6V0L
PDGFR-b Promoter Forms a G-Vacancy Quadruplex that Can be Complemented by dGMP: Molecular Structure and Recognition of Guanine Derivatives and Metabolites
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7 | 760 mmHg | 278 | Bruker AVANCE III 800 |
| 2 | 2D 1H-1H NOESY | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7.0 | 760 mmHg | 288 | Bruker AVANCE III 800 |
| 6 | 2D 1H-1H NOESY | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7 | 760 mmHg | 298 | Bruker AVANCE III 800 |
| 5 | 2D 1H-1H NOESY | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7 | 760 mmHg | 278 | Bruker AVANCE III 800 |
| 3 | 2D 1H-1H COSY | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7 | 760 mmHg | 278 | Bruker AVANCE III 800 |
| 4 | 2D 1H-13C HSQC | 3600 uM 1H DNA (5'-D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*(DA3)P*-3')(DGP) | 90% H2O/10% D2O | 50 mM | 7 | 760 mmHg | 298 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 2 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics | X-PLOR NIH | |
| simulated annealing | molecular dynamics | Amber |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | Sparky | Goddard | |
| 2 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 3 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 4 | peak picking | Sparky | Goddard | |
| 5 | processing | TopSpin | Bruker Biospin | |
| 6 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 7 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
