data_16286 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; d(CGAGCTCG)2 assignments ; _BMRB_accession_number 16286 _BMRB_flat_file_name bmr16286.str _Entry_type original _Submission_date 2009-05-07 _Accession_date 2009-05-07 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details '1H assignments for d(CGAGCTCG)2' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Waywell Phil . . 2 Thomas James A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 46 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2010-01-28 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16280 'shorter oligo' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural analysis of the binding of the diquaternary pyridophenazine derivative dqdppn to B-DNA oligonucleotides.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20090983 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Waywell Philip . . 2 Thomas James A. . 3 Williamson Mike P. . stop_ _Journal_abbreviation 'Org. Biomol. Chem.' _Journal_name_full 'Organic & biomolecular chemistry' _Journal_volume 8 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 648 _Page_last 654 _Year 2010 _Details . loop_ _Keyword intercalation 'major groove' 'induced CD' 'chemical shift' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name d(CGAGCTCG)2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label d(CGAGCTCG),1 $d(CGAGCTCG)2 d(CGAGCTCG),2 $d(CGAGCTCG)2 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_d(CGAGCTCG)2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common d(CGAGCTCG)2 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence CGAGCTCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DA 4 DG 5 DC 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(CGAGCTCG)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(CGAGCTCG)2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details 'DNA only' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $d(CGAGCTCG)2 2 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name Felix _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_1 save_ save_2D_31P-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 31P-1H COSY' _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 temperature 298 . K pH 7 . pH pressure 1 . atm 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 0.00 internal direct . . . 1.000000000 'sodium phosphate' P 31 phosphorus ppm 0.00 internal direct . . . 1.00000 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 DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '2D 31P-1H COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name d(CGAGCTCG),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 DC H1' H 5.63 0.02 1 2 1 1 DC H2' H 1.75 0.02 2 3 1 1 DC H2'' H 2.24 0.02 2 4 1 1 DC H3' H 4.59 0.02 1 5 1 1 DC H5 H 5.82 0.02 1 6 1 1 DC H6 H 7.51 0.02 1 7 1 1 DC P P -0.97 0.02 1 8 2 2 DG H1' H 5.28 0.02 1 9 2 2 DG H2' H 2.60 0.02 2 10 2 2 DG H2'' H 2.67 0.02 2 11 2 2 DG H3' H 4.88 0.02 1 12 2 2 DG H8 H 7.86 0.02 1 13 2 2 DG P P -0.94 0.02 1 14 3 3 DA H1' H 6.03 0.02 1 15 3 3 DA H2' H 2.63 0.02 2 16 3 3 DA H2'' H 2.84 0.02 2 17 3 3 DA H3' H 4.98 0.02 1 18 3 3 DA H8 H 8.04 0.02 1 19 3 3 DA P P -1.07 0.02 1 20 4 4 DG H1' H 5.65 0.02 1 21 4 4 DG H2' H 2.44 0.02 2 22 4 4 DG H2'' H 2.52 0.02 2 23 4 4 DG H3' H 4.86 0.02 1 24 4 4 DG H8 H 7.55 0.02 1 25 4 4 DG P P -0.96 0.02 1 26 5 5 DC H1' H 5.77 0.02 1 27 5 5 DC H2' H 1.95 0.02 2 28 5 5 DC H2'' H 2.40 0.02 2 29 5 5 DC H3' H 4.57 0.02 1 30 5 5 DC H5 H 5.11 0.02 1 31 5 5 DC H6 H 7.26 0.02 1 32 5 5 DC P P -1.16 0.02 1 33 6 6 DT H1' H 5.99 0.02 1 34 6 6 DT H2' H 2.05 0.02 2 35 6 6 DT H2'' H 2.39 0.02 2 36 6 6 DT H3' H 4.77 0.02 1 37 6 6 DT H6 H 7.39 0.02 1 38 6 6 DT H71 H 1.51 0.02 1 39 6 6 DT H72 H 1.51 0.02 1 40 6 6 DT H73 H 1.51 0.02 1 41 6 6 DT P P -1.09 0.02 1 42 7 7 DC H1' H 5.59 0.02 1 43 7 7 DC H2' H 1.93 0.02 1 44 7 7 DC H2'' H 2.26 0.02 1 45 7 7 DC H3' H 4.75 0.02 1 46 7 7 DC H5 H 5.65 0.02 1 47 7 7 DC H6 H 7.42 0.02 1 48 7 7 DC P P -0.87 0.02 1 49 8 8 DG H1' H 6.07 0.02 1 50 8 8 DG H2' H 2.27 0.02 2 51 8 8 DG H2'' H 2.53 0.02 2 52 8 8 DG H3' H 4.60 0.02 1 53 8 8 DG H8 H 7.87 0.02 1 stop_ save_