DC DC 16 16 16 N 9 -4.40 0.70 121.90 117.50 B B B N3 C2 O2 DC DC DC 16 16 16 N 9 7.51 1.20 119.70 127.21 B B B C3' O3' P DC DC DT 16 16 17 Y 9 -3.65 0.60 122.90 119.25 B B B C6 C5 C7 DT DT DT 17 17 17 N 9 2.56 0.30 108.30 110.86 B B B O4' C1' N1 DT DT DT 20 20 20 N 9 -3.68 0.60 122.90 119.22 B B B C6 C5 C7 DT DT DT 20 20 20 N 9 1.96 0.30 108.30 110.26 B B B O4' C1' N1 DC DC DC 21 21 21 N 9 -3.91 0.60 122.90 118.99 B B B C6 C5 C7 DT DT DT 22 22 22 N 9 -3.73 0.60 122.90 119.17 B B B C6 C5 C7 DT DT DT 23 23 23 N 9 2.22 0.30 108.30 110.52 B B B O4' C1' N1 DT DT DT 24 24 24 N 9 3.53 0.30 108.30 111.83 B B B O4' C1' N9 DG DG DG 25 25 25 N 10 -5.58 0.80 105.90 100.32 A A A O4' C1' C2' DC DC DC 1 1 1 N 10 4.61 0.30 108.30 112.91 A A A O4' C1' N1 DC DC DC 1 1 1 N 10 3.68 0.60 118.90 122.58 A A A N1 C2 O2 DC DC DC 1 1 1 N 10 -5.21 0.70 121.90 116.69 A A A N3 C2 O2 DC DC DC 1 1 1 N 10 -4.51 0.70 121.90 117.39 A A A N3 C2 O2 DC DC DC 2 2 2 N 10 -4.79 0.60 118.60 113.81 A A A N1 C6 N6 DA DA DA 3 3 3 N 10 -4.05 0.60 118.60 114.55 A A A N1 C6 N6 DA DA DA 4 4 4 N 10 -4.43 0.60 118.60 114.17 A A A N1 C6 N6 DA DA DA 5 5 5 N 10 -3.07 0.50 117.00 113.93 A A A C4 C5 C6 DA DA DA 7 7 7 N 10 -5.77 0.60 118.60 112.83 A A A N1 C6 N6 DA DA DA 7 7 7 N 10 2.96 0.30 108.30 111.26 A A A O4' C1' N9 DG DG DG 8 8 8 N 10 -3.88 0.60 118.60 114.72 A A A N1 C6 N6 DA DA DA 10 10 10 N 10 2.40 0.30 108.30 110.70 A A A O4' C1' N9 DG DG DG 11 11 11 N 10 2.44 0.30 108.30 110.74 B B B O4' C1' N1 DC DC DC 14 14 14 N 10 -4.27 0.70 121.90 117.63 B B B N3 C2 O2 DC DC DC 14 14 14 N 10 5.35 0.30 108.30 113.65 B B B O4' C1' N9 DG DG DG 15 15 15 N 10 -3.93 0.60 122.90 118.97 B B B C6 C5 C7 DT DT DT 17 17 17 N 10 -4.16 0.60 122.90 118.74 B B B C6 C5 C7 DT DT DT 20 20 20 N 10 -3.89 0.60 122.90 119.01 B B B C6 C5 C7 DT DT DT 23 23 23 N 10 7.93 1.20 119.70 127.63 B B B C3' O3' P DT DT DT 23 23 24 Y 10 7.40 1.20 119.70 127.10 B B B C3' O3' P DT DT DG 24 24 25 Y 10 2.82 0.30 108.30 111.12 B B B O4' C1' N9 DG DG DG 25 25 25 N 10 3.38 0.30 108.30 111.68 B B B O4' C1' N9 DG DG DG 26 26 26 N 11 4.12 0.30 108.30 112.42 A A A O4' C1' N1 DC DC DC 1 1 1 N 11 3.95 0.60 118.90 122.85 A A A N1 C2 O2 DC DC DC 1 1 1 N 11 -5.42 0.70 121.90 116.48 A A A N3 C2 O2 DC DC DC 1 1 1 N 11 -3.10 0.50 117.00 113.90 A A A C4 C5 C6 DA DA DA 4 4 4 N 11 3.03 0.50 117.70 120.73 A A A C5 C6 N1 DA DA DA 4 4 4 N 11 -4.51 0.60 118.60 114.09 A A A N1 C6 N6 DA DA DA 4 4 4 N 11 -4.01 0.60 118.60 114.59 A A A N1 C6 N6 DA DA DA 5 5 5 N 11 -3.07 0.50 117.00 113.93 A A A C4 C5 C6 DA DA DA 7 7 7 N 11 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 7 7 7 N 11 -4.16 0.60 118.60 114.44 A A A N1 C6 N6 DA DA DA 7 7 7 N 11 4.42 0.30 108.30 112.72 A A A O4' C1' N9 DG DG DG 8 8 8 N 11 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 9 9 9 N 11 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DA DA DA 10 10 10 N 11 2.71 0.30 108.30 111.01 A A A O4' C1' N9 DG DG DG 11 11 11 N 11 -4.01 0.60 119.90 115.89 A A A N1 C6 O6 DG DG DG 11 11 11 N 11 2.90 0.30 108.30 111.20 A A A O4' C1' N1 DC DC DC 12 12 12 N 11 -4.43 0.70 121.90 117.47 A A A N3 C2 O2 DC DC DC 12 12 12 N 11 2.52 0.30 108.30 110.82 A A A O4' C1' N9 DG DG DG 13 13 13 N 11 3.09 0.30 108.30 111.39 B B B O4' C1' N1 DC DC DC 14 14 14 N 11 -3.66 0.60 122.30 118.64 B B B N3 C2 O2 DT DT DT 17 17 17 N 11 2.14 0.30 108.30 110.44 B B B O4' C1' N1 DC DC DC 21 21 21 N 11 -4.46 0.70 121.90 117.44 B B B N3 C2 O2 DC DC DC 21 21 21 N 11 2.01 0.30 108.30 110.31 B B B O4' C1' N1 DT DT DT 23 23 23 N 11 -4.03 0.60 122.90 118.87 B B B C6 C5 C7 DT DT DT 23 23 23 N 11 1.99 0.30 108.30 110.29 B B B O4' C1' N9 DG DG DG 25 25 25 N 11 2.70 0.30 108.30 111.00 B B B O4' C1' N9 DG DG DG 26 26 26 N NMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-Im-Py-Beta-Dp) with the Tridecamer DNA Duplex 5'-CCAAAGAGAAGCG-3' 1 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 26 B N1 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 26 B O6 DG 13 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 26 B N2 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 25 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 25 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 25 B N2 DG 12 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 24 B N3 DT 11 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 24 B O4 DT 11 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 23 B N3 DT 10 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 23 B O4 DT 10 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 22 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 22 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 21 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 21 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 21 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 B DT 20 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 B DT 20 B O4 DT 7 1_555 hydrog WATSON-CRICK A DG 8 A N1 DG 8 1_555 B DC 19 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 8 A N2 DG 8 1_555 B DC 19 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 8 A O6 DG 8 1_555 B DC 19 B N4 DC 6 1_555 hydrog WATSON-CRICK A DA 9 A N1 DA 9 1_555 B DT 18 B N3 DT 5 1_555 hydrog WATSON-CRICK A DA 9 A N6 DA 9 1_555 B DT 18 B O4 DT 5 1_555 hydrog WATSON-CRICK A DA 10 A N1 DA 10 1_555 B DT 17 B N3 DT 4 1_555 hydrog WATSON-CRICK A DA 10 A N6 DA 10 1_555 B DT 17 B O4 DT 4 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 16 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 16 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 16 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 15 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 15 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 15 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 13 A N1 DG 13 1_555 B DC 14 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A N2 DG 13 1_555 B DC 14 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 13 A O6 DG 13 1_555 B DC 14 B N4 DC 1 1_555 DNA POLYAMIDE, PURINE TRACT, BETA ALANINE, MINOR GROOVE, DNA 1LEJ PDB 1 1LEJ 1LEJ PDB 2 1LEJ 1 13 1LEJ 1 13 1LEJ A 1 1 13 14 26 1LEJ 14 26 1LEJ B 2 1 13 BINDING SITE FOR RESIDUE P11 A 27 A P11 27 Software 21 A DA 3 A DA 3 21 1_555 A DA 4 A DA 4 21 1_555 A DA 5 A DA 5 21 1_555 A DG 6 A DG 6 21 1_555 A DA 7 A DA 7 21 1_555 A DG 8 A DG 8 21 1_555 A DA 9 A DA 9 21 1_555 A DA 10 A DA 10 21 1_555 A DG 11 A DG 11 21 1_555 A DC 12 A DC 12 21 1_555 A DG 13 A DG 13 21 1_555 B DT 17 B DT 4 21 1_555 B DT 18 B DT 5 21 1_555 B DC 19 B DC 6 21 1_555 B DT 20 B DT 7 21 1_555 B DC 21 B DC 8 21 1_555 B DT 22 B DT 9 21 1_555 B DT 23 B DT 10 21 1_555 B DT 24 B DT 11 21 1_555 B DG 25 B DG 12 21 1_555 B DG 26 B DG 13 21 1_555