Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from intron of N-myc gene
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') | 90% H2O/10% D2O | 120 | 6.5 | ambient | 298.15 | |
| 2 | 2D 1H-15N HSQC | 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') | 90% H2O/10% D2O | 120 | 6.5 | ambient | 298.15 | |
| 3 | 2D 31P-1H COSY | 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') | 90% H2O/10% D2O | 120 | 6.5 | ambient | 298.15 | |
| 4 | 2D 1H-1H DQF COSY | 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') | 90% H2O/10% D2O | 120 | 6.5 | ambient | 298.15 | |
| 5 | 2D 1H-15N HMQC | 0.4-6.6 mM DNA (5'-D(*TP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*GP*GP*GP*AP*A)-3') | 90% H2O/10% D2O | 120 | 6.5 | ambient | 298.15 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | VNMRS | 800 |
| 2 | Varian | VNMRS | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 2 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm | |
