data_30058 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIY G-Quadruplexes: Solution Structure of d(GGGGTTTGGGGTTTTGGGGAAGGGG) in sodium ; _BMRB_accession_number 30058 _BMRB_flat_file_name bmr30058.str _Entry_type original _Submission_date 2016-04-05 _Accession_date 2016-04-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dvorkin S. A. . 2 Karsisiotis A. I. . 3 'Webba da Silva' M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 256 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-19 update BMRB 'update entry citation' 2017-05-04 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30045 'DIY G-Quadruplexes: d(GGGTTTGGGTTTTGGGAGGG)' 30055 'DIY G-Quadruplexes: d(GGTTTGGTTTTGGTTTGG)' 30056 'DIY G-Quadruplexes: d(GGTTTGGTTTTGGTTGG)' stop_ _Original_release_date 2016-04-06 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Encoding canonical DNA quadruplex structure. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30182059 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dvorkin Scarlett A. . 2 Karsisiotis Andreas I. . 3 'Webba da Silva' Mateus . . stop_ _Journal_abbreviation 'Sci Adv' _Journal_name_full 'Science advances' _Journal_volume 4 _Journal_issue 8 _Journal_ISSN 2375-2548 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first eaat3007 _Page_last eaat3007 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA (25-MER)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (25-MER)' _Molecular_mass 7978.100 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; GGGGTTTGGGGTTTTGGGGA AGGGG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DG 3 3 DG 4 4 DG 5 5 DT 6 6 DT 7 7 DT 8 8 DG 9 9 DG 10 10 DG 11 11 DG 12 12 DT 13 13 DT 14 14 DT 15 15 DT 16 16 DG 17 17 DG 18 18 DG 19 19 DG 20 20 DA 21 21 DA 22 22 DG 23 23 DG 24 24 DG 25 25 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . 32644 . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2 mM DNA (25-MER), 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 2 mM none NaPi 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VNMRS _Field_strength 500 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 20 0.02 mM pH 6.8 . pH pressure 1 . atm temperature 293.15 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 na indirect . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 DG H1 H 11.52 0.02 . 2 1 1 DG H1' H 6.03 0.02 . 3 1 1 DG H2' H 3.08 0.02 . 4 1 1 DG H2'' H 2.83 0.02 . 5 1 1 DG H3' H 4.95 0.02 . 6 1 1 DG H4' H 4.43 0.02 . 7 1 1 DG H5' H 3.88 0.02 . 8 1 1 DG H5'' H 3.89 0.02 . 9 1 1 DG H8 H 7.30 0.02 . 10 1 1 DG H21 H 10.19 0.02 . 11 1 1 DG H22 H 5.82 0.02 . 12 2 2 DG H1 H 11.51 0.02 . 13 2 2 DG H1' H 6.19 0.02 . 14 2 2 DG H2' H 2.84 0.02 . 15 2 2 DG H2'' H 2.70 0.02 . 16 2 2 DG H3' H 5.09 0.02 . 17 2 2 DG H4' H 4.47 0.02 . 18 2 2 DG H5' H 4.12 0.02 . 19 2 2 DG H5'' H 4.41 0.02 . 20 2 2 DG H8 H 7.97 0.02 . 21 2 2 DG H21 H 9.25 0.02 . 22 2 2 DG H22 H 6.03 0.02 . 23 3 3 DG H1 H 10.87 0.02 . 24 3 3 DG H1' H 5.96 0.02 . 25 3 3 DG H2' H 2.82 0.02 . 26 3 3 DG H2'' H 3.21 0.02 . 27 3 3 DG H3' H 5.08 0.02 . 28 3 3 DG H4' H 4.35 0.02 . 29 3 3 DG H5' H 4.39 0.02 . 30 3 3 DG H5'' H 4.11 0.02 . 31 3 3 DG H8 H 7.24 0.02 . 32 3 3 DG H21 H 8.92 0.02 . 33 4 4 DG H1 H 11.35 0.02 . 34 4 4 DG H1' H 6.10 0.02 . 35 4 4 DG H2' H 2.52 0.02 . 36 4 4 DG H2'' H 2.80 0.02 . 37 4 4 DG H3' H 5.12 0.02 . 38 4 4 DG H4' H 4.47 0.02 . 39 4 4 DG H5' H 4.22 0.02 . 40 4 4 DG H5'' H 4.24 0.02 . 41 4 4 DG H8 H 8.13 0.02 . 42 4 4 DG H21 H 9.69 0.02 . 43 4 4 DG H22 H 6.16 0.02 . 44 5 5 DT H1' H 6.28 0.02 . 45 5 5 DT H2' H 2.39 0.02 . 46 5 5 DT H2'' H 2.51 0.02 . 47 5 5 DT H3' H 4.73 0.02 . 48 5 5 DT H4' H 4.25 0.02 . 49 5 5 DT H5' H 4.15 0.02 . 50 5 5 DT H5'' H 4.12 0.02 . 51 5 5 DT H6 H 7.34 0.02 . 52 5 5 DT H71 H 1.91 0.02 . 53 5 5 DT H72 H 1.91 0.02 . 54 5 5 DT H73 H 1.91 0.02 . 55 6 6 DT H1' H 5.36 0.02 . 56 6 6 DT H2' H 2.21 0.02 . 57 6 6 DT H2'' H 1.45 0.02 . 58 6 6 DT H3' H 4.50 0.02 . 59 6 6 DT H4' H 3.91 0.02 . 60 6 6 DT H5' H 3.54 0.02 . 61 6 6 DT H5'' H 3.84 0.02 . 62 6 6 DT H6 H 6.53 0.02 . 63 6 6 DT H71 H 0.99 0.02 . 64 6 6 DT H72 H 0.99 0.02 . 65 6 6 DT H73 H 0.99 0.02 . 66 7 7 DT H1' H 6.03 0.02 . 67 7 7 DT H2' H 2.17 0.02 . 68 7 7 DT H2'' H 1.82 0.02 . 69 7 7 DT H3' H 4.55 0.02 . 70 7 7 DT H4' H 4.17 0.02 . 71 7 7 DT H5' H 3.57 0.02 . 72 7 7 DT H5'' H 2.76 0.02 . 73 7 7 DT H6 H 6.90 0.02 . 74 7 7 DT H71 H 0.83 0.02 . 75 7 7 DT H72 H 0.83 0.02 . 76 7 7 DT H73 H 0.83 0.02 . 77 8 8 DG H1 H 11.66 0.02 . 78 8 8 DG H1' H 6.00 0.02 . 79 8 8 DG H2' H 3.14 0.02 . 80 8 8 DG H2'' H 2.96 0.02 . 81 8 8 DG H3' H 4.72 0.02 . 82 8 8 DG H4' H 4.39 0.02 . 83 8 8 DG H5' H 4.32 0.02 . 84 8 8 DG H5'' H 4.17 0.02 . 85 8 8 DG H8 H 7.46 0.02 . 86 8 8 DG H21 H 9.46 0.02 . 87 8 8 DG H22 H 5.86 0.02 . 88 9 9 DG H1 H 11.45 0.02 . 89 9 9 DG H1' H 6.17 0.02 . 90 9 9 DG H2' H 2.79 0.02 . 91 9 9 DG H2'' H 2.63 0.02 . 92 9 9 DG H3' H 5.04 0.02 . 93 9 9 DG H4' H 4.48 0.02 . 94 9 9 DG H5' H 4.31 0.02 . 95 9 9 DG H5'' H 4.09 0.02 . 96 9 9 DG H8 H 7.99 0.02 . 97 9 9 DG H21 H 9.69 0.02 . 98 9 9 DG H22 H 6.08 0.02 . 99 10 10 DG H1 H 10.99 0.02 . 100 10 10 DG H1' H 5.90 0.02 . 101 10 10 DG H2' H 2.65 0.02 . 102 10 10 DG H2'' H 3.04 0.02 . 103 10 10 DG H3' H 5.03 0.02 . 104 10 10 DG H4' H 4.49 0.02 . 105 10 10 DG H5' H 4.10 0.02 . 106 10 10 DG H5'' H 4.32 0.02 . 107 10 10 DG H8 H 7.24 0.02 . 108 10 10 DG H21 H 8.74 0.02 . 109 10 10 DG H22 H 6.03 0.02 . 110 11 11 DG H1 H 11.34 0.02 . 111 11 11 DG H1' H 5.97 0.02 . 112 11 11 DG H2' H 2.68 0.02 . 113 11 11 DG H2'' H 2.53 0.02 . 114 11 11 DG H3' H 4.99 0.02 . 115 11 11 DG H4' H 4.44 0.02 . 116 11 11 DG H5' H 4.18 0.02 . 117 11 11 DG H5'' H 4.13 0.02 . 118 11 11 DG H8 H 7.91 0.02 . 119 12 12 DT H1' H 5.60 0.02 . 120 12 12 DT H2' H 2.12 0.02 . 121 12 12 DT H2'' H 1.82 0.02 . 122 12 12 DT H3' H 4.62 0.02 . 123 12 12 DT H4' H 4.33 0.02 . 124 12 12 DT H5' H 3.90 0.02 . 125 12 12 DT H5'' H 4.06 0.02 . 126 12 12 DT H6 H 7.10 0.02 . 127 12 12 DT H71 H 1.78 0.02 . 128 12 12 DT H72 H 1.78 0.02 . 129 12 12 DT H73 H 1.78 0.02 . 130 13 13 DT H1' H 5.67 0.02 . 131 13 13 DT H2' H 2.03 0.02 . 132 13 13 DT H2'' H 1.88 0.02 . 133 13 13 DT H3' H 4.50 0.02 . 134 13 13 DT H4' H 3.70 0.02 . 135 13 13 DT H6 H 7.32 0.02 . 136 13 13 DT H71 H 1.67 0.02 . 137 13 13 DT H72 H 1.67 0.02 . 138 13 13 DT H73 H 1.67 0.02 . 139 14 14 DT H1' H 5.73 0.02 . 140 14 14 DT H2' H 2.04 0.02 . 141 14 14 DT H2'' H 1.82 0.02 . 142 14 14 DT H4' H 4.35 0.02 . 143 14 14 DT H5' H 4.34 0.02 . 144 14 14 DT H5'' H 3.82 0.02 . 145 14 14 DT H6 H 7.18 0.02 . 146 14 14 DT H71 H 1.41 0.02 . 147 14 14 DT H72 H 1.41 0.02 . 148 14 14 DT H73 H 1.41 0.02 . 149 15 15 DT H1' H 6.06 0.02 . 150 15 15 DT H2' H 2.43 0.02 . 151 15 15 DT H2'' H 1.87 0.02 . 152 15 15 DT H6 H 7.21 0.02 . 153 15 15 DT H71 H 1.67 0.02 . 154 15 15 DT H72 H 1.67 0.02 . 155 15 15 DT H73 H 1.67 0.02 . 156 16 16 DG H1 H 11.28 0.02 . 157 16 16 DG H1' H 6.14 0.02 . 158 16 16 DG H2' H 3.04 0.02 . 159 16 16 DG H2'' H 3.50 0.02 . 160 16 16 DG H3' H 4.85 0.02 . 161 16 16 DG H4' H 4.64 0.02 . 162 16 16 DG H5' H 4.12 0.02 . 163 16 16 DG H5'' H 4.11 0.02 . 164 16 16 DG H8 H 7.59 0.02 . 165 16 16 DG H21 H 9.32 0.02 . 166 16 16 DG H22 H 7.22 0.02 . 167 17 17 DG H1 H 11.39 0.02 . 168 17 17 DG H1' H 6.16 0.02 . 169 17 17 DG H2' H 2.71 0.02 . 170 17 17 DG H2'' H 2.57 0.02 . 171 17 17 DG H3' H 5.04 0.02 . 172 17 17 DG H4' H 4.46 0.02 . 173 17 17 DG H5' H 4.23 0.02 . 174 17 17 DG H5'' H 4.08 0.02 . 175 17 17 DG H8 H 7.87 0.02 . 176 17 17 DG H21 H 9.39 0.02 . 177 17 17 DG H22 H 6.02 0.02 . 178 18 18 DG H1 H 11.09 0.02 . 179 18 18 DG H1' H 6.03 0.02 . 180 18 18 DG H2' H 3.30 0.02 . 181 18 18 DG H2'' H 2.88 0.02 . 182 18 18 DG H3' H 5.16 0.02 . 183 18 18 DG H4' H 4.57 0.02 . 184 18 18 DG H5' H 4.36 0.02 . 185 18 18 DG H5'' H 4.07 0.02 . 186 18 18 DG H8 H 7.23 0.02 . 187 18 18 DG H21 H 8.43 0.02 . 188 18 18 DG H22 H 5.97 0.02 . 189 19 19 DG H1 H 11.00 0.02 . 190 19 19 DG H1' H 6.20 0.02 . 191 19 19 DG H2' H 2.62 0.02 . 192 19 19 DG H2'' H 2.80 0.02 . 193 19 19 DG H3' H 5.15 0.02 . 194 19 19 DG H4' H 4.94 0.02 . 195 19 19 DG H5' H 4.40 0.02 . 196 19 19 DG H5'' H 4.42 0.02 . 197 19 19 DG H8 H 8.13 0.02 . 198 20 20 DA H1' H 6.32 0.02 . 199 20 20 DA H2 H 8.10 0.02 . 200 20 20 DA H2' H 2.54 0.02 . 201 20 20 DA H2'' H 2.70 0.02 . 202 20 20 DA H3' H 4.94 0.02 . 203 20 20 DA H4' H 4.44 0.02 . 204 20 20 DA H5' H 4.18 0.02 . 205 20 20 DA H5'' H 4.16 0.02 . 206 20 20 DA H8 H 8.24 0.02 . 207 21 21 DA H1' H 6.32 0.02 . 208 21 21 DA H2 H 7.64 0.02 . 209 21 21 DA H2' H 2.54 0.02 . 210 21 21 DA H2'' H 2.70 0.02 . 211 21 21 DA H3' H 4.94 0.02 . 212 21 21 DA H4' H 4.44 0.02 . 213 21 21 DA H5' H 4.18 0.02 . 214 21 21 DA H5'' H 4.16 0.02 . 215 21 21 DA H8 H 8.24 0.02 . 216 22 22 DG H1 H 10.77 0.02 . 217 22 22 DG H1' H 5.73 0.02 . 218 22 22 DG H2' H 2.84 0.02 . 219 22 22 DG H2'' H 3.02 0.02 . 220 22 22 DG H3' H 4.89 0.02 . 221 22 22 DG H4' H 4.36 0.02 . 222 22 22 DG H5' H 4.33 0.02 . 223 22 22 DG H5'' H 4.23 0.02 . 224 22 22 DG H8 H 7.08 0.02 . 225 22 22 DG H21 H 9.34 0.02 . 226 22 22 DG H22 H 6.63 0.02 . 227 23 23 DG H1' H 6.09 0.02 . 228 23 23 DG H2' H 2.66 0.02 . 229 23 23 DG H2'' H 2.41 0.02 . 230 23 23 DG H3' H 4.99 0.02 . 231 23 23 DG H4' H 4.48 0.02 . 232 23 23 DG H5' H 4.05 0.02 . 233 23 23 DG H5'' H 4.06 0.02 . 234 23 23 DG H8 H 7.68 0.02 . 235 24 24 DG H1 H 11.02 0.02 . 236 24 24 DG H1' H 6.00 0.02 . 237 24 24 DG H2' H 2.83 0.02 . 238 24 24 DG H2'' H 3.25 0.02 . 239 24 24 DG H3' H 5.07 0.02 . 240 24 24 DG H4' H 4.59 0.02 . 241 24 24 DG H5' H 4.45 0.02 . 242 24 24 DG H5'' H 4.05 0.02 . 243 24 24 DG H8 H 7.22 0.02 . 244 24 24 DG H21 H 8.61 0.02 . 245 24 24 DG H22 H 6.17 0.02 . 246 25 25 DG H1 H 11.29 0.02 . 247 25 25 DG H1' H 6.22 0.02 . 248 25 25 DG H2' H 2.64 0.02 . 249 25 25 DG H2'' H 2.41 0.02 . 250 25 25 DG H3' H 4.75 0.02 . 251 25 25 DG H4' H 4.26 0.02 . 252 25 25 DG H5' H 4.19 0.02 . 253 25 25 DG H5'' H 4.26 0.02 . 254 25 25 DG H8 H 8.19 0.02 . 255 25 25 DG H21 H 8.73 0.02 . 256 25 25 DG H22 H 6.04 0.02 . stop_ save_