5B81
Solution NMR structure of a 16-mer DNA duplex containing quadruple GC mismatches showing staggered base pairing, and consequent rescue of canonical double helical characteristics
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 | 350 uM Unlabelled Mismatched DNA | 95% H2O/5% D2O | 50, sodium, chloride mM | 7.2 | 1 atm | 288 | Bruker AVANCE III 500 |
2 | 2D 1H-1H NOESY | 350 uM Unlabelled Mismatched DNA | 95% H2O/5% D2O | 50, sodium, chloride mM | 7.2 | 1 atm | 288 | Bruker AVANCE III 700 |
3 | 2D 1H-1H TOCSY | 350 uM Unlabelled Mismatched DNA | 95% H2O/5% D2O | 50, sodium, chloride mM | 7.2 | 1 atm | 288 | Bruker AVANCE III 500 |
4 | 2D DQF-COSY | 350 uM Unlabelled Mismatched DNA | 95% H2O/5% D2O | 50, sodium, chloride mM | 7.2 | 1 atm | 288 | Bruker AVANCE III 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 500 |
2 | Bruker | AVANCE III | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
2 | structure calculation | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
3 | chemical shift assignment | Sparky | 3.114 | Goddard |
4 | peak picking | Sparky | 3.114 | Goddard |