Structure of a Stable Interstrand DNA Crosslink Involving an dA Amino Group and an Abasic Site
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 500 uM deoxyribonucleic acid | 100% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
| 2 | 2D 1H-1H TOCSY | 500 uM deoxyribonucleic acid | 95% H2O/5% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
| 3 | 2D 1H-1H NOESY | 500 uM deoxyribonucleic acid | 95% H2O/5% D2O | 120 mM | 8 | 1 atm | 278 | Bruker AVANCE III 900 |
| 4 | 2D 1H-1H COSY | 500 uM deoxyribonucleic acid | 100% D2O | 120 mM | 8 | 1 atm | 298 | Bruker AVANCE III 900 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | 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 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 7 | peak picking | Sparky | Goddard | |
