Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A2-DNA structure
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N SOFAST-HMQC | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| 2 | 2D 1H-13C SOFAST-HMQC | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| 3 | 2D 1H-13C HSQC aliphatic | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| 4 | 2D 1H-1H NOESY | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| 5 | 2D 1H-1H TOCSY | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Bruker AVANCE II 600 |
| 6 | 2D DQF-COSY | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Bruker AVANCE II 600 |
| 7 | 2D 1H-31P HSQC | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Bruker AVANCE II 600 |
| 8 | 2D 1H-13C TROSY | 3.5 mM DNA (5'-D(*GP*CP*AP*TP*CP*GP*AP*TP*TP*GP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| 9 | 2D 1H-13C TROSY | 3.5 mM DNA (5'-D(*GP*CP*CP*AP*AP*TP*CP*GP*AP*TP*GP*C)-3') | 90% H2O/10% D2O | 100 mM | 6.8 | 1 atm | 298 | Varian INOVA 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 800 |
| 2 | Bruker | AVANCE II | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | X-PLOR NIH | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 256 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | Sparky | NMRFAM | Goddard |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | collection | VNMR | Varian | |
| 4 | collection | TopSpin | Bruker Biospin | |
| 5 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 6 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 7 | peak picking | Sparky | NMRFAM | Goddard |
