Hybrid-1 form of human telomere DNA quadruplex with wild-type 5'-flanking in K+ solution
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 298 | Bruker AVANCE III 800 |
| 2 | 2D 1H-13C HSQC | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 298 | Bruker AVANCE III 800 |
| 3 | 2D DQF-COSY | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 298 | Bruker AVANCE III 800 |
| 4 | 2D 1H-13C HMBC | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 298 | Bruker AVANCE III 800 |
| 5 | 2D 1H-1H NOESY | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 288 | Bruker AVANCE III 800 |
| 6 | 2D 1H-13C HSQC | 1.9 mM DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 10 mM potassium cyanide | 90% H2O/10% D2O | 10 mM | 7 | 1 atm | 288 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | X-PLOR NIH | |
| simulated annealing | Amber | |
| molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | TopSpin | Bruker Biospin | |
| 2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 3 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 4 | chemical shift assignment | CcpNmr Analysis | CCPN | |
| 5 | peak picking | CcpNmr Analysis | CCPN | |
| 6 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
