2KUZ
2-Aminopurine incorporation perturbs the dynamics and structure of DNA
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HMQC | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride | 100% D2O | 7.0 | ambient | 298 | ||
2 | 2D 1H-13C HMQC | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride, 20 mg/mL Pf1 phage | 90% H2O/10% D2O | 7.0 | ambient | 298 | ||
3 | 2D 1H-1H NOESY | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride | 100% D2O | 7.0 | ambient | 298 | ||
4 | 2D 1H-1H TOCSY | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride | 100% D2O | 7.0 | ambient | 298 | ||
5 | 2D DQF-COSY | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride | 100% D2O | 7.0 | ambient | 298 | ||
6 | 2D 1H-1H NOESY | 3 mM DNAstrandI, 3 mM DNAstrandII, 10 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 7.0 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Torsion angle dynamics, 50K at 20,000K with subsequent gradual cooling to 25K in 154 steps of 0.5 ps length (34 steps to cool down to 3,000 K, followed by 120 steps to reach the end temperature) and a final minimization (3,000 steps). | CARA |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 11 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | peak picking | CARA | 1.8.4 | Keller, R. et al. |
2 | chemical shift assignment | CARA | 1.8.4 | Keller, R. et al. |
3 | structure solution | X-PLOR NIH | 2.20 | Schwieters, C. et al. |
4 | refinement | X-PLOR NIH | 2.20 | Schwieters, C. et al. |
5 | geometry optimization | X-PLOR NIH | 2.20 | Schwieters, C. et al. |
6 | collection | TopSpin | 2.0 | Bruker Biospin |
7 | processing | TopSpin | 2.0 | Bruker Biospin |
8 | data analysis | Gifa | 4 | Delsuc, M.A. et al. |
9 | data analysis | 3DNA | Lu, X.J. et al. | |
10 | data analysis | PALES | Zweckstetter, M. et al. |