data_34438 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Guanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pair ; _BMRB_accession_number 34438 _BMRB_flat_file_name bmr34438.str _Entry_type original _Submission_date 2019-09-30 _Accession_date 2019-09-30 _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 Pavc D. . . 2 Wang B. . . 3 Spindler L. . . 4 Drevensek-Olenik I. . . 5 Plavec J. . . 6 Sket P. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 132 "31P chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-07-27 original BMRB . stop_ _Original_release_date 2020-07-14 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Guanine-rich oligonucleotide with 5'- and 3'-GC ends form G-quadruplex with A(GGGG)A hexad, GCGC- and G-quartets and two symmetric GG and AA base pair ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pavc D. . . 2 Wang B. . . 3 Spindler L. . . 4 Drevensek-Olenik I. . . 5 Plavec J. . . 6 Sket P. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name GCnCG _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_1 $entity_1 unit_2 $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 entity_1 _Molecular_mass 4451.877 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; GCGGAGGGGAGGCG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DG 5 DA 6 DG 7 DG 8 DG 9 DG 10 DA 11 DG 12 DG 13 DC 14 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 . 32630 . . . . 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 '1 mM 8% 13C, 8% 15N GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM '[8% 13C; 8% 15N]' 'sodium chloride' 175 mM 'natural abundance' 'sodium phosphate buffer' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'sodium chloride' 175 mM 'natural abundance' 'sodium phosphate buffer' 10 mM 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '1 mM GCnCG, 175 mM sodium chloride, 10 mM sodium phosphate buffer, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'sodium chloride' 175 mM 'natural abundance' 'sodium phosphate buffer' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task 'chemical shift assignment' collection processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Sparky _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name Amber _Version 14 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model 'Agilent Technologies VNMRS 800 MHz NMR spectrometer' _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model 'Agilent Technologies DD2 600 MHz NMR spectrometer' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_3 save_ save_2D_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_3 save_ save_2D_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_3 save_ save_2D_DQF-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-31P_COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _Sample_label $sample_3 save_ save_2D_1H-13C_HSQC_aromatic_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _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' 175 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 175 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 175 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . 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 0.000 external direct . . . 1.0 'phosphoric acid (85%)' P 31 phosphorus ppm 0.000 external direct . . . 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_ _Experiment_label '2D NOESY' '2D TOCSY' '2D DQF-COSY' '2D 1H-31P COSY' '2D 1H-13C HSQC aromatic' stop_ loop_ _Sample_label $sample_2 $sample_3 $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name unit_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 10.999 0.081 1 2 1 1 DG H1' H 4.324 0.059 1 3 1 1 DG H2' H 2.145 0.061 1 4 1 1 DG H2'' H 2.467 0.059 1 5 1 1 DG H3' H 4.763 0.074 1 6 1 1 DG H4' H 3.528 0.046 1 7 1 1 DG H5' H 4.157 0.003 1 8 1 1 DG H5'' H 4.083 0.001 1 9 1 1 DG H8 H 6.257 0.030 1 10 1 1 DG H21 H 8.925 0.080 1 11 1 1 DG H22 H 5.978 0.079 1 12 2 2 DC H1' H 5.951 0.049 1 13 2 2 DC H2' H 1.111 0.054 1 14 2 2 DC H2'' H 2.014 0.060 1 15 2 2 DC H3' H 4.741 0.061 1 16 2 2 DC H4' H 4.073 0.035 1 17 2 2 DC H5 H 5.016 0.048 1 18 2 2 DC H5' H 3.516 0.004 2 19 2 2 DC H5'' H 3.516 0.004 2 20 2 2 DC H6 H 6.745 0.028 1 21 2 2 DC H41 H 8.725 0.079 1 22 2 2 DC H42 H 8.901 0.079 1 23 2 2 DC P P -0.990 0.002 1 24 3 3 DG H1' H 5.124 0.048 1 25 3 3 DG H2' H 2.601 0.042 1 26 3 3 DG H2'' H 2.037 0.011 1 27 3 3 DG H3' H 4.772 0.048 1 28 3 3 DG H8 H 7.916 0.068 1 29 3 3 DG P P -1.320 0.000 1 30 4 4 DG H1 H 10.991 0.076 1 31 4 4 DG H1' H 5.579 0.056 1 32 4 4 DG H2' H 2.334 0.042 1 33 4 4 DG H2'' H 2.031 0.058 1 34 4 4 DG H3' H 4.436 0.054 1 35 4 4 DG H4' H 3.081 0.004 1 36 4 4 DG H5' H 2.751 0.000 1 37 4 4 DG H5'' H 1.978 0.005 1 38 4 4 DG H8 H 7.693 0.069 1 39 4 4 DG P P -0.604 0.000 1 40 5 5 DA H1' H 6.380 0.049 1 41 5 5 DA H2 H 7.899 0.075 1 42 5 5 DA H2' H 3.011 0.036 1 43 5 5 DA H2'' H 2.925 0.040 1 44 5 5 DA H3' H 5.176 0.049 1 45 5 5 DA H4' H 4.343 0.048 1 46 5 5 DA H5' H 4.154 0.050 1 47 5 5 DA H5'' H 3.847 0.005 1 48 5 5 DA H8 H 8.419 0.059 1 49 5 5 DA P P -1.025 0.000 1 50 6 6 DG H1 H 13.181 0.078 1 51 6 6 DG H1' H 5.236 0.005 1 52 6 6 DG H2' H 2.497 0.010 1 53 6 6 DG H2'' H 2.523 0.001 1 54 6 6 DG H3' H 4.837 0.004 1 55 6 6 DG H4' H 4.355 0.039 1 56 6 6 DG H5' H 4.161 0.005 2 57 6 6 DG H5'' H 4.161 0.005 2 58 6 6 DG H8 H 7.959 0.075 1 59 6 6 DG H22 H 6.729 0.000 1 60 6 6 DG P P -0.785 0.000 1 61 7 7 DG H1 H 11.583 0.074 1 62 7 7 DG H1' H 6.024 0.050 1 63 7 7 DG H2' H 2.560 0.060 1 64 7 7 DG H2'' H 2.843 0.060 1 65 7 7 DG H3' H 5.053 0.053 1 66 7 7 DG H4' H 4.460 0.053 1 67 7 7 DG H5' H 4.214 0.043 1 68 7 7 DG H5'' H 4.172 0.043 1 69 7 7 DG H8 H 7.809 0.071 1 70 7 7 DG H21 H 10.156 0.000 1 71 7 7 DG H22 H 6.270 0.000 1 72 7 7 DG P P -0.407 0.000 1 73 8 8 DG H1 H 11.234 0.098 1 74 8 8 DG H1' H 6.218 0.048 1 75 8 8 DG H2' H 2.734 0.039 1 76 8 8 DG H2'' H 2.924 0.054 1 77 8 8 DG H3' H 5.071 0.042 1 78 8 8 DG H4' H 4.634 0.058 1 79 8 8 DG H5' H 4.350 0.039 1 80 8 8 DG H5'' H 4.326 0.051 1 81 8 8 DG H8 H 7.736 0.068 1 82 8 8 DG H21 H 9.300 0.079 1 83 8 8 DG H22 H 8.357 0.080 1 84 8 8 DG P P -1.124 0.003 1 85 9 9 DG H1 H 11.049 0.080 1 86 9 9 DG H1' H 6.159 0.063 1 87 9 9 DG H2' H 2.297 0.067 1 88 9 9 DG H2'' H 2.379 0.067 2 89 9 9 DG H3' H 4.734 0.068 1 90 9 9 DG H4' H 3.097 0.067 1 91 9 9 DG H5' H 3.860 0.051 1 92 9 9 DG H5'' H 3.821 0.050 1 93 9 9 DG H8 H 7.549 0.069 1 94 9 9 DG P P -1.083 0.001 1 95 10 10 DA H1' H 6.624 0.056 1 96 10 10 DA H2 H 8.439 0.043 1 97 10 10 DA H2' H 3.135 0.065 1 98 10 10 DA H2'' H 3.254 0.064 1 99 10 10 DA H3' H 5.483 0.072 1 100 10 10 DA H4' H 4.386 0.074 1 101 10 10 DA H5' H 4.133 0.069 1 102 10 10 DA H5'' H 3.970 0.067 1 103 10 10 DA H8 H 8.933 0.050 1 104 10 10 DA P P 0.487 0.000 1 105 11 11 DG H1 H 11.351 0.080 1 106 11 11 DG H1' H 6.219 0.056 1 107 11 11 DG H2' H 2.379 0.065 2 108 11 11 DG H2'' H 2.718 0.064 1 109 11 11 DG H3' H 5.047 0.057 1 110 11 11 DG H4' H 4.458 0.050 1 111 11 11 DG H5' H 4.273 0.051 1 112 11 11 DG H5'' H 3.884 0.053 1 113 11 11 DG H8 H 7.595 0.068 1 114 11 11 DG H21 H 9.011 0.079 1 115 11 11 DG H22 H 5.537 0.064 1 116 11 11 DG P P 0.279 0.000 1 117 12 12 DG H1 H 11.381 0.078 1 118 12 12 DG H1' H 6.223 0.046 1 119 12 12 DG H2' H 2.654 0.050 1 120 12 12 DG H2'' H 2.772 0.052 1 121 12 12 DG H3' H 5.027 0.054 1 122 12 12 DG H4' H 4.530 0.050 1 123 12 12 DG H5' H 4.312 0.039 1 124 12 12 DG H5'' H 4.231 0.038 1 125 12 12 DG H8 H 8.001 0.055 1 126 12 12 DG P P -0.521 0.001 1 127 13 13 DC H1' H 5.998 0.051 1 128 13 13 DC H2' H 1.921 0.064 1 129 13 13 DC H2'' H 2.328 0.065 1 130 13 13 DC H3' H 4.682 0.070 1 131 13 13 DC H4' H 4.215 0.061 1 132 13 13 DC H5 H 5.623 0.053 1 133 13 13 DC H5' H 4.178 0.050 1 134 13 13 DC H5'' H 4.068 0.056 1 135 13 13 DC H6 H 7.439 0.066 1 136 13 13 DC P P -0.522 0.001 1 137 14 14 DG H1' H 5.811 0.048 1 138 14 14 DG H2' H 2.263 0.055 2 139 14 14 DG H2'' H 2.263 0.055 2 140 14 14 DG H3' H 4.437 0.065 1 141 14 14 DG H4' H 3.933 0.063 1 142 14 14 DG H5' H 3.907 0.039 2 143 14 14 DG H5'' H 3.907 0.039 2 144 14 14 DG H8 H 7.361 0.068 1 145 14 14 DG P P -0.696 0.002 1 stop_ save_