data_34502 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; LNA modified G-quadruplex with flipped G-tract and central tetrad ; _BMRB_accession_number 34502 _BMRB_flat_file_name bmr34502.str _Entry_type original _Submission_date 2020-03-25 _Accession_date 2020-03-25 _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 Weisz K. . . 2 Haase L. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 125 "13C chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-08-31 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 ; Sugar pucker vs glycosidic torsion angle: Locking specific G-quadruplex topologies through LNA modifications ; _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 Weisz K. . . 2 Haase L. . . 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 "DNA (5'-D(*GP*GP*GP*AP*TP*GP*GP*GP*AP*CP*AP*CP*AP*(GF2))-R(P*(LCG))-D(P*GP*GP*AP*CP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label unit_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 entity_1 _Molecular_mass 7000.501 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; GGGATGGGACACAGXGGACG GG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DA 5 DT 6 DG 7 DG 8 DG 9 DA 10 DC 11 DA 12 DC 13 DA 14 DG 15 LCG 16 DG 17 DG 18 DA 19 DC 20 DG 21 DG 22 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_LCG _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' _BMRB_code LCG _PDB_code LCG _Standard_residue_derivative . _Molecular_mass 375.231 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C3' C3' C . 0 . ? C6' C6' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? C4 C4 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C2' C2' C . 0 . ? O6 O6 O . 0 . ? C4' C4' C . 0 . ? C1' C1' C . 0 . ? C2 C2 C . 0 . ? N1 N1 N . 0 . ? O4' O4' O . 0 . ? OP2 OP2 O . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H3' H3' H . 0 . ? H6'1 H6'1 H . 0 . ? H6'2 H6'2 H . 0 . ? H8 H8 H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? H1 H1 H . 0 . ? HOP2 HOP2 H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? HO3' HO3' H . 0 . ? HOP3 HOP3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P O5' ? ? SING P OP2 ? ? SING P OP3 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C3' C2' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING C6' C4' ? ? SING C6' O2' ? ? SING C6' H6'1 ? ? SING C6' H6'2 ? ? SING N9 C8 ? ? SING N9 C4 ? ? SING N9 C1' ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? DOUB C4 C5 ? ? SING C4 N3 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING C2' C1' ? ? SING C2' O2' ? ? SING C2' H2' ? ? SING C4' O4' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2 N1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N1 H1 ? ? SING OP2 HOP2 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING O3' HO3' ? ? SING OP3 HOP3 ? ? stop_ 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 . . synthetic construct 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 '0.4 mM L15, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.4 mM L15, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version 4.0.4 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'CcpNmr Analysis' _Version 2.4.2 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.49 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name Amber _Version 16 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 Bruker _Model 'AVANCE NEO' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_1H_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _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_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C 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' 15 . mM pH 7 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.25144953 water H 1 protons ppm 4.78 na 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 '1D 1H' '2D 1H-1H NOESY' '2D DQF-COSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _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 11.725 0.002 1 2 1 1 DG H1' H 6.106 0.001 1 3 1 1 DG H2' H 2.671 0.005 1 4 1 1 DG H2'' H 3.204 0.003 1 5 1 1 DG H3' H 5.018 0.003 1 6 1 1 DG H8 H 7.370 0.002 1 7 1 1 DG C8 C 141.070 . 1 8 2 2 DG H1 H 11.729 0.001 1 9 2 2 DG H1' H 5.871 0.004 1 10 2 2 DG H2' H 2.504 0.002 1 11 2 2 DG H2'' H 2.684 0.004 1 12 2 2 DG H3' H 5.122 0.0 1 13 2 2 DG H8 H 7.894 0.002 1 14 2 2 DG C8 C 138.350 . 1 15 3 3 DG H1 H 11.437 0.004 1 16 3 3 DG H1' H 6.285 0.001 1 17 3 3 DG H2' H 2.837 0.003 1 18 3 3 DG H2'' H 2.572 0.002 1 19 3 3 DG H3' H 5.009 0.004 1 20 3 3 DG H8 H 7.943 0.002 1 21 3 3 DG C8 C 137.018 . 1 22 4 4 DA H1' H 6.390 0.001 1 23 4 4 DA H2 H 7.293 0.002 1 24 4 4 DA H2' H 2.673 0.004 2 25 4 4 DA H2'' H 2.642 0.002 2 26 4 4 DA H3' H 5.028 0.003 1 27 4 4 DA H8 H 8.303 0.001 1 28 4 4 DA C2 C 154.536 . 1 29 4 4 DA C8 C 142.189 . 1 30 5 5 DT H1' H 6.001 0.005 1 31 5 5 DT H2' H 2.071 0.001 1 32 5 5 DT H2'' H 2.598 0.001 1 33 5 5 DT H3' H 4.874 0.002 1 34 5 5 DT H6 H 7.204 0.001 1 35 5 5 DT H71 H 1.114 0.002 1 36 5 5 DT H72 H 1.114 0.002 1 37 5 5 DT H73 H 1.114 0.002 1 38 5 5 DT C6 C 137.918 . 1 39 6 6 DG H1 H 11.432 0.002 1 40 6 6 DG H1' H 6.138 0.002 1 41 6 6 DG H2' H 3.631 0.004 1 42 6 6 DG H2'' H 3.179 0.005 1 43 6 6 DG H3' H 4.860 0.003 1 44 6 6 DG H8 H 7.314 0.002 1 45 6 6 DG C8 C 141.614 . 1 46 7 7 DG H1 H 11.269 0.002 1 47 7 7 DG H1' H 5.755 0.004 1 48 7 7 DG H2' H 2.651 0.004 1 49 7 7 DG H2'' H 2.476 0.001 1 50 7 7 DG H3' H 5.003 0.003 1 51 7 7 DG H8 H 7.237 0.001 1 52 7 7 DG C8 C 140.380 . 1 53 8 8 DG H1 H 11.232 0.004 1 54 8 8 DG H1' H 5.804 0.002 1 55 8 8 DG H2' H 2.083 0.001 1 56 8 8 DG H2'' H 2.375 0.001 1 57 8 8 DG H3' H 4.931 0.001 1 58 8 8 DG H8 H 7.581 0.002 1 59 8 8 DG C8 C 137.690 . 1 60 9 9 DA H1' H 5.925 0.003 1 61 9 9 DA H2' H 2.675 0.004 1 62 9 9 DA H2'' H 2.547 0.012 1 63 9 9 DA H3' H 4.943 0.002 1 64 9 9 DA H8 H 8.012 0.001 1 65 9 9 DA C8 C 141.706 . 1 66 10 10 DC H1' H 5.885 0.003 1 67 10 10 DC H2' H 1.779 0.004 1 68 10 10 DC H2'' H 2.159 0.002 1 69 10 10 DC H3' H 4.591 0.001 1 70 10 10 DC H5 H 5.890 0.0 1 71 10 10 DC H6 H 7.619 0.012 1 72 10 10 DC C6 C 143.721 . 1 73 11 11 DA H1' H 5.697 0.001 1 74 11 11 DA H2' H 2.342 0.001 1 75 11 11 DA H2'' H 1.864 0.003 1 76 11 11 DA H3' H 4.351 0.002 1 77 11 11 DA H8 H 7.838 0.001 1 78 11 11 DA C8 C 141.435 . 1 79 12 12 DC H1' H 5.581 0.002 1 80 12 12 DC H2' H 1.649 0.002 1 81 12 12 DC H2'' H 1.976 0.002 1 82 12 12 DC H3' H 4.395 0.003 1 83 12 12 DC H5 H 5.109 0.004 1 84 12 12 DC H6 H 7.047 0.001 1 85 12 12 DC C6 C 143.471 . 1 86 13 13 DA H1' H 6.191 0.001 1 87 13 13 DA H2 H 7.647 0.002 1 88 13 13 DA H2' H 2.517 0.002 1 89 13 13 DA H2'' H 2.275 0.001 1 90 13 13 DA H3' H 4.666 0.002 1 91 13 13 DA H8 H 7.923 0.002 1 92 13 13 DA C2 C 154.444 . 1 93 13 13 DA C8 C 141.647 . 1 94 14 14 DG H1 H 11.171 0.003 1 95 14 14 DG H1' H 6.003 0.004 1 96 14 14 DG H2' H 3.615 0.001 1 97 14 14 DG H2'' H 2.865 0.001 1 98 14 14 DG H3' H 4.943 0.003 1 99 14 14 DG H8 H 7.392 0.002 1 100 14 14 DG C8 C 141.283 . 1 101 15 15 LCG H1 H 11.773 0.002 1 102 15 15 LCG H1' H 5.526 0.002 1 103 15 15 LCG H2' H 4.664 0.001 1 104 15 15 LCG H3' H 4.342 0.002 1 105 15 15 LCG H8 H 7.483 0.002 1 106 15 15 LCG C8 C 137.196 . 1 107 16 16 DG H1 H 11.508 0.005 1 108 16 16 DG H1' H 6.028 0.003 1 109 16 16 DG H2' H 1.335 0.002 1 110 16 16 DG H2'' H 2.499 0.002 1 111 16 16 DG H3' H 4.789 0.002 1 112 16 16 DG H8 H 7.405 0.002 1 113 16 16 DG C8 C 136.789 . 1 114 17 17 DG H1' H 6.033 0.001 1 115 17 17 DG H2' H 2.640 0.004 1 116 17 17 DG H2'' H 2.385 0.001 1 117 17 17 DG H8 H 7.915 0.002 1 118 17 17 DG C8 C 138.457 . 1 119 18 18 DA H1' H 5.896 0.001 1 120 18 18 DA H2' H 2.420 0.002 1 121 18 18 DA H2'' H 2.286 0.001 1 122 18 18 DA H8 H 8.059 0.002 1 123 18 18 DA C8 C 142.307 . 1 124 19 19 DC H2' H 1.874 . 2 125 19 19 DC H2'' H 2.398 0.001 2 126 19 19 DC H5 H 5.775 0.0 1 127 19 19 DC H6 H 7.379 0.004 1 128 19 19 DC C6 C 143.145 . 1 129 20 20 DG H1 H 11.612 0.001 1 130 20 20 DG H1' H 6.067 0.001 1 131 20 20 DG H2' H 3.198 0.002 2 132 20 20 DG H2'' H 3.727 0.002 2 133 20 20 DG H3' H 4.824 0.001 1 134 20 20 DG H8 H 7.138 0.002 1 135 20 20 DG C8 C 141.304 . 1 136 21 21 DG H1 H 11.488 0.002 1 137 21 21 DG H1' H 5.743 0.002 1 138 21 21 DG H2' H 2.506 0.005 2 139 21 21 DG H2'' H 2.566 0.003 2 140 21 21 DG H3' H 5.039 0.004 1 141 21 21 DG H8 H 7.370 0.003 1 142 21 21 DG C8 C 140.892 . 1 143 22 22 DG H1 H 11.654 0.004 1 144 22 22 DG H1' H 5.936 0.003 1 145 22 22 DG H2' H 2.472 0.002 1 146 22 22 DG H2'' H 2.805 0.003 1 147 22 22 DG H3' H 4.730 0.001 1 148 22 22 DG H8 H 7.924 0.003 1 149 22 22 DG C8 C 138.659 . 1 stop_ save_