2MGN
Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 | 90% H2O/10% D2O | 45 | 7 | 298 | ||
2 | 2D 1H-1H NOESY | 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 | 100% D2O | 45 | 7 | 298 | ||
3 | 2D 1H-1H TOCSY | 0.2-2.0 mM DNA, 0.2-2.0 mM PQ3 | 100% D2O | 45 | 7 | 298 | ||
4 | 2D 1H-13C HSQC | 1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3 | 100% D2O | 90 | 7 | 298 | ||
5 | 2D 13C-filtered HSQC-NOESY | 1.0 mM DNA, 1.0 mM [U-100% 13C]-CH3 PQ3 | 100% D2O | 90 | 7 | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
2 | Bruker | AMX | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics | Extracted distances from structure of free DNA (PDB entry 2A5P) were used during calculation | 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 | geometry optimization | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
4 | chemical shift assignment | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | peak picking | Sparky | Goddard | |
7 | collection | TopSpin | Bruker Biospin | |
8 | processing | TopSpin | Bruker Biospin | |
9 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
10 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
11 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |