7D0X
NMR solution structures of the DNA minidumbbell formed by 5'-mCTTGXmCTTG-3'
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 | 0.5 mM DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 25 mM | 7.0 | 1 atm | 273 | Bruker AVANCE 500 |
2 | 2D 1H-1H COSY | 0.5 mM DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 25 mM | 7.0 | 1 atm | 273 | Bruker AVANCE 500 |
3 | 2D 1H-1H TOCSY | 0.5 mM DNA (5'-D(*(MC1)P*TP*TP*GP*(DX)P*(DMC)P*TP*TP*G)-3'), 10 mM sodium phosphate, 0.02 mM DSS | 99.96% D2O | 25 mM | 7.0 | 1 atm | 273 | Bruker AVANCE 500 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
---|---|---|
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 | 1000 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | TopSpin | Bruker Biospin | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |