1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Negi, D. 0000-0002-9001-5315 Sannapureddi, R.K.R. 0000-0002-1568-2599 Sathyamoorthy, B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-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 O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C Y 49 N N Y 50 N C Y 51 N N Y 52 N C N 53 N C N 54 N O N 55 N N N 56 N C N 57 N N N 58 N N Y 59 N C N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 N C N 85 R C N 86 N N N 87 N C N 88 N O N 89 N N N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 1 N sing N 2 N sing N 3 N doub 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 sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub 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 N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N sing N 67 N sing Y 68 N doub N 69 N doub N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N doub 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 sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing 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 doub N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing To Be Published 0353 Influence of single Inosine substitution in a parallel DNA G-quadruplex with single nucleotide loops. US J Phys Chem Lett 1948-7185 11 10016 10022 10.1021/acs.jpclett.0c02969 33179931 Characterization of DNA G-quadruplex Topologies with NMR Chemical Shifts. 2020 US Chemphyschem 1439-7641 26 e202401075 e202401075 10.1002/cphc.202401075 40229960 Loop Nucleotide Chemical Shifts as a Tool to Characterize DNA G-Quadruplexes 2025 0000-0002-9001-5315 0000-0002-1568-2599 0000-0002-1568-2599 0000-0002-1568-2599 10.2210/pdb9wih/pdb pdb_00009wih 10.13018/BMR36781 6070.918 DNA (5'-D(*AP*AP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*AP*A)-3') 1 syn polymer no no (DA)(DA)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DA)(DA) AAGGGTGGGTGGGTGGGAA A polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n -4.545 3 6 A 7 A 11 -88.972 A_DG7:DG11_A 1 -4.328 1.861 0.325 3.270 -3.300 3 6 A 8 A 12 -88.296 A_DG8:DG12_A 2 -1.889 1.899 -0.049 3.172 -13.058 3 6 A 4 A 16 86.792 A_DG4:DG16_A 3 -1.636 -2.382 1.035 -2.690 -15.287 3 6 A 3 A 15 90.851 A_DG3:DG15_A 4 8.835 -1.872 -0.187 -3.079 1.601 3 6 A 5 A 9 89.994 A_DG5:DG9_A 5 5.988 -1.442 0.469 3.632 12.071 3 6 A 17 A 13 -94.691 A_DG17:DG13_A 6 36.306 1.520 0.129 -3.223 3.216 23.132 A A 7 8 -4.039 A A 11 12 3.299 -1.615 -0.792 -0.565 AA_DG7DG8:DG12DG11_AA 1 2.720 -6.803 22.918 -0.847 2.922 -0.274 -176.023 A A 8 4 8.583 A A 12 16 -0.289 -17.156 1.692 3.271 AA_DG8DG4:DG16DG12_AA 2 4.309 2.156 -175.975 -1.637 0.846 -3.239 -28.387 A A 4 3 -12.466 A A 16 15 -3.544 6.008 0.666 0.175 AA_DG4DG3:DG15DG16_AA 3 -6.904 -14.324 -26.900 1.118 3.053 1.047 178.627 A A 5 17 -2.800 A A 9 13 1.048 -5.600 -1.978 3.228 AA_DG5DG17:DG13DG9_AA 4 -7.201 3.601 178.623 1.614 0.989 repository Initial release 1 0 2026-10-07 India Science and Engineering Research Board (SERB) bharathwaj@iiserb.ac.in 0000-0002-1568-2599 Bharathwaj Sathyamoorthy principal investigator/group leader Parallel DNA G-quadruplex formed by AA(GGGT)3GGGAA in potassium condition N PDBJ Y PDBJ 2025-08-27 REL REL 32630 synthetic construct sample 1 19 N structures with the least restraint violations 50 5 isotropic 1 2D 1H-13C HSQC isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-1H TOCSY isotropic 1 2D 1H-15N HMQC anisotropic 1 2D 1H-13C HSQC anisotropic 1 2D 1H-15N HMQC 1.5 mM natural abundance 20 mM natural abundance 50 mM natural abundance 50 uM natural abundance 5 % v/v natural abundance 1.5 mM natural abundance 20 mM natural abundance 50 mM natural abundance 50 uM natural abundance 5 % v/v natural abundance 18 mg/mL natural abundance 20 mM potassium phosphate, 50 mM KCl 0.2655 M isotropic 7 pH 1 atm 298 K 20 mM potassium phosphate, 50 mM KCl and 18 mg/mL Pf1 Phage 0.2655 M anisotropic 7 pH 1 atm 298 K DGSA-distance geometry simulated annealing DGSA-distance geometry simulated annealing 1 fewest violations 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS, 5 % v/v D2O, 95% H2O/5% D2O GGGT isotropic 95% H2O/5% D2O solution 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*AP*A)-3'), 20 mM potassium phosphate, 50 mM potassium chloride, 50 uM DSS, 5 % v/v D2O, 18 mg/mL Pf1 phage, 95% H2O/5% D2O Pf1 phage added to get RDCs (18 mg/mL) GGGT anisotropic 95% H2O/5% D2O solution Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman refinement Amber Schwieters, Kuszewski, Tjandra and Clore structure calculation X-PLOR NIH Woonghee Lee chemical shift assignment NMRFAM-SPARKY Woonghee Lee peak picking NMRFAM-SPARKY Bruker Biospin collection TopSpin Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe 700 Bruker AVANCE III DA 1 n 1 DA 1 A DA 2 n 2 DA 2 A DG 3 n 3 DG 3 A DG 4 n 4 DG 4 A DG 5 n 5 DG 5 A DT 6 n 6 DT 6 A DG 7 n 7 DG 7 A DG 8 n 8 DG 8 A DG 9 n 9 DG 9 A DT 10 n 10 DT 10 A DG 11 n 11 DG 11 A DG 12 n 12 DG 12 A DG 13 n 13 DG 13 A DT 14 n 14 DT 14 A DG 15 n 15 DG 15 A DG 16 n 16 DG 16 A DG 17 n 17 DG 17 A DA 18 n 18 DA 18 A DA 19 n 19 DA 19 A author_defined_assembly 1 monomeric not applicable NMR Distance Restraints 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 3.27 0.50 106.80 110.07 A A A O4' C1' C2' DA DA DA 1 1 1 N 1 2.22 0.30 108.30 110.52 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 3.45 0.50 117.70 121.15 A A A C5 C6 N1 DA DA DA 1 1 1 N 1 -4.28 0.60 118.60 114.32 A A A N1 C6 N6 DA DA DA 1 1 1 N 1 -3.28 0.50 117.00 113.72 A A A C4 C5 C6 DA DA DA 2 2 2 N 1 3.46 0.50 117.70 121.16 A A A C5 C6 N1 DA DA DA 2 2 2 N 1 -4.94 0.60 118.60 113.66 A A A N1 C6 N6 DA DA DA 2 2 2 N 1 4.53 0.30 108.30 112.83 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 5.29 0.30 108.30 113.59 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -6.81 1.00 110.10 103.29 A A A C1' O4' C4' DT DT DT 6 6 6 N 1 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 6 6 6 N 1 3.89 0.30 108.30 112.19 A A A O4' C1' N9 DG DG DG 8 8 8 N 1 1.93 0.30 108.30 110.23 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 -4.06 0.60 122.30 118.24 A A A N3 C2 O2 DT DT DT 10 10 10 N 1 -3.67 0.60 122.90 119.23 A A A C6 C5 C7 DT DT DT 10 10 10 N 1 5.38 0.30 108.30 113.68 A A A O4' C1' N9 DG DG DG 13 13 13 N 1 2.10 0.30 108.30 110.40 A A A O4' C1' N1 DT DT DT 14 14 14 N 1 -4.24 0.70 119.90 115.66 A A A N3 C2 N2 DG DG DG 16 16 16 N 1 -3.13 0.50 117.00 113.87 A A A C4 C5 C6 DA DA DA 18 18 18 N 1 -3.68 0.60 118.60 114.92 A A A N1 C6 N6 DA DA DA 18 18 18 N 1 8.54 1.20 119.70 128.24 A A A C3' O3' P DA DA DA 18 18 19 Y 1 -4.12 0.40 104.50 100.38 A A A O4' C4' C3' DA DA DA 19 19 19 N 1 4.90 0.30 108.30 113.20 A A A O4' C1' N9 DA DA DA 19 19 19 N 2 3.86 0.30 108.30 112.16 A A A O4' C1' N9 DA DA DA 1 1 1 N 2 3.39 0.50 117.70 121.09 A A A C5 C6 N1 DA DA DA 2 2 2 N 2 -5.24 0.60 118.60 113.36 A A A N1 C6 N6 DA DA DA 2 2 2 N 2 4.39 0.30 108.30 112.69 A A A O4' C1' N9 DG DG DG 3 3 3 N 2 3.73 0.30 108.30 112.03 A A A O4' C1' N9 DG DG DG 4 4 4 N 2 -6.92 1.00 110.10 103.18 A A A C1' O4' C4' DT DT DT 6 6 6 N 2 3.49 0.30 108.30 111.79 A A A O4' C1' N1 DT DT DT 6 6 6 N 2 3.18 0.30 108.30 111.48 A A A O4' C1' N9 DG DG DG 8 8 8 N 2 5.25 0.30 108.30 113.55 A A A O4' C1' N9 DG DG DG 13 13 13 N 2 7.36 1.20 119.70 127.06 A A A C3' O3' P DG DG DT 13 13 14 Y 2 2.98 0.30 108.30 111.28 A A A O4' C1' N1 DT DT DT 14 14 14 N 2 2.84 0.30 108.30 111.14 A A A O4' C1' N9 DG DG DG 15 15 15 N 2 8.38 1.20 119.70 128.08 A A A C3' O3' P DG DG DG 15 15 16 Y 2 3.60 0.60 106.00 109.60 A A A O4' C4' C3' DG DG DG 16 16 16 N 2 1.83 0.30 108.30 110.13 A A A O4' C1' N9 DG DG DG 17 17 17 N 2 7.29 1.20 119.70 126.99 A A A C3' O3' P DG DG DA 17 17 18 Y 2 3.80 0.30 108.30 112.10 A A A O4' C1' N9 DA DA DA 18 18 18 N 2 2.57 0.30 108.30 110.87 A A A O4' C1' N9 DA DA DA 19 19 19 N 2 -3.07 0.50 117.00 113.93 A A A C4 C5 C6 DA DA DA 19 19 19 N 2 3.26 0.50 117.70 120.96 A A A C5 C6 N1 DA DA DA 19 19 19 N 3 3.82 0.60 106.00 109.82 A A A O4' C4' C3' DA DA DA 1 1 1 N 3 -4.89 0.60 118.60 113.71 A A A N1 C6 N6 DA DA DA 1 1 1 N 3 -3.07 0.50 117.00 113.93 A A A C4 C5 C6 DA DA DA 2 2 2 N 3 3.15 0.50 117.70 120.85 A A A C5 C6 N1 DA DA DA 2 2 2 N 3 -4.97 0.60 118.60 113.63 A A A N1 C6 N6 DA DA DA 2 2 2 N 3 4.55 0.30 108.30 112.85 A A A O4' C1' N9 DG DG DG 3 3 3 N 3 4.93 0.30 108.30 113.23 A A A O4' C1' N9 DG DG DG 4 4 4 N 3 7.30 1.20 119.70 127.00 A A A C3' O3' P DG DG DG 4 4 5 Y 3 7.21 1.20 119.70 126.91 A A A C3' O3' P DG DG DG 7 7 8 Y 3 2.67 0.30 108.30 110.97 A A A O4' C1' N9 DG DG DG 8 8 8 N 3 4.78 0.60 106.00 110.78 A A A O4' C4' C3' DG DG DG 11 11 11 N 3 -5.52 0.80 102.40 96.88 A A A C3' C2' C1' DG DG DG 13 13 13 N 3 4.64 0.30 108.30 112.94 A A A O4' C1' N9 DG DG DG 13 13 13 N 3 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DT DT DT 14 14 14 N 3 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DG DG DG 15 15 15 N 3 2.84 0.30 108.30 111.14 A A A O4' C1' N9 DG DG DG 17 17 17 N 3 3.44 0.30 108.30 111.74 A A A O4' C1' N9 DA DA DA 18 18 18 N 3 3.09 0.50 117.70 120.79 A A A C5 C6 N1 DA DA DA 18 18 18 N 3 -4.84 0.60 118.60 113.76 A A A N1 C6 N6 DA DA DA 18 18 18 N 3 -3.93 0.60 118.60 114.67 A A A N1 C6 N6 DA DA DA 19 19 19 N 4 -4.36 0.60 118.60 114.24 A A A N1 C6 N6 DA DA DA 2 2 2 N 4 8.92 1.20 119.70 128.62 A A A C3' O3' P DA DA DG 2 2 3 Y 4 3.99 0.30 108.30 112.29 A A A O4' C1' N9 DG DG DG 3 3 3 N 4 2.34 0.30 108.30 110.64 A A A O4' C1' N9 DG DG DG 4 4 4 N 4 3.93 0.30 108.30 112.23 A A A O4' C1' N9 DG DG DG 5 5 5 N 4 2.51 0.30 108.30 110.81 A A A O4' C1' N9 DG DG DG 8 8 8 N 4 2.34 0.30 108.30 110.64 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 2.42 0.30 108.30 110.72 A A A O4' C1' N9 DG DG DG 11 11 11 N 4 -4.40 0.70 119.90 115.50 A A A N3 C2 N2 DG DG DG 11 11 11 N 4 4.69 0.30 108.30 112.99 A A A O4' C1' N9 DG DG DG 13 13 13 N 4 2.35 0.30 108.30 110.65 A A A O4' C1' N1 DT DT DT 14 14 14 N 4 3.81 0.30 108.30 112.11 A A A O4' C1' N9 DG DG DG 15 15 15 N 4 3.22 0.30 108.30 111.52 A A A O4' C1' N9 DA DA DA 18 18 18 N 4 2.71 0.30 108.30 111.01 A A A O4' C1' N9 DA DA DA 19 19 19 N 5 3.38 0.30 108.30 111.68 A A A O4' C1' N9 DA DA DA 1 1 1 N 5 3.01 0.50 117.70 120.71 A A A C5 C6 N1 DA DA DA 2 2 2 N 5 -4.78 0.60 118.60 113.82 A A A N1 C6 N6 DA DA DA 2 2 2 N 5 7.36 1.20 119.70 127.06 A A A C3' O3' P DA DA DG 2 2 3 Y 5 4.70 0.30 108.30 113.00 A A A O4' C1' N9 DG DG DG 3 3 3 N 5 3.37 0.30 108.30 111.67 A A A O4' C1' N9 DG DG DG 4 4 4 N 5 1.91 0.30 108.30 110.21 A A A O4' C1' N9 DG DG DG 5 5 5 N 5 2.61 0.30 108.30 110.91 A A A O4' C1' N9 DG DG DG 8 8 8 N 5 -3.74 0.60 122.90 119.16 A A A C6 C5 C7 DT DT DT 10 10 10 N 5 5.09 0.30 108.30 113.39 A A A O4' C1' N9 DG DG DG 13 13 13 N 5 7.23 1.20 119.70 126.93 A A A C3' O3' P DG DG DT 13 13 14 Y 5 2.74 0.30 108.30 111.04 A A A O4' C1' N1 DT DT DT 14 14 14 N 5 3.32 0.30 108.30 111.62 A A A O4' C1' N9 DG DG DG 15 15 15 N 5 2.01 0.30 108.30 110.31 A A A O4' C1' N9 DG DG DG 17 17 17 N 5 3.03 0.50 111.50 114.53 A A A C5 C6 N1 DG DG DG 17 17 17 N 5 3.35 0.30 108.30 111.65 A A A O4' C1' N9 DA DA DA 18 18 18 N 5 3.05 0.50 117.70 120.75 A A A C5 C6 N1 DA DA DA 18 18 18 N N Parallel DNA G-quadruplex formed by AA(GGGT)3GGGAA in potassium condition 1 N N hydrog TYPE_6_PAIR A DG 3 A N1 DG 3 1_555 A DG 7 A O6 DG 7 1_555 hydrog TYPE_6_PAIR A DG 3 A N2 DG 3 1_555 A DG 7 A N7 DG 7 1_555 hydrog TYPE_6_PAIR A DG 3 A N7 DG 3 1_555 A DG 15 A N2 DG 15 1_555 hydrog TYPE_6_PAIR A DG 3 A O6 DG 3 1_555 A DG 15 A N1 DG 15 1_555 hydrog TYPE_6_PAIR A DG 4 A N1 DG 4 1_555 A DG 8 A O6 DG 8 1_555 hydrog TYPE_6_PAIR A DG 4 A N2 DG 4 1_555 A DG 8 A N7 DG 8 1_555 hydrog TYPE_6_PAIR A DG 4 A N7 DG 4 1_555 A DG 16 A N2 DG 16 1_555 hydrog TYPE_6_PAIR A DG 4 A O6 DG 4 1_555 A DG 16 A N1 DG 16 1_555 hydrog TYPE_6_PAIR A DG 4 A N7 DG 4 1_555 A DG 17 A N2 DG 17 1_555 hydrog TYPE_6_PAIR A DG 4 A O6 DG 4 1_555 A DG 17 A N1 DG 17 1_555 hydrog TYPE_6_PAIR A DG 5 A N1 DG 5 1_555 A DG 9 A O6 DG 9 1_555 hydrog TYPE_6_PAIR A DG 5 A N2 DG 5 1_555 A DG 9 A N7 DG 9 1_555 hydrog TYPE_6_PAIR A DG 5 A N7 DG 5 1_555 A DG 17 A N2 DG 17 1_555 hydrog TYPE_6_PAIR A DG 5 A O6 DG 5 1_555 A DG 17 A N1 DG 17 1_555 hydrog TYPE_6_PAIR A DG 7 A N1 DG 7 1_555 A DG 11 A O6 DG 11 1_555 hydrog TYPE_6_PAIR A DG 7 A N2 DG 7 1_555 A DG 11 A N7 DG 11 1_555 hydrog TYPE_6_PAIR A DG 8 A N1 DG 8 1_555 A DG 12 A O6 DG 12 1_555 hydrog TYPE_6_PAIR A DG 8 A N2 DG 8 1_555 A DG 12 A N7 DG 12 1_555 hydrog TYPE_6_PAIR A DG 9 A N1 DG 9 1_555 A DG 13 A O6 DG 13 1_555 hydrog TYPE_6_PAIR A DG 9 A N2 DG 9 1_555 A DG 13 A N7 DG 13 1_555 hydrog TYPE_6_PAIR A DG 11 A N1 DG 11 1_555 A DG 15 A O6 DG 15 1_555 hydrog TYPE_6_PAIR A DG 11 A N2 DG 11 1_555 A DG 15 A N7 DG 15 1_555 hydrog TYPE_6_PAIR A DG 12 A N1 DG 12 1_555 A DG 16 A O6 DG 16 1_555 hydrog TYPE_6_PAIR A DG 12 A N2 DG 12 1_555 A DG 16 A N7 DG 16 1_555 hydrog TYPE_6_PAIR A DG 13 A N1 DG 13 1_555 A DG 17 A O6 DG 17 1_555 hydrog TYPE_6_PAIR A DG 13 A N2 DG 13 1_555 A DG 17 A N7 DG 17 1_555 DNA G-quadruplex, Parallel conformation, DNA 9WIH PDB 1 1 9WIH 1 19 9WIH 1 19 9WIH A 1 1 19