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Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-13C HSQC 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 2 2D 1H-1H TOCSY 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 3 2D DQF-COSY 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 4 2D 1H-1H NOESY 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 5 2D 1H-31P COSY 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 6 1D 31P 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 100% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600 7 2D 1H-1H NOESY 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate 90% H2O/10% D2O 100 mM 7.45 1 atm 298 Bruker AVANCE 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software molecular dynamics Amber matrix relaxation Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 2000 Conformers Submitted Total Number 10 Representative Model 1 (closest to the average)
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 N. Ulyanov 5 collection TopSpin Bruker Biospin