data_25915 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Photoswitchable G-quadruplex ; _BMRB_accession_number 25915 _BMRB_flat_file_name bmr25915.str _Entry_type original _Submission_date 2015-12-02 _Accession_date 2015-12-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Tetramolecular G-quadruplex motif with a photoresponsive azobenzene linker' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thevarpadam Julie . . 2 Bessi Irene . . 3 Binas Oliver . . 4 Goncalves Diana PN . 5 Slavov Chavdar . . 6 Jonker Hendrik RA . 7 Richter Christian . . 8 Wachtveitl Josef . . 9 Schwalbe Harald . . 10 Heckel Alexander . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 48 "13C chemical shifts" 34 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-07-22 update BMRB 'update entry citation' 2016-02-15 original author 'original release' stop_ _Original_release_date 2016-02-15 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Photoresponsive formation of an intermolecular minimal G-quadruplex motif ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26805928 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thevarpadam Julie . . 2 Bessi Irene . . 3 Binas Oliver . . 4 Goncalves Diana PN . 5 Slavov Chavdar . . 6 Jonker Hendrik RA . 7 Richter Christian . . 8 Wachtveitl Josef . . 9 Schwalbe Harald . . 10 Heckel Alexander . . stop_ _Journal_abbreviation 'Angew. Chem. Int. Ed.' _Journal_volume 55 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2738 _Page_last 2742 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Photoswitchable G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')_1" $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') "DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')_2" $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') "DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')_3" $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') "DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')_4" $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') 'POTASSIUM ION_1' $entity_K 'POTASSIUM ION_2' $entity_K 'POTASSIUM ION_3' $entity_K 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_(5'-D(*GP*GP*(AZW)P*GP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') _Molecular_mass 1252.861 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 5 _Mol_residue_sequence ; GGXGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 AZW 4 DG 5 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_AZW _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common '4-{(E)-[4-(hydroxymethyl)phenyl]diazenyl}benzyl dihydrogen phosphate' _BMRB_code AZW _PDB_code AZW _Standard_residue_derivative . _Molecular_mass 322.253 _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 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C1A C1A C . 0 . ? C2A C2A C . 0 . ? C6A C6A C . 0 . ? C3A C3A C . 0 . ? C5A C5A C . 0 . ? C4A C4A C . 0 . ? N5A N5A N . 0 . ? C1B C1B C . 0 . ? C2B C2B C . 0 . ? C6B C6B C . 0 . ? C3B C3B C . 0 . ? C5B C5B C . 0 . ? C4B C4B C . 0 . ? N5B N5B N . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? H2 H2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H2A H2A H . 0 . ? H6A H6A H . 0 . ? H3A H3A H . 0 . ? H5A H5A H . 0 . ? H2B H2B H . 0 . ? H6B H6B H . 0 . ? H3B H3B H . 0 . ? H5B H5B H . 0 . ? H3' H3' H . 0 . ? H3'' H3'' H . 0 . ? H3 H3 H . 0 . ? OP3 OP3 O . 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 OP1 P ? ? SING P OP2 ? ? SING P O5' ? ? SING C5' O5' ? ? SING C5' C1A ? ? DOUB C2A C1A ? ? SING C2A C3A ? ? SING C1A C6A ? ? DOUB C3A C4A ? ? DOUB C6A C5A ? ? SING C4A C5A ? ? SING C4A N5A ? ? DOUB N5B N5A ? ? SING N5B C4B ? ? DOUB C3B C4B ? ? SING C3B C2B ? ? SING C4B C5B ? ? DOUB C2B C1B ? ? DOUB C5B C6B ? ? SING C1B C6B ? ? SING C1B C3' ? ? SING O3' C3' ? ? SING OP2 H2 ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C2A H2A ? ? SING C6A H6A ? ? SING C3A H3A ? ? SING C5A H5A ? ? SING C2B H2B ? ? SING C6B H6B ? ? SING C3B H3B ? ? SING C5B H5B ? ? SING C3' H3' ? ? SING C3' H3'' ? ? SING O3' H3 ? ? SING P OP3 ? ? SING OP3 HOP3 ? ? stop_ save_ ############# # Ligands # ############# save_K _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_K (POTASSIUM ION)" _BMRB_code K _PDB_code K _Molecular_mass 39.098 _Mol_charge 1 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons K K K . 1 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_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_(5'-D(*GP*GP*(AZW)P*GP*G)-3') . . . . . . 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_(5'-D(*GP*GP*(AZW)P*GP*G)-3') 'DNA solid-phase synthesis' . not applicable . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_H2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') 550 uM 'natural abundance' Tris-HCl 25 mM 'natural abundance' KCl 50 mM 'natural abundance' stop_ save_ save_sample_D2O _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*GP*GP*(AZW)P*GP*G)-3') 550 uM 'natural abundance' Tris-HCl 25 mM 'natural abundance' KCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version 1.2 loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details 'development version' save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 3.2 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details 'CryoProbe 1H,13C,15N' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_D2O save_ save_2D_1H-13C_HMBC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _Sample_label $sample_H2O save_ save_2D_1H-31P_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P TOCSY' _Sample_label $sample_D2O save_ save_2D_1H-1H_P.E._COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H P.E. COSY' _Sample_label $sample_D2O save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_H2O save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_D2O save_ ####################### # Sample conditions # ####################### save_sample_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 71 . mM pH 7.4 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-13C HSQC' '2D 1H-13C HMBC' '2D 1H-1H P.E. COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_D2O $sample_H2O stop_ _Sample_conditions_label $sample_conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name "DNA (5'-D(*GP*GP*(AZW)P*GP*G)-3')_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 11.54 0.02 1 2 1 1 DG H1' H 5.78 0.02 1 3 1 1 DG H2' H 3.12 0.02 2 4 1 1 DG H2'' H 2.78 0.02 2 5 1 1 DG H3' H 4.92 0.02 1 6 1 1 DG H4' H 4.48 0.02 1 7 1 1 DG H5' H 3.98 0.02 2 8 1 1 DG H5'' H 4.03 0.02 2 9 1 1 DG H8 H 6.88 0.02 1 10 1 1 DG C1' C 86.53 0.05 1 11 1 1 DG C2' C 34.25 0.05 1 12 1 1 DG C3' C 78.50 0.05 1 13 1 1 DG C4' C 87.42 0.05 1 14 1 1 DG C5' C 62.72 0.05 1 15 1 1 DG C8 C 138.01 0.05 1 16 2 2 DG H1 H 11.67 0.02 1 17 2 2 DG H1' H 5.40 0.02 1 18 2 2 DG H2' H 2.67 0.02 2 19 2 2 DG H2'' H 2.80 0.02 2 20 2 2 DG H3' H 5.06 0.02 1 21 2 2 DG H4' H 4.47 0.02 1 22 2 2 DG H5' H 4.14 0.02 2 23 2 2 DG H5'' H 4.23 0.02 2 24 2 2 DG H8 H 8.27 0.02 1 25 2 2 DG C1' C 80.96 0.05 1 26 2 2 DG C2' C 37.01 0.05 1 27 2 2 DG C3' C 77.36 0.05 1 28 2 2 DG C4' C 84.70 0.05 1 29 2 2 DG C5' C 65.69 0.05 1 30 2 2 DG C8 C 136.08 0.05 1 31 3 3 AZW C2A C 126.50 0.05 3 32 3 3 AZW C6A C 126.50 0.05 3 33 3 3 AZW C2B C 126.98 0.05 3 34 3 3 AZW C6B C 126.98 0.05 3 35 3 3 AZW C3' C 66.19 0.05 1 36 3 3 AZW C3A C 122.64 0.05 3 37 3 3 AZW C5A C 122.64 0.05 3 38 3 3 AZW C3B C 121.67 0.05 3 39 3 3 AZW C5B C 121.67 0.05 3 40 3 3 AZW C5' C 66.54 0.05 1 41 3 3 AZW H2A H 7.46 0.02 3 42 3 3 AZW H6A H 7.46 0.02 3 43 3 3 AZW H2B H 7.06 0.02 3 44 3 3 AZW H6B H 7.06 0.02 3 45 3 3 AZW H3' H 4.97 0.02 2 46 3 3 AZW H3'' H 4.64 0.02 2 47 3 3 AZW H3A H 7.57 0.02 3 48 3 3 AZW H5A H 7.57 0.02 3 49 3 3 AZW H3B H 7.24 0.02 3 50 3 3 AZW H5B H 7.24 0.02 3 51 3 3 AZW H5' H 5.25 0.02 2 52 3 3 AZW H5'' H 5.07 0.02 2 53 4 4 DG H1 H 11.39 0.02 1 54 4 4 DG H1' H 6.00 0.02 1 55 4 4 DG H2' H 3.22 0.02 2 56 4 4 DG H2'' H 2.73 0.02 2 57 4 4 DG H3' H 4.80 0.02 1 58 4 4 DG H4' H 4.51 0.02 1 59 4 4 DG H5' H 4.18 0.02 2 60 4 4 DG H5'' H 4.73 0.02 2 61 4 4 DG H8 H 7.24 0.02 1 62 4 4 DG C1' C 86.75 0.05 1 63 4 4 DG C2' C 32.64 0.05 1 64 4 4 DG C3' C 77.64 0.05 1 65 4 4 DG C4' C 86.20 0.05 1 66 4 4 DG C5' C 67.54 0.05 1 67 4 4 DG C8 C 139.01 0.05 1 68 5 5 DG H1 H 11.43 0.02 1 69 5 5 DG H1' H 5.99 0.02 1 70 5 5 DG H2' H 2.56 0.02 2 71 5 5 DG H2'' H 2.27 0.02 2 72 5 5 DG H3' H 4.78 0.02 1 73 5 5 DG H4' H 4.17 0.02 1 74 5 5 DG H5' H 4.17 0.02 2 75 5 5 DG H5'' H 4.29 0.02 2 76 5 5 DG H8 H 7.44 0.02 1 77 5 5 DG C1' C 80.92 0.05 1 78 5 5 DG C2' C 38.98 0.05 1 79 5 5 DG C3' C 69.36 0.05 1 80 5 5 DG C4' C 84.53 0.05 1 81 5 5 DG C5' C 63.89 0.05 1 82 5 5 DG C8 C 136.13 0.05 1 stop_ save_