data_34071 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 2'F-ANA/DNA Chimeric TBA Quadruplex structure ; _BMRB_accession_number 34071 _BMRB_flat_file_name bmr34071.str _Entry_type original _Submission_date 2016-12-02 _Accession_date 2016-12-02 _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 Lietard J. . . 2 'Abou Assi' H. . . 3 Gomez-Pinto I. . . 4 Gonzalez C. . . 5 Somoza M. M. . 6 Damha M. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 146 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-27 update BMRB 'update entry citation' 2017-01-26 original author 'original release' stop_ _Original_release_date 2017-01-25 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Mapping the affinity landscape of Thrombin-binding aptamers on 2'F-ANA/DNA chimeric G-Quadruplex microarrays. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28100695 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lietard J. . . 2 'Abou Assi' H. . . 3 Gomez-Pinto I. . . 4 Gonzalez C. . . 5 Somoza M. M. . 6 Damha M. J. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 45 _Journal_issue 4 _Journal_ASTM NARHAD _Journal_ISSN 1362-4962 _Journal_CSD 0389 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1619 _Page_last 1632 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _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 entity_1 _Molecular_mass 4761.042 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; GGXTGGTGTGGTTGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 TAF 4 DT 5 DG 6 DG 7 DT 8 DG 9 DT 10 DG 11 DG 12 DT 13 DT 14 DG 15 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_TAF _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common "2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE" _BMRB_code TAF _PDB_code TAF _Standard_residue_derivative . _Molecular_mass 340.199 _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 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 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 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C5M C5M C . 0 . ? F2' F2' F . 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 . ? HOP1 HOP1 H . 0 . ? HOP2 HOP2 H . 0 . ? H6 H6 H . 0 . ? H3 H3 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 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 . ? HO'3 HO'3 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 OP1 ? ? SING P OP2 ? ? DOUB P OP3 ? ? SING P O5' ? ? SING OP1 HOP1 ? ? 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 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? SING C5M H71 ? ? SING C5M H72 ? ? SING C5M H73 ? ? SING F2' C2' ? ? SING C2' C1' ? ? SING C2' C3' ? ? 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' HO'3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "1.0 mg/mL DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mg/mL 'natural abundance' NaPi 10 mM 'natural abundance' KCl 25 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 800 _Details . save_ save_NMR_spectrometer_2 _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 35 . mM pH 7.0 . pH pressure 1 . atm temperature 279.6 . 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 0.0 internal 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' '2D 1H-1H TOCSY' 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 entity_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 DG H1 H 12.120 0.027 . 2 1 1 DG H1' H 6.090 0.017 . 3 1 1 DG H2' H 3.000 0.010 . 4 1 1 DG H2'' H 3.000 0.000 . 5 1 1 DG H3' H 5.000 0.002 . 6 1 1 DG H4' H 4.420 0.010 . 7 1 1 DG H5' H 4.290 0.000 . 8 1 1 DG H5'' H 4.290 0.000 . 9 1 1 DG H8 H 7.410 0.025 . 10 2 2 DG H1 H 12.210 0.000 . 11 2 2 DG H1' H 6.030 0.017 . 12 2 2 DG H2' H 3.110 0.029 . 13 2 2 DG H2'' H 2.310 0.021 . 14 2 2 DG H3' H 5.210 0.026 . 15 2 2 DG H4' H 4.420 0.008 . 16 2 2 DG H5' H 4.280 0.000 . 17 2 2 DG H5'' H 4.280 0.000 . 18 2 2 DG H8 H 8.220 0.025 . 19 3 3 TAF H1' H 6.290 0.017 . 20 3 3 TAF H2'' H 5.620 0.020 . 21 3 3 TAF H3 H 11.390 0.000 . 22 3 3 TAF H3' H 4.970 0.019 . 23 3 3 TAF H4' H 4.270 0.020 . 24 3 3 TAF H6 H 8.020 0.014 . 25 3 3 TAF H71 H 2.030 0.021 . 26 3 3 TAF H72 H 2.030 0.021 . 27 3 3 TAF H73 H 2.030 0.021 . 28 4 4 DT H1' H 5.990 0.033 . 29 4 4 DT H2' H 1.930 0.015 . 30 4 4 DT H2'' H 2.660 0.021 . 31 4 4 DT H3 H 11.330 0.025 . 32 4 4 DT H3' H 4.880 0.009 . 33 4 4 DT H4' H 4.295 0.003 . 34 4 4 DT H5' H 3.960 0.020 . 35 4 4 DT H5'' H 3.960 0.000 . 36 4 4 DT H6 H 6.980 0.093 . 37 4 4 DT H71 H 0.870 0.017 . 38 4 4 DT H72 H 0.870 0.017 . 39 4 4 DT H73 H 0.870 0.017 . 40 5 5 DG H1 H 12.270 0.019 . 41 5 5 DG H1' H 6.045 0.006 . 42 5 5 DG H2' H 3.340 0.011 . 43 5 5 DG H2'' H 2.920 0.006 . 44 5 5 DG H3' H 4.872 0.006 . 45 5 5 DG H4' H 4.420 0.004 . 46 5 5 DG H5' H 4.290 0.007 . 47 5 5 DG H5'' H 4.290 0.015 . 48 5 5 DG H8 H 7.460 0.011 . 49 6 6 DG H1 H 12.210 0.019 . 50 6 6 DG H1' H 5.950 0.019 . 51 6 6 DG H2' H 2.800 0.015 . 52 6 6 DG H2'' H 2.610 0.004 . 53 6 6 DG H3' H 5.130 0.006 . 54 6 6 DG H4' H 4.440 0.015 . 55 6 6 DG H5' H 4.290 0.005 . 56 6 6 DG H5'' H 4.240 0.002 . 57 6 6 DG H8 H 7.690 0.011 . 58 7 7 DT H1' H 6.490 0.010 . 59 7 7 DT H2' H 2.515 0.005 . 60 7 7 DT H2'' H 2.623 0.011 . 61 7 7 DT H3 H 11.330 0.000 . 62 7 7 DT H3' H 4.862 0.003 . 63 7 7 DT H4' H 4.444 0.014 . 64 7 7 DT H5' H 4.300 0.024 . 65 7 7 DT H5'' H 4.240 0.002 . 66 7 7 DT H6 H 7.934 0.006 . 67 7 7 DT H71 H 1.980 0.006 . 68 7 7 DT H72 H 1.980 0.006 . 69 7 7 DT H73 H 1.980 0.006 . 70 8 8 DG H1 H 10.714 0.000 . 71 8 8 DG H1' H 5.775 0.020 . 72 8 8 DG H2' H 1.995 0.027 . 73 8 8 DG H2'' H 2.329 0.009 . 74 8 8 DG H3' H 4.786 0.006 . 75 8 8 DG H4' H 3.988 0.015 . 76 8 8 DG H5' H 4.120 0.009 . 77 8 8 DG H5'' H 4.120 0.013 . 78 8 8 DG H8 H 7.479 0.028 . 79 9 9 DT H1' H 5.830 0.017 . 80 9 9 DT H2' H 1.980 0.006 . 81 9 9 DT H2'' H 2.420 0.022 . 82 9 9 DT H3 H 10.760 0.018 . 83 9 9 DT H3' H 4.640 0.009 . 84 9 9 DT H4' H 3.790 0.015 . 85 9 9 DT H5' H 3.030 0.010 . 86 9 9 DT H5'' H 3.570 0.028 . 87 9 9 DT H6 H 7.271 0.008 . 88 9 9 DT H71 H 1.810 0.016 . 89 9 9 DT H72 H 1.810 0.016 . 90 9 9 DT H73 H 1.810 0.016 . 91 10 10 DG H1 H 11.950 0.007 . 92 10 10 DG H1' H 6.070 0.010 . 93 10 10 DG H2' H 3.740 0.015 . 94 10 10 DG H2'' H 2.930 0.009 . 95 10 10 DG H3' H 4.928 0.005 . 96 10 10 DG H4' H 4.340 0.011 . 97 10 10 DG H8 H 7.451 0.020 . 98 11 11 DG H1 H 12.110 0.014 . 99 11 11 DG H1' H 6.030 0.010 . 100 11 11 DG H2' H 2.990 0.010 . 101 11 11 DG H2'' H 2.320 0.010 . 102 11 11 DG H3' H 5.150 0.008 . 103 11 11 DG H4' H 4.410 0.006 . 104 11 11 DG H5' H 4.330 0.010 . 105 11 11 DG H5'' H 4.330 0.004 . 106 11 11 DG H8 H 8.220 0.012 . 107 12 12 DT H1' H 6.170 0.029 . 108 12 12 DT H2' H 2.240 0.013 . 109 12 12 DT H2'' H 2.610 0.012 . 110 12 12 DT H3 H 11.390 0.002 . 111 12 12 DT H3' H 4.920 0.044 . 112 12 12 DT H4' H 4.260 0.025 . 113 12 12 DT H6 H 7.920 0.012 . 114 12 12 DT H71 H 1.990 0.011 . 115 12 12 DT H72 H 1.990 0.011 . 116 12 12 DT H73 H 1.990 0.011 . 117 13 13 DT H1' H 6.100 0.008 . 118 13 13 DT H2' H 2.060 0.010 . 119 13 13 DT H2'' H 2.741 0.007 . 120 13 13 DT H3 H 11.331 0.017 . 121 13 13 DT H3' H 4.920 0.007 . 122 13 13 DT H4' H 4.290 0.007 . 123 13 13 DT H5' H 3.932 0.002 . 124 13 13 DT H5'' H 4.240 0.010 . 125 13 13 DT H6 H 7.200 0.050 . 126 13 13 DT H71 H 0.940 0.019 . 127 13 13 DT H72 H 0.940 0.019 . 128 13 13 DT H73 H 0.940 0.019 . 129 14 14 DG H1 H 12.181 0.006 . 130 14 14 DG H1' H 6.090 0.020 . 131 14 14 DG H2' H 3.500 0.007 . 132 14 14 DG H2'' H 2.980 0.012 . 133 14 14 DG H3' H 4.930 0.003 . 134 14 14 DG H4' H 4.440 0.018 . 135 14 14 DG H5' H 4.280 0.000 . 136 14 14 DG H5'' H 4.280 0.000 . 137 14 14 DG H8 H 7.485 0.005 . 138 15 15 DG H1 H 12.350 0.014 . 139 15 15 DG H1' H 6.160 0.018 . 140 15 15 DG H2' H 2.700 0.000 . 141 15 15 DG H2'' H 2.450 0.017 . 142 15 15 DG H3' H 4.810 0.004 . 143 15 15 DG H4' H 4.280 0.012 . 144 15 15 DG H5' H 4.190 0.000 . 145 15 15 DG H5'' H 4.190 0.000 . 146 15 15 DG H8 H 8.090 0.009 . stop_ save_