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Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-13C JR HMBC 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 90% H2O/10% D2O 100mM K+ 7 ambient 298 2 2D 1H-1H JR NOESY 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 90% H2O/10% D2O 100mM K+ 7 ambient 298 3 2D 1H-1H NOESY 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 100% D2O 100mM K+ 7 ambient 298 4 2D 1H-1H COSY 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 100% D2O 100mM K+ 7 ambient 298 5 2D 1H-1H TOCSY 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 100% D2O 100mM K+ 7 ambient 298 6 2D 1H-13C HSQC 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 100% D2O 100mM K+ 7 ambient 298 7 H-D exchange 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 100% D2O 100mM K+ 7 ambient 298 8 15N-filtered 0.5-2.0 mM [U-2% 15N; U-2% 13C] DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-3 90% H2O/10% D2O 100mM K+ 7 ambient 298 9 D-labeled 0.5-2.0 mM [U-100% 2H] DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4 90% H2O/10% D2O 100mM K+ 7 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Bruker AVANCE 700
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics refinement in vacuo, distance-restrained molecular dynamics refinement in explicit solvent TopSpin
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 processing TopSpin 2.1 Bruker Biospin 2 peak picking Felix 2007 Felix NMR, Inc. 3 structure solution X-PLOR NIH 2.27 Schwieters, Kuszewski, Tjandra and Clore 4 refinement Amber 10 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm 5 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore