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NMR Structural Studies on the Covalent DNA Binding of a Pyrrolobenzodiazepine-Naphthalimide Conjugate
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 90% H2O/10% D2O 90% H2O/10% D2O 0.28 7 ambient 298 2 2D 1H-1H NOESY 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O 100% D2O 3 2D DQF-COSY 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O 100% D2O 4 2D 1H-1H TOCSY 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O 100% D2O 5 2D-1H-1H ROESY 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O 100% D2O 6 2D 31P-1H HETCOR 1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O 100% D2O
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria representative conformers of production runs Conformers Calculated Total Number 20000 Conformers Submitted Total Number 5 Representative Model 1 (closest to the average and energy minimized)
Computation: NMR Software # Classification Version Software Name Author 1 restrained molecular dynamics Amber 9 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm 2 refinement Amber 9 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm