5I2V
NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region
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 | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 800 |
8 | 2D 1H-1H NOESY | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 700 |
2 | 2D 1H-1H COSY | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 800 |
3 | 2D 1H-13C HSQC | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 800 |
4 | 2D 1H-1H TOCSY | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 800 |
5 | 2D 1H-15N HSQC | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 800 |
6 | 2D 1H-13C HMBC | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 700 |
7 | 1D 1H-15N HSQC | 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N | 90% H2O/10% D2O | 90 mM | 6.6 | 1 atm | 293 | Bruker AVANCE III 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
2 | Bruker | AVANCE III | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 11 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | Sparky | Goddard | |
2 | collection | TopSpin | Bruker Biospin | |
3 | data analysis | CcpNmr Analysis | CCPN | |
4 | structure calculation | ARIA | Linge, O'Donoghue and Nilges | |
5 | structure calculation | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
6 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |