data_50278 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Canonical and modified dsDNA 12mers ; _BMRB_accession_number 50278 _BMRB_flat_file_name bmr50278.str _Entry_type original _Submission_date 2020-05-17 _Accession_date 2020-05-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details ; Data deposition for manuscript: Impact of 5-Formylcytosine on the Melting Kineticsof DNA by 1H NMR Chemical Exchange. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dubini 'Romeo Cosimo Arrigo' . . 2 Schon Alexander . . 3 Muller Markus . . 4 Carell Thomas . . 5 Rovo Petra . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 159 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-06-30 original BMRB . stop_ _Original_release_date 2020-05-18 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Impact of 5-Formylcytosine on the Melting Kineticsof DNA by 1H NMR Chemical Exchange ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Dubini 'Romeo Cosimo Arrigo' . . 2 Schon Alexander . . 3 Muller Markus . . 4 Carell Thomas . . 5 Rovo Petra . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name dsDNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Mod12 dsDNA' $entity_1 'Can12 dsDNA' $entity_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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'Mod12 dsDNA' _Molecular_mass . _Mol_thiol_state 'not present' _Details 'The residue 6 is: 5-formylcytosine, whose consensus abbreviation is 5fC.' ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; GCGATXGATCGC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DT 6 5FC 7 DG 8 DA 9 DT 10 DC 11 DG 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'Can12 dsDNA' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence ; GCGATCGATCGC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DT 6 DC 7 DG 8 DA 9 DT 10 DC 11 DG 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_5FC _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE _BMRB_code 5FC _PDB_code 5FC _Standard_residue_derivative . _Molecular_mass 335.207 _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 . ? OP2 OP2 O . 0 . ? OP1 OP1 O . 0 . ? O5' O5' O . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? C2' C2' C . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C5A C5A C . 0 . ? O5A O5A O . 0 . ? OP3 OP3 O . 0 . ? HOP2 HOP2 H . 0 . ? H6 H6 H . 0 . ? HN41 HN41 H . 0 . ? HN42 HN42 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H5A H5A H . 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 SING P OP2 ? ? DOUB P OP1 ? ? SING P O5' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING N1 C6 ? ? SING N1 C2 ? ? SING N1 C1' ? ? DOUB C6 C5 ? ? SING C6 H6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? DOUB N3 C4 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 HN41 ? ? SING N4 HN42 ? ? SING C5 C5A ? ? SING C2' C1' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' H1' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? DOUB C5A O5A ? ? SING C5A H5A ? ? SING OP3 HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . . . . . . $entity_2 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'chemical synthesis' . . . . . $entity_2 'chemical synthesis' . . . . . 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 $entity_1 1.58 mM 'natural abundance' D2O 5 % 'natural abundance' H2O 95 % 'natural abundance' DSS 25 uM 'natural abundance' 'sodium phosphate' 15 mM 'natural abundance' 'sodium azide' 0.02 % 'natural abundance' 'sodium chloride' 25 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 $entity_1 1.00 mM 'natural abundance' D2O 5 % 'natural abundance' H2O 95 % 'natural abundance' DSS 25 uM 'natural abundance' 'sodium phosphate' 15 mM 'natural abundance' 'sodium azide' 0.02 % 'natural abundance' 'sodium chloride' 25 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name SPARKY _Version 1.414 loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name TOPSPIN _Version 4 loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details Cryoprobe save_ ############################# # NMR applied experiments # ############################# save_1D_1H_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _Sample_label $sample_1 save_ save_1D_1H_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _Sample_label $sample_2 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_1H-1H_NOESY_4 _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 pH 7 . pH temperature 310 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 310 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'Mod12 dsDNA' _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 5.968 0.001 1 2 1 1 DG H2' H 2.556 0.001 1 3 1 1 DG H2'' H 2.755 0.001 1 4 1 1 DG H4' H 3.697 0.000 1 5 1 1 DG H8 H 7.933 0.000 1 6 2 2 DC H1' H 5.674 0.000 1 7 2 2 DC H2' H 2.020 0.001 1 8 2 2 DC H2'' H 2.387 0.002 1 9 2 2 DC H4' H 4.133 0.029 1 10 2 2 DC H5 H 5.374 0.001 1 11 2 2 DC H6 H 7.355 0.000 1 12 2 2 DC H41 H 6.438 0.000 1 13 2 2 DC H42 H 8.416 0.000 1 14 3 3 DG H1' H 5.657 0.004 1 15 3 3 DG H2' H 2.691 0.001 1 16 3 3 DG H2'' H 2.807 0.001 1 17 3 3 DG H3' H 5.006 0.000 1 18 3 3 DG H4' H 4.343 0.001 1 19 3 3 DG H8 H 7.869 0.000 1 20 4 4 DA H1' H 6.216 0.001 1 21 4 4 DA H2 H 7.758 0.000 1 22 4 4 DA H2' H 2.588 0.001 1 23 4 4 DA H2'' H 2.884 0.003 1 24 4 4 DA H3' H 4.987 0.000 1 25 4 4 DA H4' H 4.232 0.000 1 26 4 4 DA H8 H 8.132 0.000 1 27 5 5 DT H1' H 5.845 0.001 1 28 5 5 DT H2' H 1.873 0.001 1 29 5 5 DT H2'' H 2.470 0.002 1 30 5 5 DT H6 H 6.966 0.001 1 31 5 5 DT H71 H 1.262 0.002 1 32 5 5 DT H72 H 1.262 0.002 1 33 5 5 DT H73 H 1.262 0.002 1 34 6 6 5FC H1' H 5.643 0.001 1 35 6 6 5FC H2' H 2.078 0.000 1 36 6 6 5FC H2'' H 2.461 0.002 1 37 6 6 5FC H4' H 4.120 0.000 1 38 6 6 5FC H6 H 8.337 0.000 1 39 6 6 5FC H7 H 9.360 0.000 1 40 6 6 5FC H41 H 7.857 0.000 1 41 6 6 5FC H42 H 9.122 0.000 1 42 7 7 DG H1' H 5.699 0.000 1 43 7 7 DG H2' H 2.677 0.000 1 44 7 7 DG H2'' H 2.800 0.000 1 45 7 7 DG H3' H 4.985 0.001 1 46 7 7 DG H4' H 4.451 0.000 1 47 7 7 DG H8 H 7.888 0.000 1 48 8 8 DA H1' H 6.181 0.001 1 49 8 8 DA H2 H 7.708 0.000 1 50 8 8 DA H2' H 2.528 0.000 1 51 8 8 DA H2'' H 2.869 0.000 1 52 8 8 DA H3' H 4.947 0.001 1 53 8 8 DA H4' H 4.406 0.000 1 54 8 8 DA H8 H 8.047 0.000 1 55 9 9 DT H1' H 5.881 0.001 1 56 9 9 DT H2' H 2.027 0.003 1 57 9 9 DT H2'' H 2.423 0.000 1 58 9 9 DT H4' H 4.153 0.000 1 59 9 9 DT H6 H 7.135 0.001 1 60 9 9 DT H71 H 1.287 0.000 1 61 9 9 DT H72 H 1.287 0.000 1 62 9 9 DT H73 H 1.287 0.000 1 63 10 10 DC H1' H 5.700 0.000 1 64 10 10 DC H2' H 1.995 0.005 1 65 10 10 DC H2'' H 2.373 0.001 1 66 10 10 DC H3' H 4.984 0.000 1 67 10 10 DC H4' H 4.098 0.002 1 68 10 10 DC H5 H 5.577 0.001 1 69 10 10 DC H6 H 7.407 0.001 1 70 10 10 DC H41 H 6.689 0.001 1 71 10 10 DC H42 H 8.376 0.001 1 72 11 11 DG H1' H 5.940 0.001 1 73 11 11 DG H2' H 2.600 0.000 1 74 11 11 DG H2'' H 2.720 0.001 1 75 11 11 DG H3' H 4.964 0.000 1 76 11 11 DG H8 H 7.895 0.000 1 77 12 12 DC H1' H 6.183 0.001 1 78 12 12 DC H2' H 2.146 0.001 1 79 12 12 DC H2'' H 2.183 0.001 1 80 12 12 DC H3' H 4.962 0.000 1 81 12 12 DC H4' H 4.040 0.001 1 82 12 12 DC H5 H 5.520 0.000 1 83 12 12 DC H6 H 7.460 0.001 1 stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ 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 $chem_shift_reference_1 _Mol_system_component_name 'Can12 dsDNA' _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 5.970 0.001 1 2 1 1 DG H2' H 2.570 0.001 1 3 1 1 DG H2'' H 2.758 0.006 1 4 1 1 DG H8 H 7.937 0.000 1 5 2 2 DC H1' H 5.682 0.001 1 6 2 2 DC H2' H 2.027 0.001 1 7 2 2 DC H2'' H 2.394 0.001 1 8 2 2 DC H5 H 5.382 0.001 1 9 2 2 DC H6 H 7.371 0.000 1 10 2 2 DC H41 H 6.441 0.001 1 11 2 2 DC H42 H 8.428 0.000 1 12 3 3 DG H1 H 12.727 0.000 1 13 3 3 DG H1' H 5.664 0.000 1 14 3 3 DG H2' H 2.706 0.000 1 15 3 3 DG H2'' H 2.816 0.002 1 16 3 3 DG H3' H 5.017 0.000 1 17 3 3 DG H8 H 7.890 0.001 1 18 4 4 DA H1' H 6.234 0.001 1 19 4 4 DA H2 H 7.777 0.000 1 20 4 4 DA H2' H 2.593 0.002 1 21 4 4 DA H2'' H 2.926 0.005 1 22 4 4 DA H3' H 4.995 0.000 1 23 4 4 DA H8 H 8.154 0.000 1 24 5 5 DT H1' H 5.847 0.001 1 25 5 5 DT H2' H 1.980 0.001 1 26 5 5 DT H2'' H 2.407 0.004 1 27 5 5 DT H3 H 13.452 0.000 1 28 5 5 DT H6 H 7.089 0.000 1 29 5 5 DT H71 H 1.318 0.000 1 30 5 5 DT H72 H 1.318 0.000 1 31 5 5 DT H73 H 1.318 0.000 1 32 6 6 DC H1' H 5.610 0.001 1 33 6 6 DC H2' H 1.918 0.001 1 34 6 6 DC H2'' H 2.332 0.001 1 35 6 6 DC H5 H 5.514 0.001 1 36 6 6 DC H6 H 7.352 0.000 1 37 6 6 DC H41 H 6.584 0.001 1 38 6 6 DC H42 H 8.302 0.000 1 39 7 7 DG H1 H 12.524 0.000 1 40 7 7 DG H1' H 5.610 0.001 1 41 7 7 DG H2' H 2.675 0.001 1 42 7 7 DG H2'' H 2.780 0.002 1 43 7 7 DG H3' H 4.986 0.000 1 44 7 7 DG H8 H 7.858 0.001 1 45 8 8 DA H1' H 6.194 0.001 1 46 8 8 DA H2 H 7.738 0.001 1 47 8 8 DA H2' H 2.573 0.007 1 48 8 8 DA H2'' H 2.898 0.002 1 49 8 8 DA H3' H 4.968 0.000 1 50 8 8 DA H8 H 8.117 0.000 1 51 9 9 DT H1' H 5.871 0.001 1 52 9 9 DT H2' H 2.011 0.002 1 53 9 9 DT H2'' H 2.431 0.005 1 54 9 9 DT H3 H 13.463 0.000 1 55 9 9 DT H6 H 7.112 0.001 1 56 9 9 DT H71 H 1.311 0.000 1 57 9 9 DT H72 H 1.311 0.000 1 58 9 9 DT H73 H 1.311 0.000 1 59 10 10 DC H1' H 5.707 0.001 1 60 10 10 DC H2' H 2.001 0.001 1 61 10 10 DC H2'' H 2.375 0.003 1 62 10 10 DC H5 H 5.579 0.000 1 63 10 10 DC H6 H 7.411 0.000 1 64 10 10 DC H41 H 6.700 0.001 1 65 10 10 DC H42 H 8.389 0.001 1 66 11 11 DG H1 H 13.013 0.000 1 67 11 11 DG H1' H 5.944 0.001 1 68 11 11 DG H2' H 2.608 0.002 1 69 11 11 DG H2'' H 2.722 0.003 1 70 11 11 DG H3' H 4.968 0.000 1 71 11 11 DG H8 H 7.897 0.000 1 72 12 12 DC H1' H 6.186 0.001 1 73 12 12 DC H2' H 2.152 0.001 1 74 12 12 DC H2'' H 2.187 0.000 1 75 12 12 DC H5 H 5.519 0.001 1 76 12 12 DC H6 H 7.458 0.001 1 stop_ save_