Structure of Exocyclic R,R N6,N6-(2,3-Dihydroxy-1,4-butadiyl)-2'-Deoxyadenosine Adduct Induced by 1,2,3,4-Diepoxybutane in DNA
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.7 mM 5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3', 0.7 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 100% D2O | 100 | 7 | ambient | 288 | |
| 2 | 2D 1H-1H TOCSY | 0.7 mM 5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3', 0.7 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 100% D2O | 100 | 7 | ambient | 288 | |
| 3 | 2D DQF-COSY | 0.7 mM 5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3', 0.7 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 100% D2O | 100 | 7 | ambient | 288 | |
| 4 | 2D 1H-1H NOESY | 0.7 mM 5'-D(*CP*GP*GP*AP*CP*(RBD)P*AP*GP*AP*AP*G)-3', 0.7 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate | 90% H2O/10% D2O | 100 | 7 | ambient | 278 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | CORMA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
| Conformers Calculated Total Number | 8 |
| Conformers Submitted Total Number | 8 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | CORMA | Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar | |
| 2 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 3 | conversion of intensities to distance restraints | MARDIGRAS | Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli | |
| 4 | chemical shift assignment | Sparky | Goddard | |
| 5 | peak picking | Sparky | Goddard | |
| 6 | chemical shift calculation | Sparky | Goddard | |
| 7 | collection | TopSpin | Bruker Biospin | |
| 8 | processing | TopSpin | Bruker Biospin | |
| 9 | data analysis | Curves | plus web server | Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, Richard Lavery |
| 10 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
