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Dodecamer DNA containing the synthetic base pair P-Z in complex with a pyrrole-imidazole polyamide
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 100% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600 2 2D DQF-COSY 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 100% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600 3 2D 1H-1H TOCSY 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 100% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600 4 2D 1H-13C HSQC 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 100% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600 5 31P -1H COSY 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 100% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600 6 2D NOESY 1.3 mM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3') 90% H2O/10% D2O 100 mM 7.4 1 atm 298 Bruker AVANCE II 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE II 600
NMR Refinement Method Details Software simulated annealing Amber molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with acceptable covalent geometry Conformers Calculated Total Number 5000 Conformers Submitted Total Number 10 Representative Model 1 (most represented cluster)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 3 chemical shift assignment Sparky Goddard 4 structure calculation MARDIGRAS Borgias AB