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Thallium form of the G-Quadruplex from Oxytricha Nova, d(G4T4G4)2
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 100% D2O 6.5 1 atm 298 2 DQF-COSY 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 100% D2O 6.5 1 atm 298 3 31P-1H COSY 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 100% D2O 6.5 1 atm 298 4 2D NOESY 0.005 M DNA, 0.0001 M EDTA-d12, 0.050 M Thallium-Nitrate, pH 6.0 90% H2O/10% D2O 6.5 1 atm 278
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian UNITYPLUS 600 2 Varian INOVA 500
NMR Refinement Method Details Software (1) distance geometry with simulated annealing;
(2) torsion angle dynamics (2000 K for 60 ps with 15 fs timesteps);
(3) cartesian dynamics (1000 K for 5 ps with 5 fs timesteps);
(4) restrained molecular dynamics (100 cycles of 200 steps each) VNMR
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (closest to the average)
Additional NMR Experimental Information Details This structure was determined without the use of isotopically enriched nucleotides.
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1b Varian, Inc 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax 3 data analysis Sparky 3.110 Goddard and Kneller 4 iterative matrix relaxation CNS 1.1 Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren 5 refinement CNS 1.1 Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren 6 structure solution CNS 1.1 Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren