data_19440 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of DNA duplex ; _BMRB_accession_number 19440 _BMRB_flat_file_name bmr19440.str _Entry_type original _Submission_date 2013-08-20 _Accession_date 2013-08-20 _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 Brzezinska Jolanta . . 2 Gdaniec Zofia . . 3 Popenda Lukasz . . 4 Markiewicz Wojciech T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 4 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 160 "31P chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-03 update BMRB 'update entry citation' 2014-01-23 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 19441 'spermine modified DNA duplex' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24361616 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Brzezinska Jolanta . . 2 Gdaniec Zofia . . 3 Popenda Lukasz . . 4 Markiewicz Wojciech T. . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1840 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1163 _Page_last 1170 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'N-[4,9,13-triazatridecan-1-yl]-2-deoxycytidine modified duplex DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3')' $DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 'DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3')' $DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-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(*GP*TP*CP*GP*GP*CP*TP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') _Molecular_mass 2458.635 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence GTCGGCTG loop_ _Residue_seq_code _Residue_label 1 DG 2 DT 3 DC 4 DG 5 DG 6 DC 7 DT 8 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') _Molecular_mass 2396.614 _Mol_thiol_state 'not present' _Details . _Residue_count 8 _Mol_residue_sequence CAGCCGAC loop_ _Residue_seq_code _Residue_label 1 DC 2 DA 3 DG 4 DC 5 DC 6 DG 7 DA 8 DC 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(*GP*TP*CP*GP*GP*CP*TP*G)-3') . . . . . . $DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-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(*GP*TP*CP*GP*GP*CP*TP*G)-3') 'chemical synthesis' . . . . . 'synthesized using phosphoramidite chemistry' $DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 'chemical synthesis' . . . . . 'synthesized using phosphoramidite chemistry' 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_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM 'natural abundance' $DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 0.5 mM 'natural abundance' D2O 100 % '[U-100% 2H]' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM '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_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM 'natural abundance' $DNA_(5'-D(*CP*AP*GP*CP*CP*GP*AP*C)-3') 0.5 mM 'natural abundance' D2O 10 % '[U-100% 2H]' H2O 90 % 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version v2.22 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version v2.0 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version v2002 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . 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 . 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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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 7.0 . pH pressure 1 . atm 'ionic strength' 60 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 283 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 60 . mM 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 TMP P 31 phosphorus ppm 0.00 internal indirect . . . 0.404808636 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' '2D 1H-1H TOCSY' '2D 1H-31P HSQC' 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 'DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-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 DG H1' H 6.00 0.01 1 2 1 1 DG H2' H 2.72 0.01 2 3 1 1 DG H2'' H 2.79 0.01 2 4 1 1 DG H3' H 4.81 0.01 1 5 1 1 DG H4' H 4.23 0.01 1 6 1 1 DG H5' H 3.88 0.01 2 7 1 1 DG H5'' H 3.79 0.01 2 8 1 1 DG H8 H 7.95 0.01 1 9 2 2 DT H1' H 6.16 0.01 1 10 2 2 DT H2' H 2.24 0.01 2 11 2 2 DT H2'' H 2.56 0.01 2 12 2 2 DT H3' H 4.92 0.01 1 13 2 2 DT H4' H 4.31 0.01 1 14 2 2 DT H5' H 4.15 0.01 2 15 2 2 DT H5'' H 4.15 0.01 2 16 2 2 DT H6 H 7.51 0.01 1 17 2 2 DT P P -1.39 0.01 1 18 3 3 DC H1' H 5.70 0.01 1 19 3 3 DC H2' H 2.00 0.01 2 20 3 3 DC H2'' H 2.41 0.01 2 21 3 3 DC H3' H 4.86 0.01 1 22 3 3 DC H4' H 4.13 0.01 1 23 3 3 DC H5 H 5.64 0.01 1 24 3 3 DC H5' H 4.01 0.01 2 25 3 3 DC H5'' H 4.01 0.01 2 26 3 3 DC H6 H 7.46 0.01 1 27 3 3 DC P P -1.28 0.01 1 28 4 4 DG H1' H 5.63 0.01 1 29 4 4 DG H2' H 2.70 0.01 2 30 4 4 DG H2'' H 2.75 0.01 2 31 4 4 DG H3' H 5.01 0.01 1 32 4 4 DG H4' H 4.35 0.01 1 33 4 4 DG H5' H 4.11 0.01 2 34 4 4 DG H5'' H 4.01 0.01 2 35 4 4 DG H8 H 7.90 0.01 1 36 4 4 DG P P -0.97 0.01 1 37 5 5 DG H1' H 5.94 0.01 1 38 5 5 DG H2' H 2.62 0.01 2 39 5 5 DG H2'' H 2.73 0.01 2 40 5 5 DG H3' H 4.98 0.01 1 41 5 5 DG H4' H 4.42 0.01 1 42 5 5 DG H5' H 4.20 0.01 2 43 5 5 DG H5'' H 4.18 0.01 2 44 5 5 DG H8 H 7.77 0.01 1 45 5 5 DG P P -1.03 0.01 1 46 6 6 DC H1' H 5.93 0.01 1 47 6 6 DC H2' H 2.01 0.01 2 48 6 6 DC H2'' H 2.47 0.01 2 49 6 6 DC H3' H 4.77 0.01 1 50 6 6 DC H4' H 4.18 0.01 1 51 6 6 DC H5 H 5.32 0.01 1 52 6 6 DC H5' H 4.23 0.01 2 53 6 6 DC H5'' H 4.11 0.01 2 54 6 6 DC H6 H 7.39 0.01 1 55 6 6 DC P P -1.15 0.01 1 56 7 7 DT H1' H 5.88 0.01 1 57 7 7 DT H2' H 1.99 0.01 2 58 7 7 DT H2'' H 2.39 0.01 2 59 7 7 DT H3' H 4.85 0.01 1 60 7 7 DT H4' H 4.13 0.01 1 61 7 7 DT H5' H 4.07 0.01 2 62 7 7 DT H5'' H 4.02 0.01 2 63 7 7 DT H6 H 7.34 0.01 1 64 7 7 DT P P -1.31 0.01 1 65 8 8 DG H1' H 6.17 0.01 1 66 8 8 DG H2' H 2.66 0.01 2 67 8 8 DG H2'' H 2.37 0.01 2 68 8 8 DG H3' H 4.70 0.01 1 69 8 8 DG H4' H 4.17 0.01 1 70 8 8 DG H5' H 4.08 0.01 2 71 8 8 DG H5'' H 4.08 0.01 2 72 8 8 DG H8 H 7.92 0.01 1 73 8 8 DG P P -1.04 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' '2D 1H-1H TOCSY' '2D 1H-31P HSQC' 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 'DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*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 DC H1' H 5.62 0.01 1 2 1 1 DC H2' H 1.82 0.01 2 3 1 1 DC H2'' H 2.32 0.01 2 4 1 1 DC H3' H 4.68 0.01 1 5 1 1 DC H4' H 4.04 0.01 1 6 1 1 DC H5 H 5.96 0.01 1 7 1 1 DC H5' H 3.71 0.01 2 8 1 1 DC H5'' H 3.69 0.01 2 9 1 1 DC H6 H 7.68 0.01 1 10 2 2 DA H1' H 5.98 0.01 1 11 2 2 DA H2 H 7.86 0.01 1 12 2 2 DA H2' H 2.80 0.01 2 13 2 2 DA H2'' H 2.90 0.01 2 14 2 2 DA H3' H 5.04 0.01 1 15 2 2 DA H4' H 4.38 0.01 1 16 2 2 DA H5' H 4.11 0.01 2 17 2 2 DA H5'' H 3.97 0.01 2 18 2 2 DA H8 H 8.28 0.01 1 19 2 2 DA P P -1.03 0.01 1 20 3 3 DG H1' H 5.80 0.01 1 21 3 3 DG H2' H 2.58 0.01 2 22 3 3 DG H2'' H 2.64 0.01 2 23 3 3 DG H3' H 4.98 0.01 1 24 3 3 DG H4' H 4.41 0.01 1 25 3 3 DG H5' H 4.21 0.01 2 26 3 3 DG H5'' H 4.21 0.01 2 27 3 3 DG H8 H 7.76 0.01 1 28 3 3 DG P P -1.16 0.01 1 29 4 4 DC H1' H 5.96 0.01 1 30 4 4 DC H2' H 2.04 0.01 2 31 4 4 DC H2'' H 2.45 0.01 2 32 4 4 DC H3' H 4.80 0.01 1 33 4 4 DC H4' H 4.22 0.01 1 34 4 4 DC H5 H 5.26 0.01 1 35 4 4 DC H5' H 4.16 0.01 2 36 4 4 DC H5'' H 4.05 0.01 2 37 4 4 DC H6 H 7.35 0.01 1 38 4 4 DC P P -1.08 0.01 1 39 5 5 DC H1' H 5.49 0.01 1 40 5 5 DC H2' H 1.99 0.01 2 41 5 5 DC H2'' H 2.33 0.01 2 42 5 5 DC H3' H 4.82 0.01 1 43 5 5 DC H4' H 4.07 0.01 1 44 5 5 DC H5 H 5.56 0.01 1 45 5 5 DC H5' H 4.17 0.01 2 46 5 5 DC H5'' H 4.17 0.01 2 47 5 5 DC H6 H 7.41 0.01 1 48 5 5 DC P P -1.19 0.01 1 49 6 6 DG H1' H 5.61 0.01 1 50 6 6 DG H2' H 2.71 0.01 2 51 6 6 DG H2'' H 2.77 0.01 2 52 6 6 DG H3' H 5.00 0.01 1 53 6 6 DG H4' H 4.35 0.01 1 54 6 6 DG H5' H 4.02 0.01 2 55 6 6 DG H5'' H 4.02 0.01 2 56 6 6 DG H8 H 7.91 0.01 1 57 6 6 DG P P -0.91 0.01 1 58 7 7 DA H1' H 6.27 0.01 1 59 7 7 DA H2 H 7.98 0.01 1 60 7 7 DA H2' H 2.64 0.01 2 61 7 7 DA H2'' H 2.88 0.01 2 62 7 7 DA H3' H 5.00 0.01 1 63 7 7 DA H4' H 4.44 0.01 1 64 7 7 DA H5' H 4.24 0.01 2 65 7 7 DA H5'' H 4.22 0.01 2 66 7 7 DA H8 H 8.16 0.01 1 67 7 7 DA P P -1.11 0.01 1 68 8 8 DC H1' H 6.03 0.01 1 69 8 8 DC H2' H 2.07 0.01 2 70 8 8 DC H2'' H 2.13 0.01 2 71 8 8 DC H3' H 4.46 0.01 1 72 8 8 DC H4' H 4.00 0.01 1 73 8 8 DC H5 H 5.32 0.01 1 74 8 8 DC H5' H 4.27 0.01 2 75 8 8 DC H5'' H 4.05 0.01 2 76 8 8 DC H6 H 7.31 0.01 1 77 8 8 DC P P -1.12 0.01 1 stop_ save_ save_assigned_chem_shift_list_2_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-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 2 2 DT H3 H 13.99 0.01 1 2 2 2 DT H71 H 1.35 0.01 1 3 2 2 DT H72 H 1.35 0.01 1 4 2 2 DT H73 H 1.35 0.01 1 5 3 3 DC H41 H 8.63 0.01 2 6 3 3 DC H42 H 7.06 0.01 2 7 4 4 DG H1 H 13.14 0.01 1 8 5 5 DG H1 H 13.02 0.01 1 9 6 6 DC H41 H 8.25 0.01 2 10 6 6 DC H42 H 6.69 0.01 2 11 7 7 DT H3 H 14.19 0.01 1 12 7 7 DT H71 H 1.68 0.01 1 13 7 7 DT H72 H 1.68 0.01 1 14 7 7 DT H73 H 1.68 0.01 1 stop_ save_ save_assigned_chem_shift_list_2_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA (5'-D(*CP*AP*GP*CP*CP*GP*AP*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 DC H41 H 8.50 0.01 2 2 1 1 DC H42 H 7.50 0.01 2 3 3 3 DG H1 H 12.90 0.01 1 4 4 4 DC H41 H 8.16 0.01 2 5 4 4 DC H42 H 6.42 0.01 2 6 5 5 DC H41 H 8.59 0.01 2 7 5 5 DC H42 H 6.92 0.01 2 8 6 6 DG H1 H 12.93 0.01 1 9 8 8 DC H41 H 8.17 0.01 2 10 8 8 DC H42 H 6.43 0.01 2 stop_ save_