data_25724 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Universal base control oligonucleotide structure ; _BMRB_accession_number 25724 _BMRB_flat_file_name bmr25724.str _Entry_type original _Submission_date 2015-07-23 _Accession_date 2015-07-23 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Control DNA oligonucleotide for the universal base. This sequence contains a dA in place of the UB at position 5.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Spring-Connell Alexander M. . 2 Evich Marina G. . 3 Seela Frank . . 4 Germann Markus W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 133 "31P chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-10-20 update BMRB 'update entry citation' 2016-09-06 original author 'original release' stop_ _Original_release_date 2016-09-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27566150 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Spring-Connell Alexander M. . 2 Evich Marina G. . 3 Debelak Harald . . 4 Seela Frank . . 5 Germann Markus W. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 44 _Journal_issue 18 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8576 _Page_last 8587 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Control DNA oligonucleotide for the universal base' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')" $DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') "DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')" $DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 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(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') _Molecular_mass 2755.845 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence ; ATGGAGCTC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DA 2 2 DT 3 3 DG 4 4 DG 5 5 DA 6 6 DG 7 7 DC 8 8 DT 9 9 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') _Molecular_mass 2715.821 _Mol_thiol_state 'not present' _Details . _Residue_count 9 _Mol_residue_sequence ; GAGCTCCAT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 10 DG 2 11 DA 3 12 DG 4 13 DC 5 14 DT 6 15 DC 7 16 DC 8 17 DA 9 18 DT 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_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') . . . . . . $DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-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 _Details $DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') 'obtained from a vendor' . . . . . 'University of Calgary Core DNA Services' $DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 'obtained from a vendor' . . . . . 'University of Calgary Core DNA Services' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_D2O_samle _Saveframe_category sample _Sample_type solution _Details '100% D2O sample, pH* 6.36' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') 1 mM 'natural abundance' $DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM 'natural abundance' D2O 100 % 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ save_H2O_Sample _Saveframe_category sample _Sample_type solution _Details 'H2O sample' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') 1 mM 'natural abundance' $DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CORMA _Saveframe_category software _Name CORMA _Version . loop_ _Vendor _Address _Electronic_address 'Thomas James' . . stop_ loop_ _Task 'data analysis' refinement stop_ _Details . save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Thomas James' . . stop_ loop_ _Task 'data analysis' refinement 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 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_75_ms_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 75 ms' _Sample_label $D2O_samle save_ save_2D_Low_Flip_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Low Flip COSY' _Sample_label $D2O_samle save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $D2O_samle save_ save_2D_1H-1H_constant_time_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H constant time NOESY' _Sample_label $D2O_samle save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $D2O_samle save_ save_2D_1H-31P_CORR_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P CORR' _Sample_label $D2O_samle save_ save_1D_1H_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _Sample_label $D2O_samle save_ save_1D_1H_1-1_jump_and_return_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H 1-1 jump and return' _Sample_label $H2O_Sample save_ save_1D_31P_9 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 31P' _Sample_label $D2O_samle save_ save_2D_1H-1H_NOESY_150_ms_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 150 ms' _Sample_label $D2O_samle save_ save_2D_1H-1H_NOESY_250_ms_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY 250 ms' _Sample_label $D2O_samle save_ ####################### # Sample conditions # ####################### save_D2O_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH* 6.36 . pH pressure 1 . atm temperature 294 . K stop_ save_ save_H2O_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.79 . pH temperature 280 . 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 . . . 1.0 'phosphoric acid (85%)' P 31 P ppm 0 external 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_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-31P CORR' '2D 1H-1H NOESY 250 ms' stop_ loop_ _Sample_label $D2O_samle stop_ _Sample_conditions_label $D2O_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-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 DA H1' H 6.218 . 1 2 1 1 DA H2 H 7.992 . 1 3 1 1 DA H2' H 2.655 . 1 4 1 1 DA H2'' H 2.809 . 1 5 1 1 DA H3' H 4.874 . 1 6 1 1 DA H4' H 4.270 . 1 7 1 1 DA H5' H 3.781 . 1 8 1 1 DA H5'' H 3.781 . 1 9 1 1 DA H8 H 8.170 . 1 10 2 2 DT H1' H 5.611 . 1 11 2 2 DT H2' H 2.098 . 1 12 2 2 DT H2'' H 2.366 . 1 13 2 2 DT H3' H 4.853 . 1 14 2 2 DT H4' H 4.163 . 1 15 2 2 DT H6 H 7.321 . 1 16 2 2 DT H71 H 1.429 . 1 17 2 2 DT H72 H 1.429 . 1 18 2 2 DT H73 H 1.429 . 1 19 2 2 DT P P -0.678 . 1 20 3 3 DG H1' H 5.583 . 1 21 3 3 DG H2' H 2.647 . 1 22 3 3 DG H2'' H 2.728 . 1 23 3 3 DG H3' H 4.984 . 1 24 3 3 DG H4' H 4.337 . 1 25 3 3 DG H8 H 7.834 . 1 26 3 3 DG P P -0.236 . 1 27 4 4 DG H1' H 5.555 . 1 28 4 4 DG H2' H 2.608 . 1 29 4 4 DG H2'' H 2.745 . 1 30 4 4 DG H3' H 5.014 . 1 31 4 4 DG H4' H 4.375 . 1 32 4 4 DG H8 H 7.762 . 1 33 4 4 DG P P -0.319 . 1 34 5 5 DA H1' H 6.079 . 1 35 5 5 DA H2 H 7.699 . 1 36 5 5 DA H2' H 2.647 . 1 37 5 5 DA H2'' H 2.904 . 1 38 5 5 DA H3' H 5.051 . 1 39 5 5 DA H4' H 4.434 . 1 40 5 5 DA H8 H 8.053 . 1 41 5 5 DA P P -0.484 . 1 42 6 6 DG H1' H 5.708 . 1 43 6 6 DG H2' H 2.514 . 1 44 6 6 DG H2'' H 2.592 . 1 45 6 6 DG H3' H 4.944 . 1 46 6 6 DG H4' H 4.375 . 1 47 6 6 DG H8 H 7.607 . 1 48 6 6 DG P P -0.638 . 1 49 7 7 DC H1' H 5.880 . 1 50 7 7 DC H2' H 2.094 . 1 51 7 7 DC H2'' H 2.493 . 1 52 7 7 DC H3' H 4.661 . 1 53 7 7 DC H4' H 4.197 . 1 54 7 7 DC H5 H 5.205 . 1 55 7 7 DC H6 H 7.369 . 1 56 7 7 DC P P -0.298 . 1 57 8 8 DT H1' H 6.154 . 1 58 8 8 DT H2' H 2.210 . 1 59 8 8 DT H2'' H 2.544 . 1 60 8 8 DT H3' H 4.884 . 1 61 8 8 DT H4' H 4.193 . 1 62 8 8 DT H6 H 7.533 . 1 63 8 8 DT H71 H 1.646 . 1 64 8 8 DT H72 H 1.646 . 1 65 8 8 DT H73 H 1.646 . 1 66 8 8 DT P P -0.831 . 1 67 9 9 DC H1' H 6.292 . 1 68 9 9 DC H2' H 2.285 . 1 69 9 9 DC H2'' H 2.285 . 1 70 9 9 DC H3' H 4.587 . 1 71 9 9 DC H4' H 4.030 . 1 72 9 9 DC H5 H 5.811 . 1 73 9 9 DC H6 H 7.670 . 1 74 9 9 DC P P -0.425 . 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-31P CORR' '2D 1H-1H NOESY 250 ms' stop_ loop_ _Sample_label $D2O_samle stop_ _Sample_conditions_label $D2O_conditions _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-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 10 1 DG H1' H 5.570 . 1 2 10 1 DG H2' H 2.509 . 1 3 10 1 DG H2'' H 2.704 . 1 4 10 1 DG H3' H 4.841 . 1 5 10 1 DG H4' H 4.171 . 1 6 10 1 DG H5' H 3.675 . 1 7 10 1 DG H5'' H 3.675 . 1 8 10 1 DG H8 H 7.885 . 1 9 11 2 DA H1' H 6.088 . 1 10 11 2 DA H2 H 7.854 . 1 11 11 2 DA H2' H 2.772 . 1 12 11 2 DA H2'' H 2.921 . 1 13 11 2 DA H3' H 5.067 . 1 14 11 2 DA H4' H 4.438 . 1 15 11 2 DA H8 H 8.190 . 1 16 11 2 DA P P -0.482 . 1 17 12 3 DG H1' H 5.794 . 1 18 12 3 DG H2' H 2.563 . 1 19 12 3 DG H2'' H 2.634 . 1 20 12 3 DG H3' H 4.979 . 1 21 12 3 DG H4' H 4.420 . 1 22 12 3 DG H8 H 7.683 . 1 23 12 3 DG P P -0.607 . 1 24 13 4 DC H1' H 5.895 . 1 25 13 4 DC H2' H 2.083 . 1 26 13 4 DC H2'' H 2.511 . 1 27 13 4 DC H3' H 4.673 . 1 28 13 4 DC H4' H 4.236 . 1 29 13 4 DC H5 H 5.214 . 1 30 13 4 DC H6 H 7.377 . 1 31 13 4 DC P P -0.341 . 1 32 14 5 DT H1' H 6.091 . 1 33 14 5 DT H2' H 2.225 . 1 34 14 5 DT H2'' H 2.570 . 1 35 14 5 DT H3' H 4.882 . 1 36 14 5 DT H4' H 4.235 . 1 37 14 5 DT H6 H 7.480 . 1 38 14 5 DT H71 H 1.570 . 1 39 14 5 DT H72 H 1.570 . 1 40 14 5 DT H73 H 1.570 . 1 41 14 5 DT P P -0.863 . 1 42 15 6 DC H1' H 5.922 . 1 43 15 6 DC H2' H 2.146 . 1 44 15 6 DC H2'' H 2.429 . 1 45 15 6 DC H3' H 4.835 . 1 46 15 6 DC H4' H 4.166 . 1 47 15 6 DC H5 H 5.654 . 1 48 15 6 DC H6 H 7.552 . 1 49 15 6 DC P P -0.684 . 1 50 16 7 DC H1' H 5.502 . 1 51 16 7 DC H2' H 1.984 . 1 52 16 7 DC H2'' H 2.338 . 1 53 16 7 DC H3' H 4.817 . 1 54 16 7 DC H4' H 4.104 . 1 55 16 7 DC H5 H 5.662 . 1 56 16 7 DC H6 H 7.470 . 1 57 16 7 DC P P -0.383 . 1 58 17 8 DA H1' H 6.308 . 1 59 17 8 DA H2 H 7.884 . 1 60 17 8 DA H2' H 2.775 . 1 61 17 8 DA H2'' H 2.872 . 1 62 17 8 DA H3' H 5.013 . 1 63 17 8 DA H4' H 4.406 . 1 64 17 8 DA H8 H 8.328 . 1 65 17 8 DA P P -0.280 . 1 66 18 9 DT H1' H 6.116 . 1 67 18 9 DT H2' H 2.161 . 1 68 18 9 DT H2'' H 2.161 . 1 69 18 9 DT H3' H 4.519 . 1 70 18 9 DT H4' H 4.024 . 1 71 18 9 DT H6 H 7.285 . 1 72 18 9 DT H71 H 1.561 . 1 73 18 9 DT H72 H 1.561 . 1 74 18 9 DT H73 H 1.561 . 1 75 18 9 DT P P -0.607 . 1 stop_ save_