6GZN
Adenine-driven structural switch from two- to three-quartet DNA G-quadruplex
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.6 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 7.0 | 1 atm | 278 | Varian INOVA 800 |
2 | 2D 1H-1H TOCSY | 0.8 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') | 100% D2O | 100 mM | 7.0 | 1 atm | 278 | Agilent DD2 600 |
3 | 2D DQF-COSY | 0.8 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') | 100% D2O | 100 mM | 7.0 | 1 atm | 278 | Agilent DD2 600 |
4 | 2D 1H-13C HSQC aliphatic | 0.6 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 7.0 | 1 atm | 278 | Agilent DD2 600 |
5 | 2D 1H-13C HSQC aromatic | 0.6 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*CP*GP*GP*GP*AP*GP*AP*GP*GP*G)-3') | 90% H2O/10% D2O | 100 mM | 7.0 | 1 atm | 278 | Agilent DD2 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Agilent | DD2 | 600 |
2 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber |
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 | chemical shift assignment | Sparky | Goddard | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |