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Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 90% H2O/10% D2O 45 7 298 2 2D 1H-1H NOESY 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 100% D2O 45 7 298 3 2D 1H-1H TOCSY 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 100% D2O 45 7 298 4 2D 1H-13C HSQC 1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3 100% D2O 90 7 298 5 2D 13C-filtered HSQC-NOESY 1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3 100% D2O 90 7 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AMX 600 2 Bruker AMX 700
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics Extracted distances from structure of free DNA (PDB entry 2A5P) were used during calculation Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 geometry optimization Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 3 structure solution Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 4 chemical shift assignment Sparky Goddard 5 data analysis Sparky Goddard 6 peak picking Sparky Goddard 7 collection TopSpin Bruker Biospin 8 processing TopSpin Bruker Biospin 9 geometry optimization X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 10 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 11 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore