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Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H TOCSY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 40 7 298 2 2D 1H-1H TOCSY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 90% H2O/10% D2O 40 7 298 3 2D 1H-1H NOESY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 90% H2O/10% D2O 40 7 298 4 2D 1H-1H NOESY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 40 7 298 5 2D 1H-1H NOESY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 90 7 ambient atm 310 6 2D 1H-1H NOESY 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 90 7 298 7 2D 1H-13C HSQC aromatic 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 40 7 298 8 2D 1H-13C HSQC aromatic 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H 90% H2O/10% D2O 90 7 298 9 2D 1H-13C HSQC aliphatic 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 40 7 298 10 2D 1H-13C HSQC aliphatic 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H 90% H2O/10% D2O 90 7 298 11 2D 1H-13C HSQC aliphatic 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H 100% D2O 90 7 298 12 2D 1H-13C HSQC aromatic 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H 100% D2O 90 7 298 13 1D JRHMBC 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H 90% H2O/10% D2O 90 7 298 14 2D 1H-31P HSQC 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H 100% D2O 40 7 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AMX 600 2 Bruker AMX 700 3 Bruker AMX 400
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics 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 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman 2 data analysis Sparky Goddard 3 chemical shift assignment Sparky Goddard 4 peak picking Sparky Goddard 5 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 6 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 7 collection TopSpin Bruker Biospin