2N4M
Base-displaced intercalated structure of the N-(2'deoxyguanosin-8-yl)-3-aminobenzanthrone DNA adduct
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 | 352 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 352 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA | 100% D2O | 110 | 7 | ambient | 298 | |
2 | 2D 1H-1H COSY | 352 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 352 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA | 100% D2O | 110 | 7 | ambient | 298 | |
3 | 2D 1H-1H NOESY | 521 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 521 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA | 100% D2O | 110 | 7 | ambient | 288 | |
4 | 2D 1H-1H COSY | 521 uM DNA (5'-D(*GP*TP*GP*CP*(4E9)P*TP*GP*TP*TP*TP*GP*T)-3'), 521 uM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA | 100% D2O | 110 | 7 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 900 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 85 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman | |
2 | chemical shift assignment | Sparky | Goddard | |
3 | data analysis | Sparky | Goddard | |
4 | processing | TopSpin | Bruker Biospin | |
5 | data analysis | TopSpin | Bruker Biospin | |
6 | restraint calculation | MARDIGRAS | Borgias, B. A. & James, T. L. | |
7 | validation | CORMA | Borgias, B. A. & James, T. L. |