6M6K
NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CCTG repeats
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi | 99.96% D2O | 10 mM | 7.0 | 1 atm | 273 | Bruker AVANCE III 700 |
2 | 2D DQF-COSY | 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi | 99.96% D2O | 10 mM | 7.0 | 1 atm | 273 | Bruker AVANCE III 700 |
3 | 2D TOCSY | 0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaPi | 99.96% D2O | 10 mM | 7.0 | 1 atm | 273 | Bruker AVANCE 500 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
restrained molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 500 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | chemical shift assignment | TopSpin | Bruker |