data_16054 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Dimeric solution structure of the DNA loop d(TGCTTCGT) ; _BMRB_accession_number 16054 _BMRB_flat_file_name bmr16054.str _Entry_type original _Submission_date 2008-12-09 _Accession_date 2008-12-09 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Self-association of the DNA octamer d(TGCTTCGT) gives rise to a quadruplex stabilized by minor groove tetrads' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Viladoms Julia . . 2 Escaja Nuria . . 3 Frieden Miriam . . 4 Gomez-Pinto Irene . . 5 Pedroso Enrique . . 6 Gonzalez Carlos . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 83 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2009-06-10 update BMRB 'complete entry citation' 2009-04-16 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16055 5'-D(P*TP*CP*GP*TP*TP*GP*CP*T)-3' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Self-association of short DNA loops through minor groove C:G:G:C tetrads' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19321501 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Viladoms Julia . . 2 Escaja Nuria . . 3 Frieden Miriam . . 4 Gomez-Pinto Irene . . 5 Pedroso Enrique . . 6 Gonzalez Carlos . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic Acids Research' _Journal_volume 37 _Journal_issue 10 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3264 _Page_last 3275 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-D(TP*CP*GP*TP*TP*GP*CP*T)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_1 $DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3') DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_2 $DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*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(TP*GP*CP*TP*TP*CP*GP*T)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3') _Molecular_mass 2408.610 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence TGCTTCGT loop_ _Residue_seq_code _Residue_label 1 DT 2 DG 3 DC 4 DT 5 DT 6 DC 7 DG 8 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(TP*GP*CP*TP*TP*CP*GP*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 $DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3') '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3') . mM 0.1 4.0 'natural abundance' 'sodium phosphate' 25 mM . . 'natural abundance' 'sodium chloride' 100 mM . . 'natural abundance' 'magnesium chloride' 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 . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task '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' 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DPX _Field_strength 800 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-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 278 . 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 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-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 DNA_(5'-D(TP*GP*CP*TP*TP*CP*GP*T)-3')_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 DT H1' H 6.41 0.01 1 2 1 1 DT H2' H 2.48 0.01 1 3 1 1 DT H2'' H 2.62 0.01 1 4 1 1 DT H3' H 4.90 0.01 1 5 1 1 DT H4' H 4.30 0.01 1 6 1 1 DT H5' H 3.89 0.01 2 7 1 1 DT H6 H 7.72 0.01 1 8 1 1 DT H71 H 1.93 0.01 1 9 1 1 DT H72 H 1.93 0.01 1 10 1 1 DT H73 H 1.93 0.01 1 11 2 2 DG H1 H 13.52 0.01 1 12 2 2 DG H1' H 6.25 0.01 1 13 2 2 DG H2' H 2.77 0.01 1 14 2 2 DG H2'' H 2.98 0.03 1 15 2 2 DG H3' H 5.04 0.02 1 16 2 2 DG H4' H 4.62 0.01 1 17 2 2 DG H5' H 4.06 0.01 2 18 2 2 DG H5'' H 4.19 0.01 2 19 2 2 DG H8 H 8.11 0.01 1 20 2 2 DG H21 H 6.04 0.01 1 21 2 2 DG H22 H 9.11 0.01 1 22 3 3 DC H1' H 6.31 0.01 1 23 3 3 DC H2' H 2.35 0.01 1 24 3 3 DC H2'' H 2.44 0.01 1 25 3 3 DC H3' H 5.00 0.01 1 26 3 3 DC H4' H 4.34 0.01 1 27 3 3 DC H5 H 5.38 0.01 1 28 3 3 DC H5' H 4.08 0.02 2 29 3 3 DC H6 H 7.45 0.01 1 30 3 3 DC H41 H 6.55 0.02 1 31 3 3 DC H42 H 8.77 0.01 1 32 4 4 DT H1' H 5.99 0.01 1 33 4 4 DT H2' H 1.90 0.01 1 34 4 4 DT H2'' H 2.41 0.02 1 35 4 4 DT H3 H 10.47 0.01 5 36 4 4 DT H3' H 4.71 0.01 1 37 4 4 DT H4' H 3.76 0.01 1 38 4 4 DT H6 H 7.52 0.02 1 39 4 4 DT H71 H 1.66 0.01 1 40 4 4 DT H72 H 1.66 0.01 1 41 4 4 DT H73 H 1.66 0.01 1 42 5 5 DT H1' H 6.48 0.01 1 43 5 5 DT H2' H 2.32 0.01 1 44 5 5 DT H2'' H 2.54 0.01 1 45 5 5 DT H3' H 4.64 0.01 1 46 5 5 DT H5' H 3.91 0.01 2 47 5 5 DT H5'' H 4.21 0.01 2 48 5 5 DT H6 H 7.86 0.01 1 49 5 5 DT H71 H 1.94 0.01 1 50 5 5 DT H72 H 1.94 0.01 1 51 5 5 DT H73 H 1.94 0.01 1 52 6 6 DC H1' H 6.32 0.01 1 53 6 6 DC H2' H 2.26 0.01 1 54 6 6 DC H2'' H 2.72 0.01 1 55 6 6 DC H3' H 4.96 0.01 1 56 6 6 DC H4' H 4.36 0.01 1 57 6 6 DC H5 H 6.03 0.01 1 58 6 6 DC H6 H 7.78 0.01 1 59 6 6 DC H41 H 7.12 0.02 1 60 6 6 DC H42 H 9.13 0.02 1 61 7 7 DG H1 H 13.63 0.01 1 62 7 7 DG H1' H 6.22 0.01 1 63 7 7 DG H2' H 2.83 0.01 1 64 7 7 DG H2'' H 2.54 0.01 1 65 7 7 DG H3' H 5.16 0.01 1 66 7 7 DG H4' H 4.81 0.01 1 67 7 7 DG H5' H 4.23 0.01 2 68 7 7 DG H5'' H 4.35 0.01 2 69 7 7 DG H8 H 8.00 0.01 1 70 7 7 DG H21 H 7.08 0.03 1 71 7 7 DG H22 H 9.16 0.01 1 72 8 8 DT H1' H 5.83 0.01 1 73 8 8 DT H2' H 1.92 0.02 1 74 8 8 DT H2'' H 2.27 0.02 1 75 8 8 DT H3 H 10.83 0.01 5 76 8 8 DT H3' H 4.33 0.01 1 77 8 8 DT H4' H 3.61 0.01 1 78 8 8 DT H5' H 3.41 0.01 2 79 8 8 DT H5'' H 3.75 0.01 2 80 8 8 DT H6 H 7.43 0.01 1 81 8 8 DT H71 H 1.86 0.01 1 82 8 8 DT H72 H 1.86 0.01 1 83 8 8 DT H73 H 1.86 0.01 1 stop_ save_