2LWO
Solution Structure of Duplex DNA Containing a b-Carba-Fapy-dG Lesion
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 | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 100% D2O | 6.8 | ambient | 298 | ||
2 | 2D 1H-1H COSY | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 100% D2O | 6.8 | ambient | 298 | ||
3 | 2D DQF-COSY | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 100% D2O | 6.8 | ambient | 298 | ||
4 | 2D 1H-1H TOCSY | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 100% D2O | 6.8 | ambient | 298 | ||
5 | 2D 1H-13C HSQC | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 100% D2O | 6.8 | ambient | 298 | ||
6 | 2D 1H-1H NOESY | 1.1 mM 11 mer duplex oligo B-D, 25 mM phosphate buffer, 50 mM NaCl, 0.5 mM EDTA | 90% H2O/10% D2O | 6.8 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | TopSpin |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 6 |
Conformers Submitted Total Number | 7 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | data analysis | Sparky | Goddard | |
5 | peak picking | Sparky | Goddard | |
6 | peak volume calc. | Sparky | Goddard | |
7 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
8 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
9 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |