1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Robertson, S.A. Harada, K. Frankel, A.D. Wemmer, D.E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C6 H16 N5 O 1 174.224 n ARGININEAMIDE L-peptide linking 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 N 1 N N N 2 S C N 3 N C N 4 N C N 5 N C N 6 N N N 7 N C N 8 N N N 9 N N N 10 N C N 11 N O N 12 N N N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N O N 30 N P N 31 N O N 32 N O N 33 N O N 34 N C N 35 R C N 36 N O N 37 S C N 38 N O N 39 N C N 40 R C Y 41 N N Y 42 N C Y 43 N N Y 44 N C Y 45 N C N 46 N N Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N O N 66 N P N 67 N O N 68 N O N 69 N O N 70 N C N 71 R C N 72 N O N 73 S C N 74 N O N 75 N C N 76 R C N 77 N N N 78 N C N 79 N O N 80 N N N 81 N C N 82 N N N 83 N C N 84 N C N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N O N 100 N P N 101 N O N 102 N O N 103 N O N 104 N C N 105 R C N 106 N O N 107 S C N 108 N O N 109 N C N 110 R C Y 111 N N Y 112 N C Y 113 N N Y 114 N C N 115 N C N 116 N O N 117 N N N 118 N C N 119 N N N 120 N N Y 121 N C N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N O N 137 N P N 138 N O N 139 N O N 140 N O N 141 N C N 142 R C N 143 N O N 144 S C N 145 N O N 146 N C N 147 R C N 148 N N N 149 N C N 150 N O N 151 N N N 152 N C N 153 N O N 154 N C N 155 N C N 156 N C N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing Y 51 N sing Y 52 N sing Y 53 N doub N 54 N sing Y 55 N sing Y 56 N sing Y 57 N doub N 58 N sing Y 59 N doub N 60 N sing N 61 N sing Y 62 N sing Y 63 N doub N 64 N sing Y 65 N sing N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N doub N 92 N sing N 93 N doub N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing Y 124 N sing Y 125 N sing Y 126 N doub N 127 N sing Y 128 N sing N 129 N sing Y 130 N doub N 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N doub N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N sing N 172 N doub N 173 N sing N 174 N sing N 175 N sing N 176 N sing US Biochemistry BICHAW 0033 0006-2960 39 946 954 10.1021/bi9915061 10653638 Structure determination and binding kinetics of a DNA aptamer-argininamide complex. 2000 UK Embo J. EMJODG 0897 0261-4189 14 5798 5811 Identification of Two Novel Arginine Binding DNAs 1995 10.2210/pdb1db6/pdb pdb_00001db6 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 6729.329 DNA 1 syn polymer 174.224 ARGININEAMIDE 1 syn non-polymer no no (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DG)(DC)(DC)(DT)(DG)(DG)(DT) (DC)(DG) CGACCAACGTGTCGCCTGGTCG A polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -3.771 1 19 A 1 A 22 -4.012 A_DC1:DG22_A 1 -24.242 -0.142 0.457 -0.231 -0.483 1 19 A 2 A 21 -4.066 A_DG2:DC21_A 2 -21.954 0.573 0.238 -0.202 -0.558 1 20 A 3 A 20 -7.902 A_DA3:DT20_A 3 -20.722 0.292 0.274 -0.147 1.150 1 19 A 4 A 19 -6.733 A_DC4:DG19_A 4 -18.041 -0.514 0.614 -0.283 2.573 1 19 A 5 A 18 -5.733 A_DC5:DG18_A 5 -23.926 -0.528 0.392 -0.237 6.793 1 20 A 6 A 17 -11.897 A_DA6:DT17_A 6 -24.759 0.343 0.670 -0.270 -18.410 4 25 A 15 A 7 -85.381 A_DC15:DA7_A 7 17.961 3.167 1.555 -0.972 -12.807 1 19 A 9 A 16 -16.074 A_DG9:DC16_A 8 12.396 -0.010 -1.108 -0.358 -3.881 27 A 10 A 14 -156.465 A_DT10:DG14_A 9 6.053 -0.395 0.564 1.210 2.882 36.422 A A 1 2 27.037 A A 22 21 3.220 16.323 -0.094 -0.007 AA_DC1DG2:DC21DG22_AA 1 2.268 -3.757 32.594 -2.255 0.462 2.966 40.059 A A 2 3 1.731 A A 21 20 2.912 1.184 -0.820 -0.301 AA_DG2DA3:DT20DC21_AA 2 -3.840 5.615 39.865 -0.562 0.802 2.878 30.138 A A 3 4 1.067 A A 20 19 2.960 0.553 0.197 -1.224 AA_DA3DC4:DG19DT20_AA 3 -4.464 8.616 29.808 -2.454 -1.196 2.723 33.300 A A 4 5 7.002 A A 19 18 2.891 3.996 0.198 -1.313 AA_DC4DC5:DG18DG19_AA 4 3.622 -6.347 32.873 -2.867 0.176 2.827 37.349 A A 5 6 9.697 A A 18 17 3.032 6.183 -0.093 -1.038 AA_DC5DA6:DT17DG18_AA 5 -0.107 0.168 36.851 -2.357 0.133 -1.504 -176.358 A A 6 15 27.626 A A 17 7 -1.464 -55.149 0.653 -2.805 AA_DA6DC15:DA7DT17_AA 6 -147.382 -73.827 -161.365 1.362 0.438 -1.143 -129.806 A A 15 9 -10.192 A A 7 16 -2.500 15.949 0.542 6.654 AA_DC15DG9:DC16DA7_AA 7 -125.948 -80.484 -36.457 -3.497 1.691 3.058 107.525 A A 9 10 -27.625 A A 16 14 4.086 -43.400 -1.459 3.519 AA_DG9DT10:DG14DC16_AA 8 -37.403 23.808 95.311 2.882 0.300 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2000-02-03 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-05-22 _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 2ARG contains a different DNA aptamer complexed with argininamide 1OlD is a similar DNA aptamer RCSB Y RCSB 1999-11-02 REL AAR ARGININEAMIDE Sequence is derived from in-vitro selection experiments. Sequences were chemically sythethesized. sample Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14. structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy 30 10 2D NOESY DQF-COSY TOCSY 2D NOESY 0-25 mM NaCl 6.2 ambient 293 K 0-25 mM NaCl 6.2 ambient 278 K Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing and molecular dynamics 6 fewest violations 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide 99.99% D2O 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide 90% H2O/10% D2O Molecular Simulations, Inc data analysis Felix 950 Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli iterative matrix relaxation MARDIGRAS 3.2 Molecular Simulations, Inc refinement Discover 2.97 500 GE OMEGA 600 Bruker AMX AAR 23 2 AAR AAR 23 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A A 3 n 3 DA 3 A C 4 n 4 DC 4 A C 5 n 5 DC 5 A A 6 n 6 DA 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A T 10 n 10 DT 10 A G 11 n 11 DG 11 A T 12 n 12 DT 12 A C 13 n 13 DC 13 A G 14 n 14 DG 14 A C 15 n 15 DC 15 A C 16 n 16 DC 16 A T 17 n 17 DT 17 A G 18 n 18 DG 18 A G 19 n 19 DG 19 A T 20 n 20 DT 20 A C 21 n 21 DC 21 A G 22 n 22 DG 22 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 A H3 O6 DT DG 10 14 1.57 2 A A O2 H2' DT DT 10 12 1.55 2 A A H3 O6 DT DG 10 14 1.58 3 A A O2 H2' DT DT 10 12 1.58 1 A DC 1 0.067 SIDE CHAIN 1 A DC 15 0.068 SIDE CHAIN 1 A DC 16 0.109 SIDE CHAIN 2 A DC 1 0.071 SIDE CHAIN 2 A DG 14 0.068 SIDE CHAIN 2 A DC 15 0.084 SIDE CHAIN 2 A DC 16 0.060 SIDE CHAIN 3 A DC 1 0.069 SIDE CHAIN 3 A DT 10 0.069 SIDE CHAIN 3 A DG 14 0.077 SIDE CHAIN 3 A DC 15 0.089 SIDE CHAIN 3 A DC 16 0.066 SIDE CHAIN 4 A DC 1 0.072 SIDE CHAIN 4 A DG 14 0.079 SIDE CHAIN 4 A DC 15 0.056 SIDE CHAIN 4 A DC 16 0.061 SIDE CHAIN 5 A DC 8 0.057 SIDE CHAIN 5 A DT 12 0.068 SIDE CHAIN 5 A DG 14 0.076 SIDE CHAIN 5 A DC 15 0.080 SIDE CHAIN 5 A DC 16 0.079 SIDE CHAIN 6 A DC 1 0.063 SIDE CHAIN 6 A DG 14 0.079 SIDE CHAIN 6 A DC 15 0.057 SIDE CHAIN 7 A DC 1 0.070 SIDE CHAIN 7 A DG 14 0.066 SIDE CHAIN 7 A DC 15 0.101 SIDE CHAIN 7 A DC 16 0.093 SIDE CHAIN 8 A DC 1 0.068 SIDE CHAIN 8 A DG 14 0.085 SIDE CHAIN 8 A DC 15 0.113 SIDE CHAIN 8 A DC 16 0.095 SIDE CHAIN 9 A DC 1 0.068 SIDE CHAIN 9 A DG 14 0.064 SIDE CHAIN 9 A DC 15 0.089 SIDE CHAIN 9 A DC 16 0.088 SIDE CHAIN 10 A DC 1 0.064 SIDE CHAIN 10 A DG 14 0.089 SIDE CHAIN 10 A DC 15 0.080 SIDE CHAIN 10 A DC 16 0.087 SIDE CHAIN 1 2.89 0.30 108.30 111.19 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 3.57 0.30 108.30 111.87 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 3.43 0.30 108.30 111.73 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 2.45 0.30 108.30 110.75 A A A O4' C1' N9 DA DA DA 7 7 7 N 1 2.27 0.30 108.30 110.57 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 3.25 0.30 108.30 111.55 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 2.46 0.30 108.30 110.76 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 3.87 0.30 108.30 112.17 A A A O4' C1' N9 DG DG DG 11 11 11 N 1 2.44 0.30 108.30 110.74 A A A O4' C1' N1 DC DC DC 16 16 16 N 1 1.85 0.30 108.30 110.15 A A A O4' C1' N1 DT DT DT 17 17 17 N 1 3.35 0.30 108.30 111.65 A A A O4' C1' N9 DG DG DG 18 18 18 N 1 1.85 0.30 108.30 110.15 A A A O4' C1' N9 DG DG DG 19 19 19 N 1 2.10 0.30 108.30 110.40 A A A O4' C1' N1 DT DT DT 20 20 20 N 1 2.22 0.30 108.30 110.52 A A A O4' C1' N1 DC DC DC 21 21 21 N 1 3.57 0.30 108.30 111.87 A A A O4' C1' N9 DG DG DG 22 22 22 N 2 3.82 0.30 108.30 112.12 A A A O4' C1' N9 DG DG DG 2 2 2 N 2 3.12 0.30 108.30 111.42 A A A O4' C1' N1 DC DC DC 4 4 4 N 2 2.74 0.30 108.30 111.04 A A A O4' C1' N1 DC DC DC 5 5 5 N 2 2.09 0.30 108.30 110.39 A A A O4' C1' N9 DA DA DA 6 6 6 N 2 2.30 0.30 108.30 110.60 A A A O4' C1' N9 DA DA DA 7 7 7 N 2 2.99 0.30 108.30 111.29 A A A O4' C1' N1 DC DC DC 8 8 8 N 2 3.40 0.30 108.30 111.70 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 2.34 0.30 108.30 110.64 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 3.38 0.30 108.30 111.68 A A A O4' C1' N9 DG DG DG 11 11 11 N 2 3.19 0.30 108.30 111.49 A A A O4' C1' N1 DC DC DC 13 13 13 N 2 1.91 0.30 108.30 110.21 A A A O4' C1' N1 DC DC DC 16 16 16 N 2 3.52 0.30 108.30 111.82 A A A O4' C1' N9 DG DG DG 18 18 18 N 2 2.43 0.30 108.30 110.73 A A A O4' C1' N1 DC DC DC 21 21 21 N 2 3.80 0.30 108.30 112.10 A A A O4' C1' N9 DG DG DG 22 22 22 N 3 4.01 0.30 108.30 112.31 A A A O4' C1' N9 DG DG DG 2 2 2 N 3 1.98 0.30 108.30 110.28 A A A O4' C1' N9 DA DA DA 3 3 3 N 3 3.45 0.30 108.30 111.75 A A A O4' C1' N1 DC DC DC 4 4 4 N 3 2.60 0.30 108.30 110.90 A A A O4' C1' N1 DC DC DC 5 5 5 N 3 3.05 0.30 108.30 111.35 A A A O4' C1' N9 DA DA DA 7 7 7 N 3 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DC DC DC 8 8 8 N 3 2.10 0.30 108.30 110.40 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 2.23 0.30 108.30 110.53 A A A O4' C1' N9 DG DG DG 11 11 11 N 3 5.28 0.30 108.30 113.58 A A A O4' C1' N1 DT DT DT 12 12 12 N 3 -3.64 0.60 122.90 119.26 A A A C6 C5 C7 DT DT DT 12 12 12 N 3 2.97 0.30 108.30 111.27 A A A O4' C1' N1 DC DC DC 13 13 13 N 3 2.21 0.30 108.30 110.51 A A A O4' C1' N1 DC DC DC 16 16 16 N 3 4.21 0.30 108.30 112.51 A A A O4' C1' N9 DG DG DG 18 18 18 N 3 2.33 0.30 108.30 110.63 A A A O4' C1' N9 DG DG DG 19 19 19 N 3 2.42 0.30 108.30 110.72 A A A O4' C1' N1 DC DC DC 21 21 21 N 3 3.70 0.30 108.30 112.00 A A A O4' C1' N9 DG DG DG 22 22 22 N 4 4.25 0.30 108.30 112.55 A A A O4' C1' N9 DG DG DG 2 2 2 N 4 2.94 0.30 108.30 111.24 A A A O4' C1' N1 DC DC DC 4 4 4 N 4 2.55 0.30 108.30 110.85 A A A O4' C1' N1 DC DC DC 5 5 5 N 4 1.89 0.30 108.30 110.19 A A A O4' C1' N9 DA DA DA 6 6 6 N 4 2.24 0.30 108.30 110.54 A A A O4' C1' N9 DA DA DA 7 7 7 N 4 2.37 0.30 108.30 110.67 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 3.00 0.30 108.30 111.30 A A A O4' C1' N1 DT DT DT 10 10 10 N 4 3.16 0.30 108.30 111.46 A A A O4' C1' N9 DG DG DG 11 11 11 N 4 3.73 0.30 108.30 112.03 A A A O4' C1' N1 DT DT DT 12 12 12 N 4 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 12 12 12 N 4 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DC DC DC 13 13 13 N 4 2.08 0.30 108.30 110.38 A A A O4' C1' N1 DC DC DC 16 16 16 N 4 3.78 0.30 108.30 112.08 A A A O4' C1' N9 DG DG DG 18 18 18 N 4 2.02 0.30 108.30 110.32 A A A O4' C1' N9 DG DG DG 19 19 19 N 4 2.33 0.30 108.30 110.63 A A A O4' C1' N1 DT DT DT 20 20 20 N 4 2.54 0.30 108.30 110.84 A A A O4' C1' N1 DC DC DC 21 21 21 N 4 3.86 0.30 108.30 112.16 A A A O4' C1' N9 DG DG DG 22 22 22 N 5 3.24 0.30 108.30 111.54 A A A O4' C1' N1 DC DC DC 1 1 1 N 5 3.29 0.30 108.30 111.59 A A A O4' C1' N9 DG DG DG 2 2 2 N 5 3.51 0.30 108.30 111.81 A A A O4' C1' N1 DC DC DC 4 4 4 N 5 2.64 0.30 108.30 110.94 A A A O4' C1' N1 DC DC DC 5 5 5 N 5 2.00 0.30 108.30 110.30 A A A O4' C1' N9 DA DA DA 6 6 6 N 5 2.69 0.30 108.30 110.99 A A A O4' C1' N9 DA DA DA 7 7 7 N 5 2.89 0.30 108.30 111.19 A A A O4' C1' N1 DT DT DT 10 10 10 N 5 2.71 0.30 108.30 111.01 A A A O4' C1' N9 DG DG DG 11 11 11 N 5 4.40 0.30 108.30 112.70 A A A O4' C1' N1 DT DT DT 12 12 12 N 5 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DC DC DC 13 13 13 N 5 1.88 0.30 108.30 110.18 A A A O4' C1' N1 DC DC DC 16 16 16 N 5 4.09 0.30 108.30 112.39 A A A O4' C1' N9 DG DG DG 18 18 18 N 5 2.32 0.30 108.30 110.62 A A A O4' C1' N9 DG DG DG 19 19 19 N 5 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DT DT DT 20 20 20 N 5 1.80 0.30 108.30 110.10 A A A O4' C1' N1 DC DC DC 21 21 21 N 5 3.33 0.30 108.30 111.63 A A A O4' C1' N9 DG DG DG 22 22 22 N 6 4.10 0.30 108.30 112.40 A A A O4' C1' N9 DG DG DG 2 2 2 N 6 1.95 0.30 108.30 110.25 A A A O4' C1' N9 DA DA DA 3 3 3 N 6 3.88 0.30 108.30 112.18 A A A O4' C1' N1 DC DC DC 4 4 4 N 6 2.66 0.30 108.30 110.96 A A A O4' C1' N1 DC DC DC 5 5 5 N 6 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DA DA DA 6 6 6 N 6 3.37 0.30 108.30 111.67 A A A O4' C1' N9 DA DA DA 7 7 7 N 6 2.25 0.30 108.30 110.55 A A A O4' C1' N9 DG DG DG 9 9 9 N 6 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DG DG DG 11 11 11 N 6 3.94 0.30 108.30 112.24 A A A O4' C1' N1 DT DT DT 12 12 12 N 6 -3.61 0.60 122.90 119.29 A A A C6 C5 C7 DT DT DT 12 12 12 N 6 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DC DC DC 13 13 13 N 6 2.00 0.30 108.30 110.30 A A A O4' C1' N1 DC DC DC 16 16 16 N 6 3.93 0.30 108.30 112.23 A A A O4' C1' N9 DG DG DG 18 18 18 N 6 2.23 0.30 108.30 110.53 A A A O4' C1' N9 DG DG DG 19 19 19 N 6 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DT DT DT 20 20 20 N 6 2.69 0.30 108.30 110.99 A A A O4' C1' N1 DC DC DC 21 21 21 N 6 4.08 0.30 108.30 112.38 A A A O4' C1' N9 DG DG DG 22 22 22 N 7 3.21 0.30 108.30 111.51 A A A O4' C1' N9 DG DG DG 2 2 2 N 7 3.20 0.30 108.30 111.50 A A A O4' C1' N1 DC DC DC 4 4 4 N 7 3.08 0.30 108.30 111.38 A A A O4' C1' N1 DC DC DC 5 5 5 N 7 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DA DA DA 6 6 6 N 7 1.87 0.30 108.30 110.17 A A A O4' C1' N9 DA DA DA 7 7 7 N 7 2.64 0.30 108.30 110.94 A A A O4' C1' N1 DC DC DC 8 8 8 N 7 3.83 0.30 108.30 112.13 A A A O4' C1' N9 DG DG DG 9 9 9 N 7 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DT DT DT 10 10 10 N 7 2.08 0.30 108.30 110.38 A A A O4' C1' N9 DG DG DG 11 11 11 N 7 3.20 0.30 108.30 111.50 A A A O4' C1' N1 DT DT DT 12 12 12 N 7 2.78 0.30 108.30 111.08 A A A O4' C1' N1 DC DC DC 16 16 16 N 7 3.02 0.30 108.30 111.32 A A A O4' C1' N9 DG DG DG 18 18 18 N 7 2.11 0.30 108.30 110.41 A A A O4' C1' N1 DT DT DT 20 20 20 N 7 2.40 0.30 108.30 110.70 A A A O4' C1' N1 DC DC DC 21 21 21 N 7 3.43 0.30 108.30 111.73 A A A O4' C1' N9 DG DG DG 22 22 22 N 8 3.07 0.30 108.30 111.37 A A A O4' C1' N9 DG DG DG 2 2 2 N 8 3.48 0.30 108.30 111.78 A A A O4' C1' N1 DC DC DC 4 4 4 N 8 3.09 0.30 108.30 111.39 A A A O4' C1' N1 DC DC DC 5 5 5 N 8 1.83 0.30 108.30 110.13 A A A O4' C1' N9 DA DA DA 6 6 6 N 8 3.15 0.30 108.30 111.45 A A A O4' C1' N1 DC DC DC 8 8 8 N 8 4.72 0.30 108.30 113.02 A A A O4' C1' N9 DG DG DG 9 9 9 N 8 1.97 0.30 108.30 110.27 A A A O4' C1' N1 DT DT DT 10 10 10 N 8 2.71 0.30 108.30 111.01 A A A O4' C1' N9 DG DG DG 11 11 11 N 8 2.25 0.30 108.30 110.55 A A A O4' C1' N1 DC DC DC 16 16 16 N 8 1.88 0.30 108.30 110.18 A A A O4' C1' N1 DT DT DT 17 17 17 N 8 2.75 0.30 108.30 111.05 A A A O4' C1' N9 DG DG DG 18 18 18 N 8 2.42 0.30 108.30 110.72 A A A O4' C1' N1 DT DT DT 20 20 20 N 8 2.44 0.30 108.30 110.74 A A A O4' C1' N1 DC DC DC 21 21 21 N 8 3.46 0.30 108.30 111.76 A A A O4' C1' N9 DG DG DG 22 22 22 N 9 3.05 0.30 108.30 111.35 A A A O4' C1' N9 DG DG DG 2 2 2 N 9 3.94 0.30 108.30 112.24 A A A O4' C1' N1 DC DC DC 4 4 4 N 9 2.90 0.30 108.30 111.20 A A A O4' C1' N1 DC DC DC 5 5 5 N 9 2.46 0.30 108.30 110.76 A A A O4' C1' N9 DA DA DA 7 7 7 N 9 3.15 0.30 108.30 111.45 A A A O4' C1' N9 DG DG DG 9 9 9 N 9 2.62 0.30 108.30 110.92 A A A O4' C1' N1 DT DT DT 10 10 10 N 9 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DG DG DG 11 11 11 N 9 2.71 0.30 108.30 111.01 A A A O4' C1' N1 DC DC DC 16 16 16 N 9 1.82 0.30 108.30 110.12 A A A O4' C1' N1 DT DT DT 17 17 17 N 9 3.42 0.30 108.30 111.72 A A A O4' C1' N9 DG DG DG 18 18 18 N 9 1.93 0.30 108.30 110.23 A A A O4' C1' N9 DG DG DG 19 19 19 N 9 2.02 0.30 108.30 110.32 A A A O4' C1' N1 DT DT DT 20 20 20 N 9 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DC DC DC 21 21 21 N 9 3.25 0.30 108.30 111.55 A A A O4' C1' N9 DG DG DG 22 22 22 N 10 3.39 0.30 108.30 111.69 A A A O4' C1' N9 DG DG DG 2 2 2 N 10 4.10 0.30 108.30 112.40 A A A O4' C1' N1 DC DC DC 4 4 4 N 10 2.69 0.30 108.30 110.99 A A A O4' C1' N1 DC DC DC 5 5 5 N 10 2.72 0.30 108.30 111.02 A A A O4' C1' N9 DA DA DA 7 7 7 N 10 4.37 0.30 108.30 112.67 A A A O4' C1' N9 DG DG DG 9 9 9 N 10 2.60 0.30 108.30 110.90 A A A O4' C1' N1 DT DT DT 10 10 10 N 10 1.90 0.30 108.30 110.20 A A A O4' C1' N9 DG DG DG 11 11 11 N 10 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 12 12 12 N 10 2.11 0.30 108.30 110.41 A A A O4' C1' N1 DC DC DC 16 16 16 N 10 3.31 0.30 108.30 111.61 A A A O4' C1' N9 DG DG DG 18 18 18 N 10 2.30 0.30 108.30 110.60 A A A O4' C1' N9 DG DG DG 19 19 19 N 10 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DT DT DT 20 20 20 N 10 2.55 0.30 108.30 110.85 A A A O4' C1' N1 DC DC DC 21 21 21 N 10 3.70 0.30 108.30 112.00 A A A O4' C1' N9 DG DG DG 22 22 22 N SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE 1 N N 2 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 22 A N1 DG 22 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 22 A O6 DG 22 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 22 A N2 DG 22 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 21 A N3 DC 21 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 21 A O2 DC 21 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 21 A N4 DC 21 1_555 hydrog DA-DG MISPAIR A DA 3 A N6 DA 3 1_555 A DG 19 A O6 DG 19 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 20 A N3 DT 20 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 20 A O4 DT 20 1_555 hydrog DC-DG PAIR A DC 4 A N4 DC 4 1_555 A DG 18 A O6 DG 18 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 A DG 19 A N1 DG 19 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 A DG 19 A O6 DG 19 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 A DG 19 A N2 DG 19 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 18 A N1 DG 18 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 18 A O6 DG 18 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 18 A N2 DG 18 1_555 hydrog TYPE_25_PAIR A DA 6 A N6 DA 6 1_555 A DC 15 A N3 DC 15 1_555 hydrog TYPE_25_PAIR A DA 6 A N7 DA 6 1_555 A DC 15 A N4 DC 15 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 A DT 17 A N3 DT 17 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 A DT 17 A O4 DT 17 1_555 hydrog TYPE_25_PAIR A DA 7 A N6 DA 7 1_555 A DC 15 A N3 DC 15 1_555 hydrog TYPE_25_PAIR A DA 7 A N7 DA 7 1_555 A DC 15 A N4 DC 15 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 A DC 16 A N3 DC 16 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 A DC 16 A O2 DC 16 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 A DC 16 A N4 DC 16 1_555 hydrog TYPE_27_PAIR A DT 10 A N3 DT 10 1_555 A DG 14 A O6 DG 14 1_555 hydrog TYPE_27_PAIR A DT 10 A O4 DT 10 1_555 A DG 14 A N1 DG 14 1_555 DNA APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA 1DB6 PDB 1 1DB6 1 22 1DB6 1 22 1DB6 A 1 1 22 BINDING SITE FOR RESIDUE AAR A 23 A AAR 23 Software 8 A DC 8 A DC 8 8 1_555 A DG 9 A DG 9 8 1_555 A DT 12 A DT 12 8 1_555 A DC 13 A DC 13 8 1_555 A DG 14 A DG 14 8 1_555 A DC 16 A DC 16 8 1_555 A DT 17 A DT 17 8 1_555 A DG 18 A DG 18 8 1_555 1 P 1