1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hoehn, S.T. Turner, C.J. Stubbe, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 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 C5 H11 O7 P 214.110 2-DEOXY-5-PHOSPHONO-RIBOSE saccharide UK Nucleic Acids Res. NARHAD 0389 0305-1048 29 3413 3423 10.1093/nar/29.16.3413 11504879 Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation. 2001 10.2210/pdb1g5d/pdb pdb_00001g5d 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 3892.526 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*TP*GP*GP*G)-3' 1 syn polymer 3942.572 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3' 1 syn polymer no yes (DC)(DC)(DA)(DA)(DA)(DG)(ORP)(DA)(DC)(DT)(DG)(DG)(DG) CCAAAGXACTGGG A polydeoxyribonucleotide no no (DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG) CCCAGTACTTTGG 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 39.797 1 19 A 1 B 26 -0.296 A_DC1:DG26_B 1 -28.551 0.654 -0.456 -0.110 27.111 1 19 A 2 B 25 -1.085 A_DC2:DG25_B 2 -23.866 0.406 -0.368 -0.181 -17.235 1 20 A 3 B 24 1.207 A_DA3:DT24_B 3 -11.896 0.074 -0.057 -0.178 -15.443 1 20 A 4 B 23 -0.261 A_DA4:DT23_B 4 -6.528 -0.041 0.037 -0.208 -13.876 1 20 A 5 B 22 -7.257 A_DA5:DT22_B 5 -1.433 -0.054 0.114 -0.187 1.014 1 19 A 6 B 21 -4.516 A_DG6:DC21_B 6 -9.657 -0.593 0.454 -0.369 8.826 1 20 A 8 B 19 -10.639 A_DA8:DT19_B 7 -5.710 0.114 0.270 -0.109 8.731 1 19 A 9 B 18 -1.124 A_DC9:DG18_B 8 -7.980 0.460 0.466 -0.270 8.515 1 20 A 10 B 17 -0.951 A_DT10:DA17_B 9 -7.538 -0.156 0.163 -0.198 -14.142 1 19 A 11 B 16 -1.219 A_DG11:DC16_B 10 -18.270 -0.234 0.033 -0.242 -29.166 1 19 A 12 B 15 -1.459 A_DG12:DC15_B 11 -22.952 -0.490 -0.065 -0.195 -25.304 1 19 A 13 B 14 -3.516 A_DG13:DC14_B 12 -10.436 -0.617 0.136 -0.260 3.694 38.501 A A 1 2 2.924 B B 26 25 3.693 1.927 0.760 -0.282 AA_DC1DC2:DG25DG26_BB 1 1.066 -1.617 38.440 -0.697 -1.003 3.754 45.563 A A 2 3 16.133 B B 25 24 4.071 12.353 0.310 -0.699 AA_DC2DA3:DT24DG25_BB 2 0.228 -0.298 43.942 -2.227 -0.376 3.230 37.019 A A 3 4 -4.984 B B 24 23 3.198 -3.161 -0.292 -0.457 AA_DA3DA4:DT23DT24_BB 3 -0.685 1.080 36.882 -0.302 0.369 3.278 33.985 A A 4 5 -2.240 B B 23 22 3.219 -1.308 -0.712 -0.469 AA_DA4DA5:DT22DT23_BB 4 -2.572 4.405 33.866 -0.594 0.809 2.999 34.918 A A 5 6 -10.285 B B 22 21 2.928 -6.136 -0.470 -0.515 AA_DA5DG6:DC21DT22_BB 5 -2.529 4.239 34.301 -0.010 0.434 6.114 84.547 A A 6 8 -10.467 B B 21 19 6.232 -14.027 -0.393 0.533 AA_DG6DA8:DT19DC21_BB 6 -7.416 5.534 83.322 1.021 -0.039 3.301 35.650 A A 8 9 -4.212 B B 19 18 3.334 -2.574 0.257 -0.063 AA_DA8DC9:DG18DT19_BB 7 -2.788 4.563 35.454 0.278 -0.831 3.460 36.266 A A 9 10 -11.562 B B 18 17 3.332 -7.150 0.161 -0.973 AA_DC9DT10:DA17DG18_BB 8 1.652 -2.671 35.541 -0.512 -0.015 3.619 41.548 A A 10 11 4.618 B B 17 16 3.691 3.270 -0.177 -0.872 AA_DT10DG11:DC16DA17_BB 9 -2.707 3.822 41.340 -1.618 -0.072 3.341 39.322 A A 11 12 8.304 B B 16 15 3.507 5.568 -0.132 -0.904 AA_DG11DG12:DC15DC16_BB 10 1.857 -2.769 38.898 -2.039 0.429 3.172 39.115 A A 12 13 -0.454 B B 15 14 3.146 -0.304 -0.617 -0.310 AA_DG12DG13:DC14DC15_BB 11 -1.750 2.615 39.076 -0.428 0.718 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-08-22 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 _struct_conn.pdbx_leaving_atom_flag Apyrimidinic Dna With Bound Water At The Damaged Site, Alpha Form, Nmr, 1 Structure Apyrimidinic Dna With Bound Water At The Damaged Site, Beta Form, Nmr, 1 Structure Minimized Average Structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Alpha Anomer Ensemble: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer Minimized average structure: NMR Structure of an Oligonucleotide Containing an Abasic Site: Beta Anomer RCSB Y RCSB 2000-10-31 REL The abasic site deoxyribose 1H-1H coupling constants and the DNA 31P-H3' coupling constants were experimentally determined. This information was used in the modeling protocol. all calculated structures submitted 10 10 NOESY PE-COSY watergate-NOESY 31P-HCOSY 31P-decoupled-PE-COSY 31P-decoupled-J-scaled-DQCOSY 10 mM sodium phosphate buffer 6.8 ambient 293 K 10 mM sodium phosphate buffer 6.8 ambient 278 K 10 mM sodium phosphate buffer 6.8 ambient 298 K The structure is based on 475 NOE-derived distance constraints and 101 dihedral angle restraints. molecular dynamics 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer D2O 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer 10% D2O, 90% H2O 3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer D2O Brunger structure solution X-PLOR 3.851 MSI processing Felix 95.0 MSI data analysis Felix 95.0 Brunger refinement X-PLOR 3.851 750 Home-built home-built 600 Home-built home-built 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 D1P 7 n 7 ORP 7 A A 8 n 8 DA 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A G 11 n 11 DG 11 A G 12 n 12 DG 12 A G 13 n 13 DG 13 A C 14 n 1 DC 14 B C 15 n 2 DC 15 B C 16 n 3 DC 16 B A 17 n 4 DA 17 B G 18 n 5 DG 18 B T 19 n 6 DT 19 B A 20 n 7 DA 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 1 A DA 8 0.083 SIDE CHAIN 1 A DC 9 0.072 SIDE CHAIN 1 A DG 11 0.075 SIDE CHAIN 1 B DA 20 0.057 SIDE CHAIN 1 B DT 22 0.058 SIDE CHAIN 1 B DT 23 0.063 SIDE CHAIN 1 B DG 25 0.055 SIDE CHAIN 2 A DG 6 0.082 SIDE CHAIN 2 A DA 8 0.097 SIDE CHAIN 2 A DT 10 0.068 SIDE CHAIN 2 A DG 11 0.086 SIDE CHAIN 2 B DC 16 0.071 SIDE CHAIN 2 B DA 20 0.062 SIDE CHAIN 2 B DG 25 0.082 SIDE CHAIN 3 A DG 6 0.091 SIDE CHAIN 3 A DA 8 0.105 SIDE CHAIN 3 A DG 11 0.086 SIDE CHAIN 3 B DC 16 0.068 SIDE CHAIN 3 B DG 25 0.082 SIDE CHAIN 4 A DG 6 0.088 SIDE CHAIN 4 A DA 8 0.076 SIDE CHAIN 4 A DC 9 0.081 SIDE CHAIN 4 A DG 11 0.082 SIDE CHAIN 4 B DG 25 0.076 SIDE CHAIN 5 A DG 6 0.079 SIDE CHAIN 5 A DG 11 0.085 SIDE CHAIN 5 B DG 25 0.080 SIDE CHAIN 6 A DG 6 0.093 SIDE CHAIN 6 A DA 8 0.099 SIDE CHAIN 6 A DC 9 0.076 SIDE CHAIN 6 A DG 11 0.074 SIDE CHAIN 6 B DA 20 0.058 SIDE CHAIN 6 B DG 25 0.085 SIDE CHAIN 7 A DG 6 0.091 SIDE CHAIN 7 A DA 8 0.104 SIDE CHAIN 7 A DG 11 0.086 SIDE CHAIN 7 B DC 16 0.067 SIDE CHAIN 7 B DG 25 0.077 SIDE CHAIN 8 A DG 6 0.093 SIDE CHAIN 8 A DA 8 0.098 SIDE CHAIN 8 A DC 9 0.080 SIDE CHAIN 8 A DG 11 0.073 SIDE CHAIN 8 A DG 13 0.056 SIDE CHAIN 8 B DA 20 0.057 SIDE CHAIN 8 B DG 25 0.090 SIDE CHAIN 9 A DG 6 0.079 SIDE CHAIN 9 A DA 8 0.090 SIDE CHAIN 9 A DT 10 0.068 SIDE CHAIN 9 A DG 11 0.085 SIDE CHAIN 9 B DC 16 0.076 SIDE CHAIN 9 B DA 20 0.068 SIDE CHAIN 9 B DG 25 0.081 SIDE CHAIN 10 A DG 6 0.096 SIDE CHAIN 10 A DA 8 0.108 SIDE CHAIN 10 A DG 11 0.082 SIDE CHAIN 10 B DG 25 0.077 SIDE CHAIN 1 4.03 0.60 118.60 122.63 A A A N1 C6 N6 DA DA DA 3 3 3 N 1 5.45 0.60 118.60 124.05 A A A N1 C6 N6 DA DA DA 5 5 5 N 1 -4.91 0.80 123.70 118.79 A A A C5 C6 N6 DA DA DA 5 5 5 N 1 5.38 0.70 119.90 125.28 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 5.26 0.60 118.60 123.86 A A A N1 C6 N6 DA DA DA 8 8 8 N 1 -5.06 0.80 123.70 118.64 A A A C5 C6 N6 DA DA DA 8 8 8 N 1 5.12 0.70 119.90 125.02 A A A N3 C2 N2 DG DG DG 12 12 12 N 1 4.91 0.70 119.90 124.81 A A A N3 C2 N2 DG DG DG 13 13 13 N 1 4.31 0.60 118.60 122.91 B B B N1 C6 N6 DA DA DA 17 17 17 N 1 7.72 1.20 119.70 127.42 B B B C3' O3' P DA DA DG 17 17 18 Y 1 4.71 0.70 119.90 124.61 B B B N3 C2 N2 DG DG DG 18 18 18 N 1 5.12 0.60 118.60 123.72 B B B N1 C6 N6 DA DA DA 20 20 20 N 1 9.66 1.20 119.70 129.36 B B B C3' O3' P DC DC DT 21 21 22 Y 1 4.48 0.70 119.90 124.38 B B B N3 C2 N2 DG DG DG 25 25 25 N 1 4.85 0.70 119.90 124.75 B B B N3 C2 N2 DG DG DG 26 26 26 N 2 3.89 0.60 118.60 122.49 A A A N1 C6 N6 DA DA DA 3 3 3 N 2 5.06 0.60 118.60 123.66 A A A N1 C6 N6 DA DA DA 5 5 5 N 2 4.49 0.70 119.90 124.39 A A A N3 C2 N2 DG DG DG 6 6 6 N 2 4.88 0.60 118.60 123.48 A A A N1 C6 N6 DA DA DA 8 8 8 N 2 4.49 0.70 119.90 124.39 A A A N3 C2 N2 DG DG DG 12 12 12 N 2 4.96 0.70 119.90 124.86 A A A N3 C2 N2 DG DG DG 13 13 13 N 2 2.70 0.30 108.30 111.00 B B B O4' C1' N1 DC DC DC 14 14 14 N 2 4.21 0.60 118.60 122.81 B B B N1 C6 N6 DA DA DA 17 17 17 N 2 7.49 1.20 119.70 127.19 B B B C3' O3' P DA DA DG 17 17 18 Y 2 4.38 0.70 119.90 124.28 B B B N3 C2 N2 DG DG DG 18 18 18 N 2 9.31 1.20 119.70 129.01 B B B C3' O3' P DC DC DT 21 21 22 Y 2 4.66 0.70 119.90 124.56 B B B N3 C2 N2 DG DG DG 26 26 26 N 3 3.94 0.60 118.60 122.54 A A A N1 C6 N6 DA DA DA 3 3 3 N 3 4.94 0.60 118.60 123.54 A A A N1 C6 N6 DA DA DA 5 5 5 N 3 5.37 0.70 119.90 125.27 A A A N3 C2 N2 DG DG DG 6 6 6 N 3 4.25 0.60 118.60 122.85 A A A N1 C6 N6 DA DA DA 8 8 8 N 3 4.45 0.70 119.90 124.35 A A A N3 C2 N2 DG DG DG 12 12 12 N 3 5.01 0.70 119.90 124.91 A A A N3 C2 N2 DG DG DG 13 13 13 N 3 2.98 0.30 108.30 111.28 B B B O4' C1' N1 DC DC DC 14 14 14 N 3 3.85 0.60 118.60 122.45 B B B N1 C6 N6 DA DA DA 17 17 17 N 3 4.39 0.70 119.90 124.29 B B B N3 C2 N2 DG DG DG 18 18 18 N 3 4.19 0.60 118.60 122.79 B B B N1 C6 N6 DA DA DA 20 20 20 N 3 9.29 1.20 119.70 128.99 B B B C3' O3' P DC DC DT 21 21 22 Y 3 5.06 0.70 119.90 124.96 B B B N3 C2 N2 DG DG DG 26 26 26 N 4 4.01 0.60 118.60 122.61 A A A N1 C6 N6 DA DA DA 3 3 3 N 4 5.07 0.60 118.60 123.67 A A A N1 C6 N6 DA DA DA 5 5 5 N 4 5.17 0.70 119.90 125.07 A A A N3 C2 N2 DG DG DG 6 6 6 N 4 5.20 0.60 118.60 123.80 A A A N1 C6 N6 DA DA DA 8 8 8 N 4 5.04 0.70 119.90 124.94 A A A N3 C2 N2 DG DG DG 12 12 12 N 4 5.92 0.70 119.90 125.82 A A A N3 C2 N2 DG DG DG 13 13 13 N 4 3.86 0.30 108.30 112.16 B B B O4' C1' N1 DC DC DC 14 14 14 N 4 4.83 0.60 118.60 123.43 B B B N1 C6 N6 DA DA DA 17 17 17 N 4 4.94 0.70 119.90 124.84 B B B N3 C2 N2 DG DG DG 18 18 18 N 4 3.87 0.60 118.60 122.47 B B B N1 C6 N6 DA DA DA 20 20 20 N 4 9.16 1.20 119.70 128.86 B B B C3' O3' P DC DC DT 21 21 22 Y 4 4.75 0.70 119.90 124.65 B B B N3 C2 N2 DG DG DG 26 26 26 N 5 4.05 0.60 118.60 122.65 A A A N1 C6 N6 DA DA DA 3 3 3 N 5 3.70 0.60 118.60 122.30 A A A N1 C6 N6 DA DA DA 4 4 4 N 5 5.25 0.60 118.60 123.85 A A A N1 C6 N6 DA DA DA 5 5 5 N 5 5.28 0.70 119.90 125.18 A A A N3 C2 N2 DG DG DG 6 6 6 N 5 5.61 0.60 118.60 124.21 A A A N1 C6 N6 DA DA DA 8 8 8 N 5 -5.33 0.80 123.70 118.37 A A A C5 C6 N6 DA DA DA 8 8 8 N 5 5.59 0.70 119.90 125.49 A A A N3 C2 N2 DG DG DG 12 12 12 N 5 5.93 0.70 119.90 125.83 A A A N3 C2 N2 DG DG DG 13 13 13 N 5 4.15 0.30 108.30 112.45 B B B O4' C1' N1 DC DC DC 14 14 14 N 5 4.37 0.60 118.60 122.97 B B B N1 C6 N6 DA DA DA 17 17 17 N 5 7.32 1.20 119.70 127.02 B B B C3' O3' P DT DT DA 19 19 20 Y 5 10.48 1.20 119.70 130.18 B B B C3' O3' P DC DC DT 21 21 22 Y 5 4.95 0.70 119.90 124.85 B B B N3 C2 N2 DG DG DG 26 26 26 N 6 3.91 0.60 118.60 122.51 A A A N1 C6 N6 DA DA DA 3 3 3 N 6 5.02 0.60 118.60 123.62 A A A N1 C6 N6 DA DA DA 5 5 5 N 6 5.10 0.70 119.90 125.00 A A A N3 C2 N2 DG DG DG 6 6 6 N 6 4.50 0.60 118.60 123.10 A A A N1 C6 N6 DA DA DA 8 8 8 N 6 5.77 0.70 119.90 125.67 A A A N3 C2 N2 DG DG DG 13 13 13 N 6 3.17 0.30 108.30 111.47 B B B O4' C1' N1 DC DC DC 14 14 14 N 6 3.70 0.60 118.90 122.60 B B B N1 C2 O2 DC DC DC 14 14 14 N 6 4.08 0.60 118.60 122.68 B B B N1 C6 N6 DA DA DA 17 17 17 N 6 4.95 0.70 119.90 124.85 B B B N3 C2 N2 DG DG DG 18 18 18 N 6 3.97 0.60 118.60 122.57 B B B N1 C6 N6 DA DA DA 20 20 20 N 6 8.69 1.20 119.70 128.39 B B B C3' O3' P DC DC DT 21 21 22 Y 6 4.79 0.70 119.90 124.69 B B B N3 C2 N2 DG DG DG 26 26 26 N 7 3.98 0.60 118.60 122.58 A A A N1 C6 N6 DA DA DA 3 3 3 N 7 5.13 0.60 118.60 123.73 A A A N1 C6 N6 DA DA DA 5 5 5 N 7 5.48 0.70 119.90 125.38 A A A N3 C2 N2 DG DG DG 6 6 6 N 7 4.20 0.60 118.60 122.80 A A A N1 C6 N6 DA DA DA 8 8 8 N 7 4.42 0.70 119.90 124.32 A A A N3 C2 N2 DG DG DG 12 12 12 N 7 4.95 0.70 119.90 124.85 A A A N3 C2 N2 DG DG DG 13 13 13 N 7 2.98 0.30 108.30 111.28 B B B O4' C1' N1 DC DC DC 14 14 14 N 7 3.83 0.60 118.60 122.43 B B B N1 C6 N6 DA DA DA 17 17 17 N 7 4.22 0.70 119.90 124.12 B B B N3 C2 N2 DG DG DG 18 18 18 N 7 4.42 0.60 118.60 123.02 B B B N1 C6 N6 DA DA DA 20 20 20 N 7 8.98 1.20 119.70 128.68 B B B C3' O3' P DC DC DT 21 21 22 Y 7 4.72 0.70 119.90 124.62 B B B N3 C2 N2 DG DG DG 26 26 26 N 8 3.88 0.60 118.60 122.48 A A A N1 C6 N6 DA DA DA 3 3 3 N 8 5.04 0.60 118.60 123.64 A A A N1 C6 N6 DA DA DA 5 5 5 N 8 5.12 0.70 119.90 125.02 A A A N3 C2 N2 DG DG DG 6 6 6 N 8 4.50 0.60 118.60 123.10 A A A N1 C6 N6 DA DA DA 8 8 8 N 8 5.60 0.70 119.90 125.50 A A A N3 C2 N2 DG DG DG 13 13 13 N 8 3.30 0.30 108.30 111.60 B B B O4' C1' N1 DC DC DC 14 14 14 N 8 4.40 0.60 118.60 123.00 B B B N1 C6 N6 DA DA DA 17 17 17 N 8 5.03 0.70 119.90 124.93 B B B N3 C2 N2 DG DG DG 18 18 18 N 8 3.98 0.60 118.60 122.58 B B B N1 C6 N6 DA DA DA 20 20 20 N 8 8.61 1.20 119.70 128.31 B B B C3' O3' P DC DC DT 21 21 22 Y 8 4.24 0.70 119.90 124.14 B B B N3 C2 N2 DG DG DG 25 25 25 N 8 4.81 0.70 119.90 124.71 B B B N3 C2 N2 DG DG DG 26 26 26 N 9 3.93 0.60 118.60 122.53 A A A N1 C6 N6 DA DA DA 3 3 3 N 9 5.04 0.60 118.60 123.64 A A A N1 C6 N6 DA DA DA 5 5 5 N 9 4.49 0.70 119.90 124.39 A A A N3 C2 N2 DG DG DG 6 6 6 N 9 5.10 0.60 118.60 123.70 A A A N1 C6 N6 DA DA DA 8 8 8 N 9 5.40 0.70 119.90 125.30 A A A N3 C2 N2 DG DG DG 12 12 12 N 9 4.69 0.70 119.90 124.59 A A A N3 C2 N2 DG DG DG 13 13 13 N 9 4.54 0.60 118.60 123.14 B B B N1 C6 N6 DA DA DA 17 17 17 N 9 7.38 1.20 119.70 127.08 B B B C3' O3' P DA DA DG 17 17 18 Y 9 4.39 0.70 119.90 124.29 B B B N3 C2 N2 DG DG DG 18 18 18 N 9 9.24 1.20 119.70 128.94 B B B C3' O3' P DC DC DT 21 21 22 Y 9 4.86 0.70 119.90 124.76 B B B N3 C2 N2 DG DG DG 26 26 26 N 10 3.97 0.60 118.60 122.57 A A A N1 C6 N6 DA DA DA 3 3 3 N 10 5.11 0.60 118.60 123.71 A A A N1 C6 N6 DA DA DA 5 5 5 N 10 5.35 0.70 119.90 125.25 A A A N3 C2 N2 DG DG DG 6 6 6 N 10 4.63 0.60 118.60 123.23 A A A N1 C6 N6 DA DA DA 8 8 8 N 10 4.64 0.70 119.90 124.54 A A A N3 C2 N2 DG DG DG 12 12 12 N 10 5.47 0.70 119.90 125.37 A A A N3 C2 N2 DG DG DG 13 13 13 N 10 1.81 0.30 108.30 110.11 B B B O4' C1' N1 DC DC DC 14 14 14 N 10 4.30 0.60 118.60 122.90 B B B N1 C6 N6 DA DA DA 17 17 17 N 10 4.54 0.70 119.90 124.44 B B B N3 C2 N2 DG DG DG 18 18 18 N 10 4.17 0.60 118.60 122.77 B B B N1 C6 N6 DA DA DA 20 20 20 N 10 9.19 1.20 119.70 128.89 B B B C3' O3' P DC DC DT 21 21 22 Y 10 4.24 0.70 119.90 124.14 B B B N3 C2 N2 DG DG DG 25 25 25 N 10 4.84 0.70 119.90 124.74 B B B N3 C2 N2 DG DG DG 26 26 26 N 1 A A N9 C4 DA DA 4 4 0.037 0.006 1.374 1.411 N 1 A A C5' C4' DT DT 10 10 0.044 0.007 1.512 1.556 N 1 B B C8 N9 DG DG 25 25 -0.043 0.007 1.374 1.331 N 2 A A N9 C4 DA DA 4 4 0.036 0.006 1.374 1.410 N 2 A A C5' C4' DT DT 10 10 0.043 0.007 1.512 1.555 N 2 B B C5' C4' DT DT 24 24 0.043 0.007 1.512 1.555 N 3 A A N9 C4 DA DA 4 4 0.037 0.006 1.374 1.411 N 4 A A N9 C4 DA DA 4 4 0.036 0.006 1.374 1.410 N 4 A A C5' C4' DT DT 10 10 0.043 0.007 1.512 1.555 N 4 B B C5' C4' DC DC 16 16 0.042 0.007 1.512 1.554 N 4 B B C5' C4' DT DT 24 24 0.043 0.007 1.512 1.555 N 5 A A N9 C4 DA DA 4 4 0.036 0.006 1.374 1.410 N 5 B B C5' C4' DC DC 16 16 0.042 0.007 1.512 1.554 N 5 B B C5' C4' DA DA 17 17 0.042 0.007 1.512 1.554 N 6 B B C5' C4' DT DT 24 24 0.043 0.007 1.512 1.555 N 7 B B C5' C4' DT DT 24 24 0.043 0.007 1.512 1.555 N 8 A A N9 C4 DA DA 4 4 0.036 0.006 1.374 1.410 N 8 A A C5' C4' DT DT 10 10 0.043 0.007 1.512 1.555 N 9 A A C5' C4' DT DT 10 10 0.043 0.007 1.512 1.555 N 9 B B C5' C4' DA DA 20 20 0.043 0.007 1.512 1.555 N 9 B B C5' C4' DT DT 24 24 0.043 0.007 1.512 1.555 N 10 A A N9 C4 DA DA 4 4 0.038 0.006 1.374 1.412 N NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER 1 N N 2 N N covale 1.580 both A DG 6 A O3' DG 6 1_555 A ORP 7 A P ORP 7 1_555 covale 1.586 one A ORP 7 A O3 ORP 7 1_555 A DA 8 A P DA 8 1_555 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 8 A N1 DA 8 1_555 B DT 19 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 19 B O4 DT 6 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B DG 18 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B DG 18 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B DG 18 B N2 DG 5 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 17 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 17 B N6 DA 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 DG 12 A N1 DG 12 1_555 B DC 15 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 15 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 15 B N4 DC 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 damaged DNA, apyrimidinic site, DNA 1G5D PDB 1 1G5D 1G5D PDB 2 1G5D 1 13 1G5D 1 13 1G5D A 1 1 13 14 26 1G5D 14 26 1G5D B 2 1 13