data_27829 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Chemical shifts for intercalation complex between d(CGATATCG)2 and C-1305 ; _BMRB_accession_number 27829 _BMRB_flat_file_name bmr27829.str _Entry_type original _Submission_date 2019-03-06 _Accession_date 2019-03-06 _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 Andralojc Witold . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 3 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 109 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-08-03 update BMRB 'update entry citation' 2019-03-07 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 27828 'd(CGATATCG)2; free form' stop_ _Original_release_date 2019-03-06 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; A strong preference for the TA/TA dinucleotide step discovered for an acridine-based, potent antitumor dsDNA intercalator, C-1305: NMR-driven structural and sequence-specificity studies ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 32678133 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Laskowski Tomasz . . 2 Andralojc Witold . . 3 Grynda Jakub . . 4 Gwarda Paulina . . 5 Mazerski Jan . . 6 Gdaniec Zofia . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_name_full 'Scientific reports' _Journal_volume 10 _Journal_issue 1 _Journal_ISSN 2045-2322 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11697 _Page_last 11697 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'd(CGATATCG)2 : C-1305 complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA d(CGATATCG)2, chain A' $d(CGATATCG)2 'DNA d(CGATATCG)2, chain B' $d(CGATATCG)2 'ligand C1305' $C1305 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details ; The component C-1305 is: 5-[[3-(dimethylamino)propyl]amino]-8-hydroxy-6H-v-triazolo[4,5,1-de]acridin-6-one (C1305). ; save_ ######################## # Monomeric polymers # ######################## save_d(CGATATCG)2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common d(CGATATCG)2 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; CGATATCG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DA 4 DT 5 DA 6 DT 7 DC 8 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 $d(CGATATCG)2 . . . . . . 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 $d(CGATATCG)2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_complex _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $d(CGATATCG)2 1.25 mM 'natural abundance' (C1305) 1.5 mM 'natural abundance' cacodylate 2.5 mM 'natural abundance' 'sodium chloride' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.13 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _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 $complex 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' 0.01 . M pH 5.0 . pH pressure 1 . atm temperature 278 . 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 TSP H 1 'methyl protons' ppm 0.00 internal indirect . . . 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_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $complex stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA d(CGATATCG)2, chain A' _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 DC H1' H 5.682 0.01 1 2 1 1 DC H2' H 1.933 0.01 1 3 1 1 DC H2'' H 2.392 0.01 1 4 1 1 DC H3' H 4.705 0.01 1 5 1 1 DC H5 H 5.848 0.01 1 6 1 1 DC H6 H 7.616 0.01 1 7 2 2 DG H1' H 5.627 0.01 1 8 2 2 DG H2' H 2.717 0.01 1 9 2 2 DG H2'' H 2.760 0.01 1 10 2 2 DG H3' H 5.006 0.01 1 11 2 2 DG H8 H 7.920 0.01 1 12 3 3 DA H1' H 6.198 0.01 1 13 3 3 DA H2 H 7.758 0.01 1 14 3 3 DA H2' H 2.523 0.01 1 15 3 3 DA H2'' H 2.849 0.01 1 16 3 3 DA H3' H 4.972 0.01 1 17 3 3 DA H8 H 8.121 0.01 1 18 4 4 DT H1' H 6.023 0.01 1 19 4 4 DT H2' H 2.502 0.01 1 20 4 4 DT H2'' H 2.570 0.01 1 21 4 4 DT H3' H 4.995 0.01 1 22 4 4 DT H6 H 7.195 0.01 1 23 4 4 DT H71 H 1.239 0.01 1 24 4 4 DT H72 H 1.239 0.01 1 25 4 4 DT H73 H 1.239 0.01 1 26 5 5 DA H1' H 6.250 0.01 1 27 5 5 DA H2 H 7.116 0.01 1 28 5 5 DA H2' H 2.796 0.01 1 29 5 5 DA H2'' H 2.952 0.01 1 30 5 5 DA H3' H 5.003 0.01 1 31 5 5 DA H8 H 8.417 0.01 1 32 6 6 DT H1' H 5.908 0.01 1 33 6 6 DT H2' H 2.082 0.01 1 34 6 6 DT H2'' H 2.407 0.01 1 35 6 6 DT H3' H 4.857 0.01 1 36 6 6 DT H6 H 7.248 0.01 1 37 6 6 DT H71 H 1.197 0.01 1 38 6 6 DT H72 H 1.197 0.01 1 39 6 6 DT H73 H 1.197 0.01 1 40 7 7 DC H1' H 5.697 0.01 1 41 7 7 DC H2' H 1.972 0.01 1 42 7 7 DC H2'' H 2.377 0.01 1 43 7 7 DC H3' H 4.840 0.01 1 44 7 7 DC H5 H 5.622 0.01 1 45 7 7 DC H6 H 7.485 0.01 1 46 8 8 DG H1' H 6.153 0.01 1 47 8 8 DG H2' H 2.629 0.01 1 48 8 8 DG H2'' H 2.383 0.01 1 49 8 8 DG H3' H 4.699 0.01 1 50 8 8 DG H8 H 7.969 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $complex stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA d(CGATATCG)2, chain B' _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 DC H1' H 5.672 0.01 1 2 1 1 DC H2' H 1.933 0.01 1 3 1 1 DC H2'' H 2.392 0.01 1 4 1 1 DC H3' H 4.701 0.01 1 5 1 1 DC H5 H 5.848 0.01 1 6 1 1 DC H6 H 7.616 0.01 1 7 2 2 DG H1' H 5.527 0.01 1 8 2 2 DG H2' H 2.703 0.01 1 9 2 2 DG H2'' H 2.755 0.01 1 10 2 2 DG H3' H 5.004 0.01 1 11 2 2 DG H8 H 7.929 0.01 1 12 3 3 DA H1' H 6.218 0.01 1 13 3 3 DA H2 H 7.757 0.01 1 14 3 3 DA H2' H 2.596 0.01 1 15 3 3 DA H2'' H 2.924 0.01 1 16 3 3 DA H3' H 5.057 0.01 1 17 3 3 DA H8 H 8.224 0.01 1 18 4 4 DT H1' H 5.855 0.01 1 19 4 4 DT H2' H 2.326 0.01 1 20 4 4 DT H2'' H 2.397 0.01 1 21 4 4 DT H3' H 5.009 0.01 1 22 4 4 DT H6 H 7.192 0.01 1 23 4 4 DT H71 H 1.456 0.01 1 24 4 4 DT H72 H 1.456 0.01 1 25 4 4 DT H73 H 1.456 0.01 1 26 5 5 DA H1' H 6.156 0.01 1 27 5 5 DA H2 H 7.285 0.01 1 28 5 5 DA H2' H 2.751 0.01 1 29 5 5 DA H2'' H 2.932 0.01 1 30 5 5 DA H3' H 4.969 0.01 1 31 5 5 DA H8 H 8.454 0.01 1 32 6 6 DT H1' H 5.893 0.01 1 33 6 6 DT H2' H 2.098 0.01 1 34 6 6 DT H2'' H 2.459 0.01 1 35 6 6 DT H3' H 4.854 0.01 1 36 6 6 DT H6 H 7.242 0.01 1 37 6 6 DT H71 H 1.246 0.01 1 38 6 6 DT H72 H 1.246 0.01 1 39 6 6 DT H73 H 1.246 0.01 1 40 7 7 DC H1' H 5.697 0.01 1 41 7 7 DC H2' H 1.972 0.01 1 42 7 7 DC H2'' H 2.377 0.01 1 43 7 7 DC H3' H 4.840 0.01 1 44 7 7 DC H5 H 5.622 0.01 1 45 7 7 DC H6 H 7.485 0.01 1 46 8 8 DG H1' H 6.153 0.01 1 47 8 8 DG H2' H 2.629 0.01 1 48 8 8 DG H2'' H 2.383 0.01 1 49 8 8 DG H3' H 4.699 0.01 1 50 8 8 DG H8 H 7.969 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $complex stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'ligand C1305' _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 C1305 H3 H 6.968 0.01 1 2 1 1 C1305 H4 H 6.171 0.01 1 3 1 1 C1305 H7 H 6.396 0.01 1 4 1 1 C1305 H9 H 7.048 0.01 1 5 1 1 C1305 H10 H 7.820 0.01 1 6 1 1 C1305 H15 H 3.472 0.01 1 7 1 1 C1305 H16 H 2.114 0.01 1 8 1 1 C1305 H17 H 3.294 0.01 1 9 1 1 C1305 H18 H 2.987 0.01 1 stop_ save_