6H1K
The major G-quadruplex form of HIV-1 LTR
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER) | 90% H2O/10% D2O | 70mM KCL, 20mM KPi | 7.0 | 1 Pa | 298 | Bruker AVANCE II 600 |
2 | 2D 1H-1H TOCSY | 70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER) | 90% H2O/10% D2O | 70mM KCL, 20mM KPi | 7.0 | 1 Pa | 298 | Bruker AVANCE II 600 |
3 | 2D 1H-13C HSQC | 70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER) | 90% H2O/10% D2O | 70mM KCL, 20mM KPi | 7.0 | 1 Pa | 298 | Bruker AVANCE II 600 |
4 | 2D 1H-13C HMBC | 70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER) | 90% H2O/10% D2O | 70mM KCL, 20mM KPi | 7.0 | 1 Pa | 298 | Bruker AVANCE II 600 |
5 | 2D 1H-13C HSQC aromatic | 70 mM NA potassium chloride, 20 mM NA potassium phosphate, 1 mM DNA (28-MER) | 90% H2O/10% D2O | 70mM KCL, 20mM KPi | 7.0 | 1 Pa | 298 | Bruker AVANCE II 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE II | 600 |
2 | Bruker | AVANCE II | 700 |
NMR Refinement | ||
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Method | Details | Software |
DGSA-distance geometry simulated annealing | Xplor-NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (structures with the lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Xplor-NIH | Schwieters, Kuszewski, Tjandra and Clore | |
2 | structure calculation | Xplor-NIH | Schwieters, Kuszewski, Tjandra and Clore | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard |