data_19381 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes ; _BMRB_accession_number 19381 _BMRB_flat_file_name bmr19381.str _Entry_type original _Submission_date 2013-07-22 _Accession_date 2013-07-22 _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 Li Zhe . . 2 Lech Christopher . . 3 Adrian Michael . . 4 Heddi Brahim . . 5 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 186 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-02-02 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19386 'Parallel-stranded G-quadruplex in DNA poly-G stretches' 19389 'Stacked dimeric G-quadruplex' stop_ _Original_release_date 2015-02-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Engineering G4: Towards effective incorporation of locked nucleic acid into G-quadruplexes' _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 Li Zhe . . 2 Lech Christopher . . 3 Adrian Michael . . 4 Heddi Brahim . . 5 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _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/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')' $DNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*TP*TP*GP*LGP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3') _Molecular_mass 7607.944 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; TTGXGTTAGGGTTAGGGTTA GGGA ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DG 4 LCG 5 DG 6 DT 7 DT 8 DA 9 DG 10 DG 11 DG 12 DT 13 DT 14 DA 15 DG 16 DG 17 DG 18 DT 19 DT 20 DA 21 DG 22 DG 23 DG 24 DA 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 $DNA . . . . . . 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 $DNA 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 1.5 mM 'natural abundance' DSS 20 uM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA 1.5 mM 'natural abundance' DSS 20 uM 'natural abundance' 'potassium phosphate' 20 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_2 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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_2 save_ save_2D_1H-1H_COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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' 30 . mM pH 7 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 internal direct . . . 1.00000000 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D 1H-1H COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA/RNA (5'-D(*TP*TP*G)-R(P*(LG))-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')' _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 DT H1' H 5.792 . . 2 1 1 DT H2' H 1.775 . . 3 1 1 DT H2'' H 2.332 . . 4 1 1 DT H3' H 4.637 . . 5 1 1 DT H4' H 4.295 . . 6 1 1 DT H6 H 7.423 . . 7 1 1 DT H71 H 1.432 . . 8 1 1 DT H72 H 1.432 . . 9 1 1 DT H73 H 1.432 . . 10 2 2 DT H1' H 6.218 . . 11 2 2 DT H2' H 2.147 . . 12 2 2 DT H2'' H 2.350 . . 13 2 2 DT H3' H 4.703 . . 14 2 2 DT H4' H 3.890 . . 15 2 2 DT H6 H 7.532 . . 16 2 2 DT H71 H 1.430 . . 17 2 2 DT H72 H 1.430 . . 18 2 2 DT H73 H 1.430 . . 19 3 3 DG H1 H 11.963 . . 20 3 3 DG H1' H 6.243 . . 21 3 3 DG H2' H 3.692 . . 22 3 3 DG H2'' H 3.045 . . 23 3 3 DG H3' H 4.858 . . 24 3 3 DG H4' H 4.466 . . 25 3 3 DG H8 H 7.637 . . 26 4 4 LCG H1 H 11.843 . . 27 4 4 LCG H1' H 5.626 . . 28 4 4 LCG H2' H 4.513 . . 29 4 4 LCG H3' H 4.734 . . 30 4 4 LCG H5' H 4.462 . . 31 4 4 LCG H5'' H 4.355 . . 32 4 4 LCG H6'1 H 3.956 . . 33 4 4 LCG H6'2 H 3.925 . . 34 4 4 LCG H8 H 7.508 . . 35 5 5 DG H1 H 11.278 . . 36 5 5 DG H1' H 6.445 . . 37 5 5 DG H2' H 2.589 . . 38 5 5 DG H2'' H 2.667 . . 39 5 5 DG H3' H 5.027 . . 40 5 5 DG H4' H 4.561 . . 41 5 5 DG H8 H 7.981 . . 42 6 6 DT H1' H 6.440 . . 43 6 6 DT H2' H 2.446 . . 44 6 6 DT H2'' H 2.587 . . 45 6 6 DT H3' H 4.937 . . 46 6 6 DT H4' H 4.415 . . 47 6 6 DT H6 H 7.780 . . 48 6 6 DT H71 H 2.066 . . 49 6 6 DT H72 H 2.066 . . 50 6 6 DT H73 H 2.066 . . 51 7 7 DT H1' H 6.216 . . 52 7 7 DT H2' H 1.893 . . 53 7 7 DT H2'' H 2.359 . . 54 7 7 DT H3' H 4.851 . . 55 7 7 DT H4' H 4.282 . . 56 7 7 DT H6 H 7.594 . . 57 7 7 DT H71 H 2.040 . . 58 7 7 DT H72 H 2.040 . . 59 7 7 DT H73 H 2.040 . . 60 8 8 DA H1' H 6.611 . . 61 8 8 DA H2 H 8.345 . . 62 8 8 DA H2' H 3.142 . . 63 8 8 DA H2'' H 2.903 . . 64 8 8 DA H3' H 5.205 . . 65 8 8 DA H4' H 4.601 . . 66 8 8 DA H8 H 8.607 . . 67 9 9 DG H1 H 11.683 . . 68 9 9 DG H1' H 5.988 . . 69 9 9 DG H2' H 3.367 . . 70 9 9 DG H2'' H 3.026 . . 71 9 9 DG H3' H 5.084 . . 72 9 9 DG H4' H 4.430 . . 73 9 9 DG H8 H 7.339 . . 74 10 10 DG H1 H 12.104 . . 75 10 10 DG H1' H 5.878 . . 76 10 10 DG H2' H 2.534 . . 77 10 10 DG H2'' H 2.809 . . 78 10 10 DG H3' H 5.147 . . 79 10 10 DG H4' H 4.361 . . 80 10 10 DG H8 H 7.990 . . 81 11 11 DG H1 H 11.520 . . 82 11 11 DG H1' H 6.251 . . 83 11 11 DG H2' H 2.762 . . 84 11 11 DG H2'' H 2.604 . . 85 11 11 DG H3' H 5.108 . . 86 11 11 DG H4' H 4.547 . . 87 11 11 DG H8 H 8.011 . . 88 12 12 DT H1' H 6.250 . . 89 12 12 DT H2' H 2.410 . . 90 12 12 DT H2'' H 2.491 . . 91 12 12 DT H3' H 4.749 . . 92 12 12 DT H4' H 4.247 . . 93 12 12 DT H6 H 7.587 . . 94 12 12 DT H71 H 1.905 . . 95 12 12 DT H72 H 1.905 . . 96 12 12 DT H73 H 1.905 . . 97 13 13 DT H1' H 5.418 . . 98 13 13 DT H2' H 1.370 . . 99 13 13 DT H2'' H 2.124 . . 100 13 13 DT H3' H 4.535 . . 101 13 13 DT H4' H 3.961 . . 102 13 13 DT H6 H 6.706 . . 103 13 13 DT H71 H 1.443 . . 104 13 13 DT H72 H 1.443 . . 105 13 13 DT H73 H 1.443 . . 106 14 14 DA H1' H 6.329 . . 107 14 14 DA H2 H 7.424 . . 108 14 14 DA H2' H 2.335 . . 109 14 14 DA H2'' H 2.584 . . 110 14 14 DA H3' H 4.721 . . 111 14 14 DA H4' H 4.126 . . 112 14 14 DA H8 H 7.857 . . 113 15 15 DG H1 H 11.368 . . 114 15 15 DG H1' H 6.118 . . 115 15 15 DG H2' H 3.623 . . 116 15 15 DG H2'' H 3.108 . . 117 15 15 DG H3' H 4.912 . . 118 15 15 DG H4' H 4.516 . . 119 15 15 DG H8 H 7.304 . . 120 16 16 DG H1 H 11.259 . . 121 16 16 DG H1' H 5.769 . . 122 16 16 DG H2' H 2.562 . . 123 16 16 DG H2'' H 2.490 . . 124 16 16 DG H3' H 5.056 . . 125 16 16 DG H4' H 4.266 . . 126 16 16 DG H8 H 7.356 . . 127 17 17 DG H1 H 11.753 . . 128 17 17 DG H1' H 6.018 . . 129 17 17 DG H2' H 2.678 . . 130 17 17 DG H2'' H 2.621 . . 131 17 17 DG H3' H 5.204 . . 132 17 17 DG H4' H 4.444 . . 133 17 17 DG H8 H 7.709 . . 134 18 18 DT H1' H 6.375 . . 135 18 18 DT H2' H 2.363 . . 136 18 18 DT H2'' H 2.539 . . 137 18 18 DT H3' H 4.957 . . 138 18 18 DT H4' H 4.463 . . 139 18 18 DT H6 H 7.947 . . 140 18 18 DT H71 H 2.073 . . 141 18 18 DT H72 H 2.073 . . 142 18 18 DT H73 H 2.073 . . 143 19 19 DT H1' H 5.766 . . 144 19 19 DT H2' H 1.011 . . 145 19 19 DT H2'' H 1.757 . . 146 19 19 DT H3' H 4.718 . . 147 19 19 DT H4' H 4.204 . . 148 19 19 DT H6 H 7.259 . . 149 19 19 DT H71 H 1.540 . . 150 19 19 DT H72 H 1.540 . . 151 19 19 DT H73 H 1.540 . . 152 20 20 DA H1' H 6.117 . . 153 20 20 DA H2 H 8.032 . . 154 20 20 DA H2' H 2.922 . . 155 20 20 DA H2'' H 2.835 . . 156 20 20 DA H3' H 5.016 . . 157 20 20 DA H4' H 4.353 . . 158 20 20 DA H8 H 8.105 . . 159 21 21 DG H1 H 11.457 . . 160 21 21 DG H1' H 6.040 . . 161 21 21 DG H2' H 3.426 . . 162 21 21 DG H2'' H 2.967 . . 163 21 21 DG H3' H 4.999 . . 164 21 21 DG H4' H 4.465 . . 165 21 21 DG H8 H 7.342 . . 166 22 22 DG H1 H 11.967 . . 167 22 22 DG H1' H 5.794 . . 168 22 22 DG H2' H 2.570 . . 169 22 22 DG H2'' H 2.737 . . 170 22 22 DG H3' H 5.092 . . 171 22 22 DG H4' H 4.389 . . 172 22 22 DG H8 H 7.901 . . 173 23 23 DG H1 H 10.823 . . 174 23 23 DG H1' H 5.930 . . 175 23 23 DG H2' H 2.202 . . 176 23 23 DG H2'' H 2.523 . . 177 23 23 DG H3' H 4.961 . . 178 23 23 DG H4' H 4.408 . . 179 23 23 DG H8 H 7.544 . . 180 24 24 DA H1' H 6.151 . . 181 24 24 DA H2 H 7.559 . . 182 24 24 DA H2' H 2.658 . . 183 24 24 DA H2'' H 2.435 . . 184 24 24 DA H3' H 4.679 . . 185 24 24 DA H4' H 4.231 . . 186 24 24 DA H8 H 7.856 . . stop_ save_