2M11
Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex
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 | 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 100% D2O | 100 | 7.0 | ambient | 283 | |
2 | 2D 1H-1H COSY | 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 100% D2O | 100 | 7.0 | ambient | 283 | |
3 | 2D 1H-1H NOESY | 0.53 mM 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3', 10 mM sodium phosphate, 50 uM EDTA, 100 mM sodium chloride | 90% H2O/10% D2O | 100 | 7.0 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | collection | TopSpin | Bruker Biospin | |
3 | processing | TopSpin | Bruker Biospin | |
4 | data analysis | CORMA | Thomas L. James | |
5 | data analysis | Curves | 5.3 | Ravishankar, G. et al. |
6 | processing | MARDIGRAS | Thomas L. James | |
7 | chemical shift assignment | Sparky | Goddard | |
8 | chemical shift calculation | Sparky | Goddard |