☰ Navigation Tabs
Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1 90% H2O/10% D2O 90 7.0 ambient 298 2 2D 1H-1H TOCSY 0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1 90% H2O/10% D2O 90 7.0 ambient 298 3 2D 1H-13C HSQC aliphatic 0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1 90% H2O/10% D2O 90 7.0 ambient 298 4 1D JR-HMQC 0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1 90% H2O/10% D2O 90 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Bruker AVANCE 700
NMR Refinement Method Details Software distance geometry, DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics Sparky
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 chemical shift assignment Sparky Goddard 2 data analysis Sparky Goddard 3 peak picking Sparky Goddard 4 collection TopSpin Bruker Biospin 5 geometry optimization X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 6 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 7 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 8 structure solution Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 9 refinement X-PLOR NIH