Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by human telomeric repeats in K+ solution
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-13C HSQC | 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6 | 100% D2O | 7 | 298 | |||
| 2 | 2D 1H-1H TOCSY | 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6 | 100% D2O | 7 | 298 | |||
| 3 | 2D 1H-1H COSY | 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6 | 100% D2O | 7 | 298 | |||
| 4 | 2D 1H-1H NOESY | 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-1, 70mM potassium chloride-2, 20mM potassium phosphate-3 | 90% H2O/10% D2O | 7 | 298 | |||
| 5 | 2D 1H-1H NOESY | 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6 | 100% D2O | 7 | 298 | |||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 700 |
| 3 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | This natural sequence exhibits the same conformation as the 7BRG-substituted sequence, which has a much cleaner NMR spectrum. 10 relaxation matrix intensity-refined structures of the 7BRG form with the lowest energy were taken, the bromine atoms were replaced with hydrogen atoms, and the structures were subsequently subjected to distance-retrained molecular dynamics refinement. | Felix |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | peak picking | Felix | 2007 | Felix NMR, Inc. |
| 2 | processing | TopSpin | Bruker Biospin | |
| 3 | structure solution | X-PLOR NIH | 2.21 | Schwieters, Kuszewski, Tjandra, Clore |
| 4 | refinement | X-PLOR NIH | 2.21 | Schwieters, Kuszewski, Tjandra, Clore |
