G-quadruplexes with (4n-1) guanines in the G-tetrad core: formation of a G-triad water complex and implication for small-molecule binding
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.1-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 | 90% H2O/10% D2O | 45 | 7 | ambient | 298 | |
| 2 | 2D 1H-1H NOESY | 0.6-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-3 | 100% D2O | 45 | 7 | ambient | 298 | |
| 3 | 2D 1H-1H HMBC | 0.1-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 | 90% H2O/10% D2O | 45 | 7 | ambient | 298 | |
| 4 | 1D 15N-filtered 1H NMR | 0.2-0.4 mM [U-4% 15N] DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 90% H2O/10% D2O | 45 | 7 | ambient | 298 | |
| 5 | 1D 1H NMR | 0.2-0.4 mM [U-100% 2H] DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4 | 90% H2O/10% D2O | 45 | 7 | ambient | 298 | |
| 6 | 1D 1H NMR | 0.1-1.2 mM DNA (5'-D(*TP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 | 90% H2O/10% D2O | 45 | 7 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, DGSA-distance geometry simulated annealing, simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 10000 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 2 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
| 3 | chemical shift assignment | Sparky | Goddard | |
| 4 | peak picking | Sparky | Goddard | |
| 5 | chemical shift calculation | Sparky | Goddard | |
| 6 | data analysis | Sparky | Goddard | |
| 7 | collection | TopSpin | Bruker Biospin | |
| 8 | geometry optimization | X-PLOR | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | refinement | X-PLOR | Schwieters, Kuszewski, Tjandra and Clore | |
| 10 | data analysis | SpinWorks | http://home.cc.umanitoba.ca/~wolowiec/spinworks | |
