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Structure of AA(GGGTT)3GGGAA G-quadruplex in the presence of sodium ions
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700 2 2D 1H-13C HSQC 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700 3 2D 1H-15N HMQC 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700 4 2D DQF-COSY 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700 5 2D 1H-13C HSQC F2 coupled 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700 6 2D 1H-13C HSQC F2 coupled 1.5 mM DNA (5'-D(*AP*AP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*A)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 50 uM dss 95% H2O/5% D2O 418 mM 7 1 atm 298 Bruker AVANCE III 700
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 700
NMR Refinement Method Details Software distance geometry X-PLOR NIH simulated annealing Amber molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 50 Conformers Submitted Total Number 5 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin Bruker Biospin 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 chemical shift assignment NMRFAM-SPARKY Lee W, Tonelli M, Markley JL 4 peak picking NMRFAM-SPARKY Lee W, Tonelli M, Markley JL 5 geometry optimization X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 6 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 7 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman