2LE6
Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C JR HMBC | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 | 90% H2O/10% D2O | 100mM K+ | 7 | ambient | 298 | |
2 | 2D 1H-1H JR NOESY | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1 | 90% H2O/10% D2O | 100mM K+ | 7 | ambient | 298 | |
3 | 2D 1H-1H NOESY | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 100% D2O | 100mM K+ | 7 | ambient | 298 | |
4 | 2D 1H-1H COSY | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 100% D2O | 100mM K+ | 7 | ambient | 298 | |
5 | 2D 1H-1H TOCSY | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 100% D2O | 100mM K+ | 7 | ambient | 298 | |
6 | 2D 1H-13C HSQC | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 100% D2O | 100mM K+ | 7 | ambient | 298 | |
7 | H-D exchange | 0.5-2.0 mM DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-2 | 100% D2O | 100mM K+ | 7 | ambient | 298 | |
8 | 15N-filtered | 0.5-2.0 mM [U-2% 15N; U-2% 13C] DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-3 | 90% H2O/10% D2O | 100mM K+ | 7 | ambient | 298 | |
9 | D-labeled | 0.5-2.0 mM [U-100% 2H] DNA (5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')-4 | 90% H2O/10% D2O | 100mM K+ | 7 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
DGSA-distance geometry simulated annealing, distance-restrained molecular dynamics refinement in vacuo, distance-restrained molecular dynamics refinement in explicit solvent | TopSpin |
NMR Ensemble Information | |
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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 | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | TopSpin | 2.1 | Bruker Biospin |
2 | peak picking | Felix | 2007 | Felix NMR, Inc. |
3 | structure solution | X-PLOR NIH | 2.27 | Schwieters, Kuszewski, Tjandra and Clore |
4 | refinement | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
5 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |